Difference between revisions of "Fabry:Sequence-based mutation analysis"

Latest revision as of 12:27, 20 June 2012

Fabry Disease » Sequence-based mutation analysis

The following analyses were performed on the basis of the α-Galactosidase A sequence. Please consult the journal for the commands used to generate the results.

Dataset

Q279E
N215S
I289V
S65T
R356W
V316I
P323T
P40S
R118H
A143T

Amino acid properties

<figtable id="tab:aaProp"> Physicochemical properties of the chosen SNPs and changes of properties between wildtype (wt) and mutant (mt).
Used abbreviation in this table:
AA: Amino Acid, Pol: Side-chain polarity, Charge: Side-chain charge at pH 7.4, HI: Hydropathy index, RM: Residue Mass, iP: isoelectric point

SNP	wt AA	wt Pol	wt Charge	wt HI	wt RM	wt iP	mt AA	mt Pol	mt Charge	mt HI	mt RM	mt iP	change in Pol	change in Charge	change in HI	change in RM	change in iP
Q279E	Q	polar	neutral	-3.5	128.131	5.65	E	polar	negative	-3.5	129.116	3.15	none	neutral to negative	0	0.99	-2.5
N215S	N	polar	neutral	-3.5	114.104	5.41	S	polar	neutral	-0.8	87.078	5.68	none	none	2.7	-27.026	0.27
I289V	I	nonpolar	neutral	4.5	113.160	6.05	V	nonpolar	neutral	4.2	99.133	6.00	none	none	-0.3	-14.027	-0.05
S65T	S	polar	neutral	-0.8	87.078	5.68	T	polar	neutral	-0.7	101.105	5.60	none	none	0.1	14.027	-0.08
R356W	R	polar	positive	-4.5	156.188	10.76	W	nonpolar	neutral	-0.9	186.213	5.89	polar to nonpolar	positive to neutral	3.6	30.025	-4.87
V316I	V	nonpolar	neutral	4.2	99.133	6.00	I	nonpolar	neutral	4.5	113.160	6.05	none	none	0.3	14.027	0.05
P323T	P	nonpolar	neutral	-1.6	97.117	6.30	T	polar	neutral	-0.7	101.105	5.60	nonpolar to polar	none	0.9	3.988	-0.7
P40S	P	nonpolar	neutral	-1.6	97.117	6.30	S	polar	neutral	-0.8	87.078	5.68	nonpolar to polar	none	0.8	-10.039	-0.62
R118H	R	polar	positive	-4.5	156.188	10.76	H	polar	pos(10%), neutr(90%)	-3.2	137.142	7.60	none	positive to pos(10%), neutr(90%)	1.3	-19.046	-3.16
A143T	A	nonpolar	neutral	1.8	71.079	6.01	T	polar	neutral	-0.7	101.105	5.60	nonpolar to polar	none	-2.5	30.026	-0.41

</figtable>

The polarity of the side chain determines whether an amino acid is hydrophobic or not. Hydrophobicity is a measure of how soluble an amino acid is in water. Hydrophobic amino acids are more likely to be found inside a protein, while hydrophilic amino acids rather are in contact with the aqueous environment. <ref>Hydrophobicity Index for Common Amino Acids http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid-reference-chart.html#hydro, June 16, 2012</ref> Therefore, depending on the localisation of an amino acid, a change in the polarity due to a mutation can cause a major defect. This may be the case in the SNPs P40S, A143T, P323T and R356W.
Furthermore the type of charge (positive or negative) is important for the structure of a protein, because it controls the binding of the amino acid to close-by residues. A modification again can break the coherence of the protein, which might happen when the mutations R118H, Q279E and R356W occur.
The hydropathy index of an amino acid is a number representing the hydrophobic or hydrophilic properties of its sidechain.<ref>Kyte J, Doolittle RF (May 1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1): 105–32. PMID 7108955. </ref> The larger the number is, the more hydrophobic the amino acid, thus the most hydrophobic amino acid is isoleucine (4.5) and the most hydrophilic one is arginine (-4.5). Considering a hydropathy change greater than 1 (in both direction, positive and negative) as crucial, only one SNP highly increases the hydrophobicity (A143T) and 3 increase the hydrophilic character of the position (R118H, N215S and R356W)
The average residue mass ranges from 57.052 (Glycine) to 186.213 (Tryptophan), thus we expect an alteration of the mass of greater than 10 as critical. This concerns all mutations expect for Q279E and P323T.
The isoelectric point is the pH at which an amino acid carries no net charge. Below the pI it carries a net positive charge, above it a net negative charge. Since the pH in the human body is on average 6.7, only three amino acids are positively charged (Histidine, Lysine and Arginine). The pI ranges from 2.85 (Aspartic acid) to 10.76 (Arginine), therefore we considered a change of 0.8 as probably desease causing. This applies only for R118H, Q279E and R356W.

Simple structural analysis

P40S

The SNP P40S. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP P40S in the α-galactosidase protein is marked in purple.

</figure>

The SNP P40S. The wild type amino acid is colored in green, the mutation in red.

</figure>

S65T

The SNP S65T. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP S65T in the α-galactosidase protein is marked in purple.

</figure>

The SNP S65T. The wild type amino acid is colored in green, the mutation in red.

</figure>

R118H

The SNP R118H. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP R118H in the α-galactosidase protein is marked in purple.

</figure>

The SNP R118H. The wild type amino acid is colored in green, the mutation in red.

</figure>

A143T

The SNP A143T. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP A143T in the α-galactosidase protein is marked in purple.

</figure>

The SNP A143T. The wild type amino acid is colored in green, the mutation in red.

</figure>

N215S

The SNP N215S. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP N215S in the α-galactosidase protein is marked in purple.

</figure>

The SNP N215S. The wild type amino acid is colored in green, the mutation in red.

</figure>

Q279E

The SNP Q279E. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP Q279E in the α-galactosidase protein is marked in purple.

</figure>

The SNP Q279E. The wild type amino acid is colored in green, the mutation in red.

</figure>

I289V

The SNP I289V. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP I289V in the α-galactosidase protein is marked in purple.

</figure>

The SNP I289V. The wild type amino acid is colored in green, the mutation in red.

</figure>

V316I

The SNP V316I. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP V316I in the α-galactosidase protein is marked in purple.

</figure>

The SNP V316I. The wild type amino acid is colored in green, the mutation in red.

</figure>

P323T

The SNP P323T. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP P323T in the α-galactosidase protein is marked in purple.

</figure>

The SNP P323T. The wild type amino acid is colored in green, the mutation in red.

</figure>

R356W

The SNP R356W. The wild type amino acid is colored in green, the mutation in red.

</figure>

The position of the SNP R356W in the α-galactosidase protein is marked in purple.

</figure>

The SNP R356W. The wild type amino acid is colored in green, the mutation in red.

</figure>

Secondary Structure

<figtable id="tab:Location"> Secondary structure assignment predicted by the three methods Psipred, Reprof and DSSP in Task 3 for the mutated amino acid itself and
the ten adjacent residues to the left and to the right.
H represents a helix at this position, C represents coiled regions, E sheets and - is a not predictable region

SNP	SecStruc Psipred	SecStruc Psipred long	SecStruc Reprof	SecStruc Reprof long	SecStruc DSSP	SecStruc DSSP long
Q279E	H	CCCCCCCHHHHHHHHHHHHHH	H	EECCCCCCHHHHHHHHHHHHH	H	CCCCC--HHHHHHHHHHHHHC
N215S	H	CCCCCCCCCCHHHHHCCCCCC	H	CECCCCCCCCHHHHHHHHHHH	H	HHHCCCC---HHHHCCC-CEE
I289V	H	HHHHHHHHHHHCCCEEEECCC	H	HHHHHHHHHHHHHCHHCCCCC	C	HHHHHHHHHHCC--EEE-C-C
S65T	H	CCCCCCCCCCHHHHHHHHHHH	H	CCCCCCCHHHHHHHHHHHHHH	H	CCC-CCCC-CHHHHHHHHHHH
R356W	C	CCEEEEEEECCCCCCEEEEEE	C	HHHHHHHHHHCCCCCCCCHHH	-	CEEEEEEEE---CCC-EEEEE
V316I	H	HHHCCCCHHHHHHCCCCCCCC	E	HHHHCCCCCEEEECCCCCCCC	H	HHHHHH-HHHHHHHC-CC---
P323T	C	HHHHHHCCCCCCCCCEEEEEC	C	CCEEEECCCCCCCCCCEECCC	C	HHHHHHHC-CC----EEEE-C
P40S	C	CCCCCCCCCCCCCCCCCCCCC	C	HHCCCCCCCCCCCHHHHHHEE	-	---CC--CC--EEEECHHHHC
R118H	H	CCCCCCCCHHHHHHHHHHCCC	H	CCCCCCHHHHHHHHHHHCCCC	H	-CCC-CCHHHHHHHHHHHCC-
A143T	C	EECCCCCCCCCCCCCCCCHHH	C	EEECCCCCCCCCCCCCCCCCC	C	EEECCCE-CCCCE--CCCHHH

</figtable>

Despite the fact, we know from last weeks' task, that the disease causing mutations are spread all over the protein without any respect to the secondary structure, we assumed we had no prior knowledge about it. Thus we looked at the predicted secondary structure at the position of each point mutation and its surrounding (10 residues to the left and 10 residues to the right). The only remarkable fact is, that there are (almost) no sheets at the mutated residues. From Task 6 we know, that this happened only by chance and due to the small amount of picked SNPs.

Substitution matrices

<figtable id="tab:Subsmatr"> Substitution values for all SNPs,
assigned by the three substitution matrices
BLOSUM62, PAM1 and PAM250.

SNP	Value BLOSUM62	Value PAM1	Value PAM250
Q279E	3	27	2
N215S	1	20	1
I289V	4	33	4
S65T	2	38	1
R356W	-4	8	2
V316I	4	57	4
P323T	-2	4	0
P40S	-1	12	1
R118H	0	10	2
A143T	0	32	1

</figtable>

Since the PAM1 and the PAM250 matrices are designed for proteins of very diverse degree of kinship, 99% and ~20% relationship, respectively, those two matrices tend to give contradictory scores of how likely a substitution is. On the other hand, BLOSUM62 and PAM1, although the BLOSUM matrix was created from sequences with identity of less than 62 percent, usually provide similar predictions.

PSSM

<figtable id="tab:pssm"> The occurrence of the wild and mutation type according to the pssm generated by Psi-Blast

conservation of	P40S	S65T	R118H	A143T	N215S	Q279E	I289V	V316I	P323T	R356W
wild type	81%	16%	8%	11%	6%	12%	17%	29%	15%	15%
mutant type	2%	20%	2%	6%	4%	38%	11%	19%	7%	4%

</figtable>

Multiple sequence alignment

And another step close to evolution: Identify all mammalian homologous sequences. Create a multiple sequence alignment for them with a method of your choice. Using this you can now calculate conservation for WT and mutant residues again. Compare this to the matrix- and PSSM-derived results.

Scoring methods

SIFT

<figtable id="tab:Sift"> Sift Scores

SNP	Prediction	Sift Score	Sequences represented at this position
P40S	AFFECT PROTEIN FUNCTION	0.00	41
S65T	AFFECT PROTEIN FUNCTION	0.01	45
R118H	be TOLERATED	0.06	48
A143T	AFFECT PROTEIN FUNCTION	0.01	48
N215S	AFFECT PROTEIN FUNCTION	0.01	48
Q279E	AFFECT PROTEIN FUNCTION	0.00	48
I289V	AFFECT PROTEIN FUNCTION	0.05	48
V316I	be TOLERATED	0.75	48
P323T	AFFECT PROTEIN FUNCTION	0.01	48
R356W	AFFECT PROTEIN FUNCTION	0.01	47

</figtable>

Median sequence conservation: 2.99

SIFT

Polyphen2

<figtable id="tab:Polyphen"> Polyphen Scores

SNP	rs ID	Sec Struc	Prediction	pph2 Class	pph2 Prob	pph2 FPR	pph2 TPR	pph2 FDR
Q279E	rs28935485	H	probably damaging	deleterious	0.983	0.0387	0.745	0.0657
N215S	rs28935197	.	benign	neutral	0.048	0.167	0.941	0.194
I289V	?	H	probably damaging	deleterious	0.975	0.0436	0.762	0.072
S65T	?	.	probably damaging	deleterious	0.995	0.0277	0.681	0.0521
R356W	?	.	probably damaging	deleterious	1	0.00026	0.00018	0.0109
V316I	?	H	benign	neutral	0.308	0.113	0.904	0.144
P323T	?	T	possibly damaging	deleterious	0.612	0.091	0.872	0.124
P40S	?	.	probably damaging	deleterious	1	0.00026	0.00018	0.0109
R118H	?	H	benign	neutral	0.015	0.209	0.956	0.229
A143T	?	T	probably damaging	deleterious	1	0.00026	0.00018	0.0109

</figtable>

Polyphen2 [1]

SNAP

<xr id="tab:snap2"/> contains the SNAP2 predictions for the ten SNPs listed in section Dataset. There is also a more comprehensive results table that includes the predictions for all possible single point mutations at the ten given sequence positions.

<figtable id="tab:snap2"> Predictions by SNAP2 of the effect of SNPs relative to the wild type

Mutation	Binary prediction	Reliability Index	Expected Accuracy	Total of neutral mutations at this position	Total of non-neutral mutations at this position
P40S	Neutral	0	51%	2	17
S65T	Neutral	6	79%	17	2
R118H	Non-neutral	1	60%	5	14
A143T	Neutral	7	85%	18	1
N215S	Neutral	7	85%	18	1
Q279E	Neutral	6	79%	18	1
I289V	Neutral	8	91%	13	6
V316I	Neutral	8	91%	16	3
P323T	Neutral	4	67%	17	2
R356W	Non-neutral	5	75%	6	13

</figtable>

Results and Conclusion

<figtable id="tab:Overview"> This table gives an overview over all features examined in the sections above. The red background color indicates a disease causing prediction, the green color a non-disease causing one. In the end all red fields are summed up for each row and the resulting value leads to our prediction given in <xr id="tab:Result"/>.
Used abbreviation in this table:
AA: Amino Acid, Pol: Side-chain polarity, Charge: Side-chain charge at pH 7.4, HI: Hydropathy index, RM: Residue Mass, iP: isoelectric point

SNP	change in Pol	change in Charge	change in HI	change in RM	change in iP	SecStruc Psipred	SecStruc Reprof	SecStruc DSSP	Value BLOSUM62	Value PAM1	Value PAM250	Sift Score	pph2 Class	SNAP prediction	Sum bad scores
A143T	nonpolar to polar	none	-2.5	30.026	-0.41	C	C	C	0	32	1	0.01	deleterious	neutral	6
R356W	polar to nonpolar	positive to neutral	3.6	30.025	-4.87	C	C	-	-4	8	2	0.01	deleterious	non-neutral	10
I289V	none	none	-0.3	-14.027	-0.05	H	H	C	4	33	4	0.05	deleterious	neutral	5
V316I	none	none	0.3	14.027	0.05	H	E	H	4	57	4	0.75	neutral	neutral	4
R118H	none	positive to pos(10%), neutr(90%)	1.3	-19.046	-3.16	H	H	H	0	10	2	0.06	neutral	non-neutral	9
N215S	none	none	2.7	-27.026	0.27	H	H	H	1	20	1	0.01	neutral	neutral	7
Q279E	none	neutral to negative	0	0.99	-2.5	H	H	H	3	27	2	0.00	deleterious	neutral	7
P40S	nonpolar to polar	none	0.8	-10.039	-0.62	C	C	-	-1	12	1	0.00	deleterious	neutral	7
S65T	none	none	0.1	14.027	-0.08	H	H	H	2	38	1	0.01	deleterious	neutral	7
P323T	nonpolar to polar	none	0.9	3.988	-0.7	C	C	C	-2	4	0	0.01	deleterious	neutral	6

</figtable>

<figtable id="tab:Result"> All examined SNPs with the "sum bad score" according to <xr id="tab:Overview"/> and our resulting
prediction. The table also shows if the SNP truly is disease causing or not and whether our sequence
based prediction is true

SNP	Sum bad scores	Prediction	True classification	Result prediction
A143T	6	Non-disease causing	Disease causing	Wrong
R356W	10	Disease causing	Disease causing	Right
I289V	5	Non-disease causing	Non-disease causing	Right
V316I	4	Non-disease causing	Non-disease causing	Right
R118H	9	Disease causing	Non-disease causing	Wrong
N215S	7	Disease causing	Disease causing	Right
Q279E	7	Disease causing	Disease causing	Right
P40S	7	Disease causing	Disease causing	Right
S65T	7	Disease causing	Disease causing	Right
P323T	6	Non-disease causing	Non-disease causing	Right

</figtable>

In <xr id="tab:Overview"/> we list all afore gathered information in condensed form and highlight values that we consider as an indicator for a disease causing mutation with red color. Results contained in green colored fields are considered neutral. The summed up score of disease indicators is again shown in <xr id="tab:Result"/> along with our prediction for each SNP. Mutations with score smaller than 7 are considered neutral, greater or equal to that disease causing. Next to the prediction we show the true classification of the single nucleotide polymorphism acording to the mapping we did in Task 6. We show that only two of the ten predictions are wrong, which we consider as a surprisingly good result.

References

Difference between revisions of "Fabry:Sequence-based mutation analysis"

Latest revision as of 12:27, 20 June 2012

Contents

Dataset

Amino acid properties

Simple structural analysis

Secondary Structure

Substitution matrices

PSSM

Multiple sequence alignment

Scoring methods

SIFT

Polyphen2

SNAP

Results and Conclusion

References

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@@ Line 5: / Line 5: @@
 The following analyses were performed on the basis of the [[Fabry:Alpha-galactosidase|α-Galactosidase A]] [[Fabry:Alpha-galactosidase_sequence| sequence]]. Please consult the [[Fabry:Sequence-based_mutation_analysis/Journal|journal]] for the commands used to generate the results.
-== Dataset preparation ==
+== Dataset ==
  Q279E
  N215S
@@ Line 16: / Line 16: @@
  R118H
  A143T
+<!--
+<div style="float:left; border:thin solid lightgrey; margin: 0px 0px 0px 0px;">
+<figtable id="tab:Info">
+<caption>Information on chosen SNPs</caption>
+{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| disease/non-disease
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Evidence
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Perc_wt
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 2px 0;"| Perc_mt
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| Q279E
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| by cluster
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 16
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 59
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| N215S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| by cluster
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 9
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 3
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| I289V
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1000Genome
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 34
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 9
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| S65T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| by cluster
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 19
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 18
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| R356W
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| by cluster
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 20
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 7
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| V316I
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| by freq
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 30
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 16
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| P323T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| Not validated
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 24
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 7
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| P40S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| by cluster
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 92
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 1
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| R118H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| Not validated
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 11
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 2
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| A143T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| by cluster,freq
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 19
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0;"| 4
+|-
+|}
+</figtable>
+</div>
+-->
+<br style="clear:both">
 == Amino acid properties ==
 <div style="float:left; border:thin solid lightgrey; margin: 0px 0px 0px 0px;">
 <figtable id="tab:aaProp">
-<caption>Physicochemical properties of the chosen SNPs and changes of properties between wildtype (wt) and mutant (mt)</caption>
+<caption>Physicochemical properties of the chosen SNPs and changes of properties between wildtype (wt) and mutant (mt).<br>Used abbreviation in this table:<br> AA: Amino Acid, Pol: Side-chain polarity, Charge: Side-chain charge at pH 7.4, HI: Hydropathy index, RM: Residue Mass, iP: isoelectric point</caption>
-{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
+{| class="wikitable sortable"  style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNP
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>AA
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>Side-chain polarity
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>Pol
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>Side-chain charge (pH 7.4)
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>Charge
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>Hydropathy index
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>HI
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>Residue Mass
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>RM
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| wt<br>iP
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>AA
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>Side-chain polarity
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>Pol
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>Side-chain charge (pH 7.4)
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>Charge
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>Hydropathy index
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>HI
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>Residue Mass
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>RM
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| mt<br>iP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 2px 0;"| mt<br>iP
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in polarity
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in Pol
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in charge
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in Charge
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in hydropathy
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in HI
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in residue mass
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in RM
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 2px 0;"| change in iP
 |-
@@ Line 45: / Line 123: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −3.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -3.5
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 128.131
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.65
@@ Line 51: / Line 129: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| negative
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −3.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -3.5
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 129.116
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 3.15
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 3.15
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral  to negative
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| neutral  to<br>negative
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −3.5-−3.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 0
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 0.985000000000014
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 0.99
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| -2.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| -2.5
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| N215S
@@ Line 64: / Line 142: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −3.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -3.5
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 114.104
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.41
@@ Line 70: / Line 148: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.8
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -0.8
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 87.078
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.68
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 5.68
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.8-−3.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 2.7
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -27.026
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| -27.026
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 0.27
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| 0.27
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| I289V
@@ Line 91: / Line 169: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 4.2
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 99.133
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 6.00
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 6.00
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 4.2-4.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| -0.3
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -14.027
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| -14.027
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| -0.0499999999999998
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| -0.05
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| S65T
@@ Line 102: / Line 180: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.8
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -0.8
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 87.078
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.68
@@ Line 108: / Line 186: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -0.7
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 101.105
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.60
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 5.60
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.7-−0.8
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 0.1
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 14.027
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 14.027
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| -0.0800000000000001
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| -0.08
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R356W
@@ Line 121: / Line 199: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| positive
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −4.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -4.5
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 156.188
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 10.76
@@ Line 127: / Line 205: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| nonpolar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.9
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -0.9
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 186.213
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.89
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 5.89
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar  to nonpolar
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| polar  to<br>nonpolar
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| positive  to neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| positive  to<br>neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.9-−4.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 3.6
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 30.025
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 30.025
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| -4.87
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| -4.87
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| V316I
@@ Line 148: / Line 226: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 4.5
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 113.160
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 6.05
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 6.05
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 4.5-4.2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 0.3
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 14.027
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 14.027
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 0.0499999999999998
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| 0.05
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P323T
@@ Line 159: / Line 237: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| nonpolar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −1.6
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -1.6
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 97.117
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 6.30
@@ Line 165: / Line 243: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -0.7
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 101.105
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.60
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 5.60
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| nonpolar  to polar
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| nonpolar  to<br>polar
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.7-−1.6
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 0.9
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 3.988
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 3.988
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| -0.7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| -0.7
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P40S
@@ Line 178: / Line 256: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| nonpolar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −1.6
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -1.6
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 97.117
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 6.30
@@ Line 184: / Line 262: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.8
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -0.8
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 87.078
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.68
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 5.68
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| nonpolar  to polar
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| nonpolar  to<br>polar
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.8-−1.6
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 0.8
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -10.039
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| -10.039
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| -0.62
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| -0.62
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R118H
@@ Line 197: / Line 275: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| positive
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −4.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -4.5
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 156.188
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 10.76
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| H
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| pos(10%),neutr(90%)
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| pos(10%),<br>neutr(90%)
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −3.2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -3.2
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 137.142
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 7.60
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 7.60
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| positive  to pos(10%),neutr(90%)
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| positive to pos(10%),<br>neutr(90%)
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −3.2-−4.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 1.3
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -19.046
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| -19.046
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| -3.16
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| -3.16
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A143T
@@ Line 222: / Line 300: @@
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| polar
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| neutral
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -0.7
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 101.105
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 5.60
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 3px 1px 0; text-align:right"| 5.60
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| nonpolar  to polar
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| nonpolar  to<br>polar
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color: #F0F0F0"| none
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| −0.7-1.8
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| -2.5
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 30.026
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right;  background-color: #F0F0F0"| 30.026
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| -0.41
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right;  background-color: #F0F0F0"| -0.41
 |-
 |}
 </figtable>
 </div>
+<br style="clear:both">
+<br style="clear:both">
+The polarity of the side chain determines whether an amino acid is hydrophobic or not.
+Hydrophobicity is a measure of how soluble an amino acid is in water. Hydrophobic amino acids are more likely to be found inside a protein, while hydrophilic amino acids rather are in contact with the aqueous environment. <ref>Hydrophobicity Index for Common Amino Acids [http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid-reference-chart.html#hydro http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid-reference-chart.html#hydro], June 16, 2012</ref>
+Therefore, depending on the localisation of an amino acid, a change in the polarity due to a mutation can cause a major defect. This may be the case in the SNPs P40S, A143T, P323T and R356W.<br>
+Furthermore the type of charge (positive or negative) is important for the structure of a protein, because it controls the binding of the amino acid to close-by residues. A modification again can break the coherence of the protein, which might happen when the mutations R118H, Q279E and R356W occur.<br>
+The hydropathy index of an amino acid is a number representing the hydrophobic or hydrophilic properties of its sidechain.<ref>Kyte J, Doolittle RF (May 1982). ''A simple method for displaying the hydropathic character of a protein''. J. Mol. Biol. 157 (1): 105–32. [http://www.ncbi.nlm.nih.gov/pubmed/7108955?dopt=Abstract PMID 7108955]. </ref>
+The larger the number is, the more hydrophobic the amino acid, thus the most hydrophobic amino acid is isoleucine (4.5) and the most hydrophilic one is arginine (-4.5).
+Considering a hydropathy change greater than 1 (in both direction, positive and negative) as crucial, only one SNP highly increases the hydrophobicity (A143T) and 3 increase the hydrophilic character of the position (R118H, N215S and R356W)<br>
+The average residue mass ranges from 57.052 (Glycine) to 186.213 (Tryptophan), thus we expect an alteration of the mass of greater than 10 as critical. This concerns all mutations expect for Q279E and P323T.<br>
+The isoelectric point is the pH at which an amino acid carries no net charge. Below the pI it carries a net positive charge, above it a net negative charge. Since the pH in the human body is on average 6.7, only three amino acids are positively charged (Histidine, Lysine and Arginine). The pI ranges from 2.85 (Aspartic acid) to 10.76 (Arginine), therefore we considered a change of 0.8 as probably desease causing. This applies only for R118H, Q279E and R356W.
 == Simple structural analysis ==
-* Now take into consideration where in the protein the mutation occurs and document: Create a picture with PyMOL showing the original and mutated residue in the protein. [http://www.pymolwiki.org/index.php/Mutagenesis Use PyMOL for this]. More thorough structural analyses will be introduced in the next task.
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
-== Location ==
-<div style="float:left; border:thin solid lightgrey; margin: 0px 0px 20px 20px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">P40S</p>
+<div style="float: right;">
+<figure id="fig:P40S_rotation">
+[[File:Fabry P40S rotation.gif|150px|thumb|right|<caption>The SNP P40S. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:P40S_localization">
+[[File:Fabry P40S localization.png|150px|thumb|right|<caption>The position of the SNP P40S in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:P40S_transformation">
+[[File:Fabry P40S transformation.gif|150px|thumb|right|<caption>The SNP P40S. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">S65T</p>
+<div style="float: right;">
+<figure id="fig:S65T_rotation">
+[[File:Fabry S65T rotation.gif|150px|thumb|right|<caption>The SNP S65T. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:S65T_localization">
+[[File:Fabry S65T localization.png|150px|thumb|right|<caption>The position of the SNP S65T in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:S65T_transformation">
+[[File:Fabry S65T transformation.gif|150px|thumb|right|<caption>The SNP S65T. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">R118H</p>
+<div style="float: right;">
+<figure id="fig:R118H_rotation">
+[[File:Fabry R118H rotation.gif|150px|thumb|right|<caption>The SNP R118H. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:R118H_localization">
+[[File:Fabry R118H localization.png|150px|thumb|right|<caption>The position of the SNP R118H in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:R118H_transformation">
+[[File:Fabry R118H transformation.gif|150px|thumb|right|<caption>The SNP R118H. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">A143T</p>
+<div style="float: right;">
+<figure id="fig:A143T_rotation">
+[[File:Fabry A143T rotation.gif|150px|thumb|right|<caption>The SNP A143T. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:A143T_localization">
+[[File:Fabry A143T localization.png|150px|thumb|right|<caption>The position of the SNP A143T in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:A143T_transformation">
+[[File:Fabry A143T transformation.gif|150px|thumb|right|<caption>The SNP A143T. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">N215S</p>
+<div style="float: right;">
+<figure id="fig:N215S_rotation">
+[[File:Fabry N215S rotation.gif|150px|thumb|right|<caption>The SNP N215S. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:N215S_localization">
+[[File:Fabry N215S localization.png|150px|thumb|right|<caption>The position of the SNP N215S in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:N215S_transformation">
+[[File:Fabry N215S transformation.gif|150px|thumb|right|<caption>The SNP N215S. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">Q279E</p>
+<div style="float: right;">
+<figure id="fig:Q279E_rotation">
+[[File:Fabry Q279E rotation.gif|150px|thumb|right|<caption>The SNP Q279E. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:Q279E_localization">
+[[File:Fabry Q279E localization.png|150px|thumb|right|<caption>The position of the SNP Q279E in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:Q279E_transformation">
+[[File:Fabry Q279E transformation.gif|150px|thumb|right|<caption>The SNP Q279E. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">I289V</p>
+<div style="float: right;">
+<figure id="fig:I289V_rotation">
+[[File:Fabry I289V rotation.gif|150px|thumb|right|<caption>The SNP I289V. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:I289V_localization">
+[[File:Fabry I289V localization.png|150px|thumb|right|<caption>The position of the SNP I289V in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:I289V_transformation">
+[[File:Fabry I289V transformation.gif|150px|thumb|right|<caption>The SNP I289V. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">V316I</p>
+<div style="float: right;">
+<figure id="fig:V316I_rotation">
+[[File:Fabry V316I rotation.gif|150px|thumb|right|<caption>The SNP V316I. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:V316I_localization">
+[[File:Fabry V316I localization.png|150px|thumb|right|<caption>The position of the SNP V316I in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:V316I_transformation">
+[[File:Fabry V316I transformation.gif|150px|thumb|right|<caption>The SNP V316I. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">P323T</p>
+<div style="float: right;">
+<figure id="fig:P323T_rotation">
+[[File:Fabry P323T rotation.gif|150px|thumb|right|<caption>The SNP P323T. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:P323T_localization">
+[[File:Fabry P323T localization.png|150px|thumb|right|<caption>The position of the SNP P323T in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:P323T_transformation">
+[[File:Fabry P323T transformation.gif|150px|thumb|right|<caption>The SNP P323T. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<div style="border: 1px dotted #000; float: left; margin: 0px 10px 10px; padding-right: 5px; width: 370px;">
+<p style="float: left; font-size: 20pt; font-weight: bold; margin: 40px 10px 0px 40px;">R356W</p>
+<div style="float: right;">
+<figure id="fig:R356W_rotation">
+[[File:Fabry R356W rotation.gif|150px|thumb|right|<caption>The SNP R356W. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+<div style="float: left; margin-top: 20px;">
+<figure id="fig:R356W_localization">
+[[File:Fabry R356W localization.png|150px|thumb|right|<caption>The position of the SNP R356W in the α-galactosidase protein is marked in purple.</caption>]]
+</figure>
+</div>
+<div style="float: right;">
+<figure id="fig:R356W_transformation">
+[[File:Fabry R356W transformation.gif|150px|thumb|right|<caption>The SNP R356W. The wild type amino acid is colored in green, the mutation in red.</caption>]]
+</figure>
+</div>
+</div>
+<br style="clear: both;">
+== Secondary Structure ==
+<div style="float:left; border:thin solid lightgrey; margin: 0px 20px 0px 0px;">
 <figtable id="tab:Location">
+<caption>Secondary structure assignment predicted by the three methods Psipred, Reprof and DSSP in [[Fabry:Sequence-based_analyses#Alpha-galactosidase_A_.28P06280.29 |Task 3]] for the mutated amino acid itself and<br>the ten adjacent residues to the left and to the right.<br>H represents a helix at this position, C represents coiled regions, E sheets and - is a not predictable region</caption>
-<caption>Physicochemical properties of the chosen SNPs and changes of properties between wildtype (wt) and mutant (mt)</caption>
-{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
+{| class="wikitable sortable"  style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNP
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc Psipred
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc<br>Psipred
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc Psipred<br>long
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc Reprof
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc<br>Reprof
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc Reprof<br>long
-! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc DSSP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc<br>DSSP
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 2px 0;"| SecStruc DSSP<br>long
 |-
@@ Line 334: / Line 635: @@
 </figtable>
 </div>
+Despite the fact, we know from last weeks' task, that the disease causing mutations are spread all over the protein without any respect to the secondary structure, we assumed we had no prior knowledge about it. Thus we looked at the predicted secondary structure at the position of each point mutation and its surrounding (10 residues to the left and 10 residues to the right). The only remarkable fact is, that there are (almost) no sheets at the mutated residues. From [[Fabry:Mapping_point_mutations#Mapping | Task 6]] we know, that this happened only by chance and due to the small amount of picked SNPs.
+<br style="clear:both">
 == Substitution matrices ==
-<div style="float:left; border:thin solid lightgrey; margin: 0px 0px 20px 20px;">
+<div style="float:left; border:thin solid lightgrey; margin: 0px 20px 0px 0px;">
 <figtable id="tab:Subsmatr">
-<caption>Substitution values for all SNPs, both substitution matrices</caption>
+<caption>Substitution values for all SNPs,<br>assigned by the three substitution matrices<br>BLOSUM62, PAM1 and PAM250.</caption>
 {| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNP
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Value<br>BLOSUM62
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"|Value<br>PAM1
 ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 2px 0;"|Value<br>PAM250
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| Q279E
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 3
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 27
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 2
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| N215S
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 20
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 1
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| I289V
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 3
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 33
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 4
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| S65T
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 38
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 1
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R356W
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -3
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 8
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 2
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| V316I
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 3
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 57
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 4
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P323T
-| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 4
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 0
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P40S
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| -1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 12
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 1
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R118H
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 10
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 2
 |-
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A143T
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"| 32
 | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 1
 |-
@@ Line 387: / Line 701: @@
 </figtable>
 </div>
+Since the PAM1 and the PAM250 matrices are designed for proteins of very diverse degree of kinship, 99% and ~20% relationship, respectively, those two matrices tend to give contradictory scores of how likely a substitution is. On the other hand, BLOSUM62 and PAM1, although the BLOSUM matrix was created from sequences with identity of less than 62 percent, usually provide similar predictions.
 <br style="clear:both">
 == PSSM ==
-* Getting a bit closer to evolution you will have to create a PSSM (position specific scoring matrix) for your protein sequence using PSI-BLAST (5 iterations). How conserved are the WT residues in your mutant positions? How is the frequency of occurrence (conservation) for the mutant residue type? Anything interesting?
+<figtable id="tab:pssm">
+<caption>The occurrence of the wild and mutation type according to the [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/psi_results_big.pssm pssm] generated by Psi-Blast</caption>
+{| class="wikitable sortable" style="border-spacing: 0px;"
+! style="border: 2px solid #000; border-width: 0px 2px 2px 0px;" | conservation of
+! style="border-bottom: 2px solid #000; padding: 5px;" | P40S
+! style="border-bottom: 2px solid #000; padding: 5px;" | S65T
+! style="border-bottom: 2px solid #000; padding: 5px;" | R118H
+! style="border-bottom: 2px solid #000; padding: 5px;" | A143T
+! style="border-bottom: 2px solid #000; padding: 5px;" | N215S
+! style="border-bottom: 2px solid #000; padding: 5px;" | Q279E
+! style="border-bottom: 2px solid #000; padding: 5px;" | I289V
+! style="border-bottom: 2px solid #000; padding: 5px;" | V316I
+! style="border-bottom: 2px solid #000; padding: 5px;" | P323T
+! style="border-bottom: 2px solid #000; padding: 5px;" | R356W
+|-
+| style="border-right: 2px solid #000; padding: 5px;" | wild type
+| style="padding: 5px;" | 81%
+| style="padding: 5px;" | '''16%'''
+| style="padding: 5px;" | 8%
+| style="padding: 5px;" | 11%
+| style="padding: 5px;" | 6%
+| style="padding: 5px;" | '''12%'''
+| style="padding: 5px;" | 17%
+| style="padding: 5px;" | 29%
+| style="padding: 5px;" | 15%
+| style="padding: 5px;" | 15%
+|-
+| style="border-right: 2px solid #000; padding: 0px 5px;" | mutant type
+| style="padding: 0px 5px;" | 2%
+| style="padding: 0px 5px;" | '''20%'''
+| style="padding: 0px 5px;" | 2%
+| style="padding: 0px 5px;" | 6%
+| style="padding: 0px 5px;" | 4%
+| style="padding: 0px 5px;" | '''38%'''
+| style="padding: 0px 5px;" | 11%
+| style="padding: 0px 5px;" | 19%
+| style="padding: 0px 5px;" | 7%
+| style="padding: 0px 5px;" | 4%
+|-
+|}
+</figtable>
 == Multiple sequence alignment ==
@@ Line 396: / Line 752: @@
 == Scoring methods ==
+=== SIFT ===
-* Finally, we use three different approaches to score our mutants.
+<div style="float:left; border:thin solid lightgrey; margin: 0px 0px 0px 0px;">
-** [http://sift.jcvi.org/www/SIFT_seq_submit2.html SIFT]
+<figtable id="tab:Sift">
-** [http://genetics.bwh.harvard.edu/pph2/ Polyphen2]
+<caption>Sift Scores</caption>
-** [https://rostlab.org/owiki/index.php/Snap SNAP] is installed on the VirtualBox and should be used command-line only. -- As blast is the bottleneck of SNAP, and you are doing that anyway, we might as well look at ''all'' possible substitutions in the position of our mutations. This way we can learn much more about the nature of the given mutation: Is our mutation problematic because we introduce an unwanted effect, or because the WT residue is essential and by mutating we remove that?
+{| class="wikitable sortable"  style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Prediction
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Sift Score
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 2px 0;"| Sequences represented at this position
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P40S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| AFFECT PROTEIN FUNCTION
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.00
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 41
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| S65T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| AFFECT PROTEIN FUNCTION
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 45
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R118H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| be TOLERATED
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.06
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 48
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A143T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| AFFECT PROTEIN FUNCTION
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 48
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| N215S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| AFFECT PROTEIN FUNCTION
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 48
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| Q279E
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| AFFECT PROTEIN FUNCTION
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.00
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 48
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| I289V
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| AFFECT PROTEIN FUNCTION
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.05
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 48
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| V316I
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| be TOLERATED
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.75
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 48
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P323T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| AFFECT PROTEIN FUNCTION
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 48
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R356W
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| AFFECT PROTEIN FUNCTION
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|  0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 1px 0; text-align:right"| 47
+|-
+|}
+</figtable>
+</div>
+Median sequence conservation: 2.99
+[http://sift.jcvi.org/www/SIFT_seq_submit2.html SIFT]
+<br style="clear:both">
+=== Polyphen2 ===
+<div style="float:left; border:thin solid lightgrey; margin: 0px 0px 0px 0px;">
+<figtable id="tab:Polyphen">
+<caption>Polyphen Scores</caption>
+{| class="wikitable sortable"  style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| rs ID
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Sec Struc
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Prediction
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| pph2 Class
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| pph2 Prob
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| pph2 FPR
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| pph2 TPR
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0 2px 0;"| pph2 FDR
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| Q279E
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| rs28935485
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|  probably damaging
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|        deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.983
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|     0.0387
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.745
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|     0.0657
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| N215S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| rs28935197
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      .
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|             benign
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|            neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.048
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.167
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.941
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|      0.194
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| I289V
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| ?
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|  probably damaging
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|        deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.975
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|     0.0436
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.762
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|      0.072
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| S65T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| ?
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      .
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|  probably damaging
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|        deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.995
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|     0.0277
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.681
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|     0.0521
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R356W
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| ?
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      .
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|  probably damaging
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|        deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|          1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|    0.00026
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|    0.00018
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|     0.0109
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| V316I
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| ?
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|             benign
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|            neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.308
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.113
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.904
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|      0.144
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P323T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| ?
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|  possibly damaging
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|        deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.612
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.091
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.872
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|      0.124
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P40S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| ?
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      .
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|  probably damaging
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|        deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|          1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|    0.00026
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|    0.00018
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|     0.0109
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R118H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| ?
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|             benign
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|            neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.015
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.209
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|      0.956
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|      0.229
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A143T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| ?
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|      T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|  probably damaging
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"|        deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|          1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|    0.00026
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; text-align:right"|    0.00018
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0; text-align:right"|     0.0109
+|-
+|}
+</figtable>
+</div>
+[http://genetics.bwh.harvard.edu/pph2/ Polyphen2]
+[http://genetics.bwh.harvard.edu/pph2/dokuwiki/overview#prediction]
+<br style="clear:both">
+=== SNAP ===
+<xr id="tab:snap2"/> contains the SNAP2 predictions for the ten SNPs listed in section [[#Dataset|Dataset]]. There is also a [[Fabry:Sequence-based mutation analysis/SNAP2|more comprehensive results table]] that includes the predictions for all possible single point mutations at the ten given sequence positions.
+<figtable id="tab:snap2">
+<caption>Predictions by SNAP2 of the effect of SNPs relative to the wild type</caption>
+{| class="wikitable sortable" style="border-spacing: 0px; text-align: center;"
+! style="border-bottom: 2px solid #000; padding: 0px 5px;" | Mutation
+! style="border: 1px solid #000; border-width: 0px 0px 2px 1px; padding: 0px 5px;" | Binary prediction
+! style="border: 1px solid #000; border-width: 0px 0px 2px 1px; padding: 0px 5px;" | Reliability Index
+! style="border: 1px solid #000; border-width: 0px 0px 2px 1px; padding: 0px 5px;" | Expected Accuracy
+! style="border: 1px solid #000; border-width: 0px 0px 2px 1px; padding: 0px 5px;" | Total of neutral<br>mutations at this position
+! style="border: 1px solid #000; border-width: 0px 0px 2px 1px; padding: 0px 5px;" | Total of non-neutral<br>mutations at this position
+|-
+| P40S
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 0
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 51%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 2
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 17
+|-
+| S65T
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 6
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 79%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 17
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 2
+|-
+| R118H
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Non-neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 1
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 60%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 5
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 14
+|-
+| A143T
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 7
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 85%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 18
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 1
+|-
+| N215S
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 7
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 85%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 18
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 1
+|-
+| Q279E
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 6
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 79%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 18
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 1
+|-
+| I289V
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 8
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 91%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 13
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 6
+|-
+| V316I
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 8
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 91%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 16
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 3
+|-
+| P323T
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 4
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 67%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 17
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 2
+|-
+| R356W
+| style="border-left: 1px solid #000; padding: 0px 5px;" | Non-neutral
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 5
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 75%
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 6
+| style="border-left: 1px solid #000; padding: 0px 5px;" | 13
+|-
+|}
+</figtable>
+<br style="clear:both">
 == Results and Conclusion ==
+<div style="float:left; border:thin solid lightgrey; margin: 0px 0px 20px 0px;">
-* Compare '''ALL''' results and create an overview table.
+<figtable id="tab:Overview">
-* Try to come up with a consensus between all the findings requested above.
+<caption>This table gives an overview over all features examined in the sections above. The red background color indicates a disease causing prediction, the green color a non-disease causing one. In the end all red fields are summed up for each row and the resulting value leads to our prediction given in <xr id="tab:Result"/>.<br>Used abbreviation in this table:<br> AA: Amino Acid, Pol: Side-chain polarity, Charge: Side-chain charge at pH 7.4, HI: Hydropathy index, RM: Residue Mass, iP: isoelectric point</caption>
-* Check whether you are right in the HGMD – were you able to predict a change?
+{| class="wikitable sortable"  style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in Pol
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in Charge
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in HI
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in RM
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| change in iP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc Psipred
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc Reprof
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SecStruc DSSP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Value<br>BLOSUM62
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"|Value<br>PAM1
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"|Value<br>PAM250
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Sift Score
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| pph2 Class
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNAP prediction
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 2px 3px; text-align:right"| Sum<br>bad scores
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A143T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F"| nonpolar  to<br>polar
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -2.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 30.026
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| -0.41
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 32
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 6
+|-
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R356W
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F"| polar  to<br>nonpolar
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F"| positive  to<br>neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 3.6
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 30.025
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -4.87
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| -
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 8
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| non-neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 10
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| I289V
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| -0.3
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -14.027
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| -0.05
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 33
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0.05
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 5
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| V316I
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.3
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 14.027
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.05
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| E
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 57
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.75
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 4
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R118H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F"| positive to pos(10%),<br>neutr(90%)
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 1.3
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -19.046
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -3.16
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 10
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.06
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| non-neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 9
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| N215S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 2.7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -27.026
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.27
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 20
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 7
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| Q279E
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F"| neutral  to<br>negative
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.99
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -2.5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 3
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 27
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0.00
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 7
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P40S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F"| nonpolar  to<br>polar
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.8
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -10.039
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| -0.62
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| -
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 12
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0.00
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 7
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| S65T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 14.027
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| -0.08
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 38
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 1
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 7
+|-
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P323T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F"| nonpolar  to<br>polar
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A"| none
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 0.9
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| 3.988
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| -0.7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| C
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| -2
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| 0.01
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#FCA17F; text-align:right"| deleterious
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; background-color:#C9E69A; text-align:right"| neutral
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 3px; text-align:right"| 6
+|-
+|-
+|}
+</figtable>
+</div>
+<div style="float:left; border:thin solid lightgrey; margin: 0px 20px 0px 0px;">
+<figtable id="tab:Result">
+<caption>All examined SNPs with the "sum bad score" according to <xr id="tab:Overview"/> and our resulting<br>prediction. The table also shows if the SNP truly is disease causing or not and whether our sequence<br>based prediction is true</caption>
+{| class="wikitable sortable"  style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| SNP
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 2px 0px; text-align:right"| Sum<br>bad scores
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 2px 0px; text-align:right"| Prediction
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 2px 0px; text-align:right"| True classification
+! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 2px 0px; text-align:right"| Result prediction
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A143T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 6
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Non-disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Wrong
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R356W
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 10
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Right
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| I289V
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 5
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Non-disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Non-disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Right
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| V316I
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 4
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Non-disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Non-disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Right
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| R118H
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 9
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Non-disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Wrong
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| N215S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Right
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| Q279E
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Right
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P40S
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Right
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| S65T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 7
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Right
+|-
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| P323T
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| 6
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Non-disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 1px 1px 0px; text-align:right"| Non-disease causing
+| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0px 0px 1px 0px; text-align:right"| Right
+|-
+|}
+</figtable>
+</div>
+In <xr id="tab:Overview"/> we list all afore gathered information in condensed form and highlight values that we consider as an indicator for a disease causing mutation with red color. Results contained in green colored fields are considered neutral. The summed up score of disease indicators is again shown in <xr id="tab:Result"/> along with our prediction for each SNP. Mutations with score smaller than 7 are considered neutral, greater or equal to that disease causing. Next to the prediction we show the true classification of the single nucleotide polymorphism acording to the mapping we did in [[Fabry:Annotated_SNPs |Task 6]]. We show that only two of the ten predictions are wrong, which we consider as a surprisingly good result.<br>
+<br style="clear:both">
+== References ==
+<references/>