Difference between revisions of "Sequence-based mutation analysis (Phenylketonuria)"

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(→‎Analyze SNPs)
(→‎Analyze SNPs)
Line 58: Line 58:
 
[[File:A259V.png|thumb|right|'''<caption>''' Mutation of alanine to valine at position 259.</caption>]]
  
[[File:A259V.png|thumb|right|'''<caption>''' Mutation of alanine to valine at position 259.</caption>]]
 
</figure>
  
</figure>
  +
{| border="1"
−
*Amino acid properties: alanine is small, non-polar, neutral and hydrophobic - valine is small, aliphatic, non-polar, neutral and hydrophobic
  
  +
|-
−
*Structure: HELIX
 
  +
| Properties || alanine is small, non-polar, neutral and hydrophobic - valine is small, aliphatic, non-polar, neutral and hydrophobic
−
*Substitution Matrices: middle ranged value -> neutral substitution
 
  +
|-
−
*PSSM: Alanine seems to be highly conserved with a value of 70. Valine has a value of 1.
  
  +
|Structure || HELIX
−
*SIFT: TOLERATED with a score of 0.16
  
  +
|-
−
*PolyPhen2: probably damaging
  
  +
|Substitution Matrices || middle ranged value -> neutral substitution
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM || Alanine seems to be highly conserved with a value of 70. Valine has a value of 1.
−  
  +
|-
−
&rarr; prediction = ...
  
  +
|SIFT || TOLERATED with a score of 0.16
  +
|-
  +
|PolyPhen2 || probably damaging
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
| colspan="2" |&rarr; prediction = '''...'''
  +
|}
   
 
<br clear=all>
  
<br clear=all>
Line 75: Line 85:
 
[[File:R123I.png|thumb|right|'''<caption>''' Mutation of alanine to valine at position 259.</caption>]]
  
[[File:R123I.png|thumb|right|'''<caption>''' Mutation of alanine to valine at position 259.</caption>]]
 
</figure>
  
</figure>
  +
{| border="1"
−
*Amino acid properties: arginine is positively charged, hydrophilic and polar - isoleucine is aliphatic, neutral, non-polar and hydrophobic
  
  +
|-
−
*Substitution Matrices: low value -> bad substitution
  
  +
|Properties || arginine is positively charged, hydrophilic and polar - isoleucine is aliphatic, neutral, non-polar and hydrophobic
−
*Structure: LOOP
  
  +
|-
−
*PSSM: Arginine seems to be highly conserved with a value of 49. Isoleucine has a value of 7.
  
  +
|Substitution Matrices || low value -> bad substitution
−
*SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00
  
  +
|-
−
*PolyPhen2: possibly damaging
  
  +
|Structure ||LOOP
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM || Arginine seems to be highly conserved with a value of 49. Isoleucine has a value of 7.
−  
  +
|-
−
&rarr; prediction = non-neutral
  
  +
|SIFT || AFFECT PROTEIN FUNCTION with a score of 0.00
  +
|-
  +
|PolyPhen2 || possibly damaging
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
| colspan="2" | &rarr; prediction = '''non-neutral'''
  +
|}
   
 
===Gln-20-Leu===
  
===Gln-20-Leu===
  +
{| border="1"
−
*Amino acid properties: glutamine is neutral, polar and hydrophilic - leucine is aliphatic, neutral, non-polar and hydrophilic
 
  +
|-
−
*Substitution Matrices: low value -> bad substitution
  
  +
|Properties || glutamine is neutral, polar and hydrophilic - leucine is aliphatic, neutral, non-polar and hydrophilic
−
*Structure: LOOP
  
  +
|-
−
*PSSM: seems to be not conserved as aspartic acid has a higher value than glutamine: 17-14. Leucine has a value of 6.
  
  +
|Substitution Matrices || low value -> bad substitution
−
*SIFT: TOLERATED with a score of 0.90
  
  +
|-
−
*PolyPhen2: benign
 
  +
|Structure || LOOP
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM || seems to be not conserved as aspartic acid has a higher value than glutamine: 17-14. Leucine has a value of 6.
−  
  +
|-
−
&rarr; prediction =
  
  +
|SIFT || TOLERATED with a score of 0.90
−  
  +
|-
  +
|PolyPhen2 || benign
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
|colspan="2" | &rarr; prediction = '''...'''
  +
|}
 
===Gln-172-His===
  
===Gln-172-His===
 
<figure id="Q172H">
  
<figure id="Q172H">
 
[[File:Q172H.png|thumb|right|'''<caption>''' Mutation of glutamine to histidine at position 172.</caption>]]
  
[[File:Q172H.png|thumb|right|'''<caption>''' Mutation of glutamine to histidine at position 172.</caption>]]
 
</figure>
  
</figure>
  +
{| border="1"
−
*Amino acid properties: glutamine is neutral, polar and hydrophilic - histidine is positively charged, polar and hydrophobic
  
  +
|-
−
*Substitution Matrices:
  
  +
|Properties || glutamine is neutral, polar and hydrophilic - histidine is positively charged, polar and hydrophobic
−
*Structure:
  
  +
|-
−
*PSSM:
 
  +
|Substitution Matrices ||
−
*SIFT:
 
  +
|-
−
*PolyPhen2:
 
  +
|Structure ||
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM ||
−  
  +
|-
−
&rarr; prediction = ...
  
  +
|SIFT ||
−  
  +
|-
  +
|PolyPhen2 ||
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
| colspan="2"|&rarr; prediction = '''...'''
  +
|}
 
===Gly-103-Ser===
  
===Gly-103-Ser===
  +
{| border="1"
−
*Amino acid properties: glycine is small, neutral, non-polar and hydrophilic - serine is small, neutral, polar and hydrophilic
  
  +
|-
−
*Substitution Matrices: middle ranged value -> neutral substitution
  
  +
|Properties || glycine is small, neutral, non-polar and hydrophilic - serine is small, neutral, polar and hydrophilic
−
*Structure: HELIX
  
  +
|-
−
*PSSM: Glycine seems to be completely unconserved as every amino acid has the same value 5.
  
  +
|Substitution Matrices: middle ranged value -> neutral substitution
−
*SIFT: TOLERATED with a score of 0.05
  
  +
|-
−
*PolyPhen2: benign
 
  +
|Structure || HELIX
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM || Glycine seems to be completely unconserved as every amino acid has the same value 5.
−  
  +
|-
−
&rarr; prediction = ...
  
  +
|SIFT || TOLERATED with a score of 0.05
−  
  +
|-
  +
|PolyPhen2 || benign
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing|-
  +
|colspan="2"|&rarr; prediction = '''...'''
  +
|}
 
===Ile-421-Thr===
  
===Ile-421-Thr===
 
<figure id="I421T">
  
<figure id="I421T">
 
[[File:I421T.png|thumb|right|'''<caption>''' Mutation of isoleucine to threonine at position 421.</caption>]]
  
[[File:I421T.png|thumb|right|'''<caption>''' Mutation of isoleucine to threonine at position 421.</caption>]]
 
</figure>
  
</figure>
  +
{| border="1"
−
*Amino acid properties: isoleucine is aliphatic, neutral, non-polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
  
  +
|-
−
*Substitution Matrices: low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
 
  +
|Properties || isoleucine is aliphatic, neutral, non-polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
−
*Structure: STRAND
  
  +
|-
−
*PSSM: Isoleucine with a value of 32 seems to be not conserved as valine has a value of 41. Threonine has a value of 0.
  
  +
|Substitution Matrices || low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
−
*SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  
  +
|-
−
*PolyPhen2: probably damaging/possibly damaging
  
  +
|Structure || STRAND
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM || Isoleucine with a value of 32 seems to be not conserved as valine has a value of 41. Threonine has a value of 0.
−  
  +
|-
−
&rarr; prediction = non-neutral
  
  +
|SIFT || AFFECT PROTEIN FUNCTION with a score of 0.00.
−  
  +
|-
  +
|PolyPhen2 || probably damaging/possibly damaging
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
| colspan="2"|&rarr; prediction = '''non-neutral'''
  +
|}
 
===Lys-341-Thr===
  
===Lys-341-Thr===
 
<figure id="K341T">
  
<figure id="K341T">
 
[[File:K341T.png|thumb|right|'''<caption>''' Mutation of lysine to threonine at position 341.</caption>]]
  
[[File:K341T.png|thumb|right|'''<caption>''' Mutation of lysine to threonine at position 341.</caption>]]
 
</figure>
  
</figure>
  +
{| border="1"
−
*Amino acid properties: lysine is positively charged, polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
  
  +
|-
−
*Substitution Matrices: low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
 
  +
|Amino acid properties || lysine is positively charged, polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
−
*Structure: STRAND
  
  +
|-
−
*PSSM: Lysine seems to be conserved with a value of 39. Threonine has a value of 1.
  
  +
|Substitution Matrices || low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
−
*SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  
  +
|-
−
*PolyPhen2: probably damaging
  
  +
|Structure || STRAND
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM || Lysine seems to be conserved with a value of 39. Threonine has a value of 1.
−  
  +
|-
−
&rarr; prediction = non-neutral
  
  +
|SIFT || AFFECT PROTEIN FUNCTION with a score of 0.00.
−  
  +
|-
  +
|PolyPhen2 || probably damaging
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
|colspan="2" |&rarr; prediction = '''non-neutral'''
  +
|}
 
===Phe-392-Ser===
  
===Phe-392-Ser===
 
<figure id="F392S">
  
<figure id="F392S">
 
[[File:F392S.png|thumb|right|'''<caption>''' Mutation of phenylalanine to serine at position 392.</caption>]]
  
[[File:F392S.png|thumb|right|'''<caption>''' Mutation of phenylalanine to serine at position 392.</caption>]]
 
</figure>
  
</figure>
  +
{| border="1"
−
*Amino acid properties: phenylalanine is aromatic, neutral, non-polar and hydrophobic - serine is small, neutral, polar and hydrophilic
  
  +
|-
−
*Substitution Matrices: low value -> bad substitution
  
  +
|Properties || phenylalanine is aromatic, neutral, non-polar and hydrophobic - serine is small, neutral, polar and hydrophilic
−
*Structure: HELIX
  
  +
|-
−
*PSSM: Phenylalanine seems to be highly conserved with a value of 49. Serine has a value of 0.
  
  +
|Substitution Matrices || low value -> bad substitution
−
*Mammalian homologs:
  
  +
|-
−
*SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  
  +
|Structure || HELIX
−
*PolyPhen2: probably damaging
  
  +
|-
−
*SNAP:
  
  +
|PSSM || Phenylalanine seems to be highly conserved with a value of 49. Serine has a value of 0.
−
*MutationTaster: disease causing
  
  +
|-
−  
  +
|SIFT || AFFECT PROTEIN FUNCTION with a score of 0.00.
−
&rarr; prediction = non-neutral
  
  +
|-
−  
  +
|PolyPhen2 || probably damaging
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
|colspan="2"|&rarr; prediction = '''non-neutral'''
  +
|}
 
===Pro-416-Gln===
  
===Pro-416-Gln===
 
<figure id="P416Q">
  
<figure id="P416Q">
 
[[File:P416Q.png|thumb|right|'''<caption>''' Mutation of proline to glutamine at position 416.</caption>]]
  
[[File:P416Q.png|thumb|right|'''<caption>''' Mutation of proline to glutamine at position 416.</caption>]]
 
</figure>
  
</figure>
  +
{| border="1"
−
*Amino acid properties: proline is small, neutral, non-polar and hydrophilic - glutamine is neutral, polar and hydrophilic
  
  +
|-
−
*Substitution Matrices: low value -> bad substitution
  
  +
|Properties || proline is small, neutral, non-polar and hydrophilic - glutamine is neutral, polar and hydrophilic
−
*Structure: LOOP
  
  +
|-
−
*PSSM: Proline seems to be highly conserved with a value of 66. Glutamine has a value of 0.
  
  +
|Substitution Matrices || low value -> bad substitution
−
*SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  
  +
|-
−
*PolyPhen2: probably damaging
  
  +
|Structure || LOOP
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM || Proline seems to be highly conserved with a value of 66. Glutamine has a value of 0.
−  
  +
|-
−
&rarr; prediction = non-neutral
  
  +
|SIFT || AFFECT PROTEIN FUNCTION with a score of 0.00.
−  
  +
|-
  +
|PolyPhen2 || probably damaging
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
|colspan="2"&rarr; prediction = '''non-neutral'''
  +
|}
 
===Thr-266-Ala===
  
===Thr-266-Ala===
 
<figure id="T266A">
  
<figure id="T266A">
 
[[File:Pah_T266A.png|thumb|right|'''<caption>''' Mutation of threonine to alanine at position 266.</caption>]]
  
[[File:Pah_T266A.png|thumb|right|'''<caption>''' Mutation of threonine to alanine at position 266.</caption>]]
 
</figure>
  
</figure>
  +
{| border="1"
−
*Amino acid properties: threonine is small, neutral, polar and hydrophobic - alanine is small, non-polar, neutral and hydrophobic
  
  +
|-
−
*Substitution Matrices: middle ranged value for Blosum62 and high value for PAM1('''TODO'''PAM250: 11 neutral/high?) -> neutral or good substituion
  
  +
|Properties || threonine is small, neutral, polar and hydrophobic - alanine is small, non-polar, neutral and hydrophobic
−
*Structure: HELIX(ReProf)/LOOP(PsiPred)
  
  +
|-
−
*PSSM: Threonine seems to be conserved with a value of 43. Alanine has a value of 29.
  
  +
|Substitution Matrices || middle ranged value for Blosum62 and high value for PAM1('''TODO'''PAM250: 11 neutral/high?) -> neutral or good substituion
−
*SIFT: AFFECT PROTEIN FUNCTION with a score of 0.00.
  
  +
|-
−
*PolyPhen2: probably damaging
  
  +
|Structure || HELIX(ReProf)/LOOP(PsiPred)
−
*SNAP:
  
  +
|-
−
*MutationTaster: disease causing
  
  +
|PSSM || Threonine seems to be conserved with a value of 43. Alanine has a value of 29.
−  
  +
|-
−
&rarr; prediction = non-neutral
  
  +
|SIFT || AFFECT PROTEIN FUNCTION with a score of 0.00.
  +
|-
  +
|PolyPhen2 || probably damaging
  +
|-
  +
|SNAP ||
  +
|-
  +
|MutationTaster || disease causing
  +
|-
  +
|colspan="2"|&rarr; prediction = '''non-neutral'''
  +
|}
   
 
== Prediction ==
  
== Prediction ==

Revision as of 16:12, 2 July 2013

Summary

...

Mutation dataset

Lab journal

SNPs
AA - three letter AA - one letter Nucleotides
Ala259Val A259V C776T
Arg123Ile R123I G368T
Gln20Leu Q20L A59T
Gln172His Q172H G516T
Gly103Ser G103S G307A
Ile421Thr I421T T1262C
Lys341Thr K341T A1022C
Phe392Ser F392S T1175C
Pro416Gln P416Q C1247A
Thr266Ala T266A A796C

Analyze SNPs

Lab journal
Looking at the substitution matrices you can see that the substitutions analyzed in this task never have the worst values.
As 2pah begins at position 118 for amino acids 20 and 103 the substitutions cannot be shown with pymol.

Mammalian Homologous Sequences

We used a normal BLAST search on the mammalian database of Uniprot and filter the results per hand for double entries. Altogether we found 22 homologues sequences (<xr id="IDs"/>). <figtable id="IDs">

UniProt-IDs homologue to P00439
H2Q6R0 G3S964 G1R3M2 G7PJC2 F7HMW9 F7I717 F7BKF9
F6XY00 E2R366 G1T8B6 H2NIF5 M3YKN3 M9P0Q7 H0WTI6
M3W9R1 G3TIW0 G1LIM6 Q2KIH7 G1P4I7 P16331 M9P0Y5
UniProt IDs of the 22 mammalian homologues sequences of the PAH protein. The only ID that has a sequence that is not 100% identical to P00439 is marked in green.

</figtable>

For the creation of the multiple alignment we used clustalw. Nevertheless, only F6XY00 has a slightly different sequence. Like E2R366 F6XY00 is a homologue sequence of the human PAH in canis familiaris. On the positions of our substitutions the sequences are conserved.

Ala-259-Val

<figure id="A259V">

Mutation of alanine to valine at position 259.

</figure>

Properties alanine is small, non-polar, neutral and hydrophobic - valine is small, aliphatic, non-polar, neutral and hydrophobic
Structure HELIX
Substitution Matrices middle ranged value -> neutral substitution
PSSM Alanine seems to be highly conserved with a value of 70. Valine has a value of 1.
SIFT TOLERATED with a score of 0.16
PolyPhen2 probably damaging
SNAP
MutationTaster disease causing
→ prediction = ...


Arg-123-Ile

<figure id="R123I">

Mutation of alanine to valine at position 259.

</figure>

Properties arginine is positively charged, hydrophilic and polar - isoleucine is aliphatic, neutral, non-polar and hydrophobic
Substitution Matrices low value -> bad substitution
Structure LOOP
PSSM Arginine seems to be highly conserved with a value of 49. Isoleucine has a value of 7.
SIFT AFFECT PROTEIN FUNCTION with a score of 0.00
PolyPhen2 possibly damaging
SNAP
MutationTaster disease causing
→ prediction = non-neutral

Gln-20-Leu

Properties glutamine is neutral, polar and hydrophilic - leucine is aliphatic, neutral, non-polar and hydrophilic
Substitution Matrices low value -> bad substitution
Structure LOOP
PSSM seems to be not conserved as aspartic acid has a higher value than glutamine: 17-14. Leucine has a value of 6.
SIFT TOLERATED with a score of 0.90
PolyPhen2 benign
SNAP
MutationTaster disease causing
→ prediction = ...

Gln-172-His

<figure id="Q172H">

Mutation of glutamine to histidine at position 172.

</figure>

Properties glutamine is neutral, polar and hydrophilic - histidine is positively charged, polar and hydrophobic
Substitution Matrices
Structure
PSSM
SIFT
PolyPhen2
SNAP
MutationTaster disease causing
→ prediction = ...

Gly-103-Ser

Properties glycine is small, neutral, non-polar and hydrophilic - serine is small, neutral, polar and hydrophilic
Substitution Matrices: middle ranged value -> neutral substitution
Structure HELIX
PSSM Glycine seems to be completely unconserved as every amino acid has the same value 5.
SIFT TOLERATED with a score of 0.05
PolyPhen2 benign
SNAP
MutationTaster - → prediction = ...

Ile-421-Thr

<figure id="I421T">

Mutation of isoleucine to threonine at position 421.

</figure>

Properties isoleucine is aliphatic, neutral, non-polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
Substitution Matrices low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
Structure STRAND
PSSM Isoleucine with a value of 32 seems to be not conserved as valine has a value of 41. Threonine has a value of 0.
SIFT AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2 probably damaging/possibly damaging
SNAP
MutationTaster disease causing
→ prediction = non-neutral

Lys-341-Thr

<figure id="K341T">

Mutation of lysine to threonine at position 341.

</figure>

Amino acid properties lysine is positively charged, polar and hydrophobic - threonine is small, neutral, polar and hydrophobic
Substitution Matrices low value for Blosum62, middle ranged value for PAM1/250 -> bad or neutral substitution
Structure STRAND
PSSM Lysine seems to be conserved with a value of 39. Threonine has a value of 1.
SIFT AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2 probably damaging
SNAP
MutationTaster disease causing
→ prediction = non-neutral

Phe-392-Ser

<figure id="F392S">

Mutation of phenylalanine to serine at position 392.

</figure>

Properties phenylalanine is aromatic, neutral, non-polar and hydrophobic - serine is small, neutral, polar and hydrophilic
Substitution Matrices low value -> bad substitution
Structure HELIX
PSSM Phenylalanine seems to be highly conserved with a value of 49. Serine has a value of 0.
SIFT AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2 probably damaging
SNAP
MutationTaster disease causing
→ prediction = non-neutral

Pro-416-Gln

<figure id="P416Q">

Mutation of proline to glutamine at position 416.

</figure>

Properties proline is small, neutral, non-polar and hydrophilic - glutamine is neutral, polar and hydrophilic
Substitution Matrices low value -> bad substitution
Structure LOOP
PSSM Proline seems to be highly conserved with a value of 66. Glutamine has a value of 0.
SIFT AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2 probably damaging
SNAP
MutationTaster disease causing
colspan="2"→ prediction = non-neutral

Thr-266-Ala

<figure id="T266A">

Mutation of threonine to alanine at position 266.

</figure>

Properties threonine is small, neutral, polar and hydrophobic - alanine is small, non-polar, neutral and hydrophobic
Substitution Matrices middle ranged value for Blosum62 and high value for PAM1(TODOPAM250: 11 neutral/high?) -> neutral or good substituion
Structure HELIX(ReProf)/LOOP(PsiPred)
PSSM Threonine seems to be conserved with a value of 43. Alanine has a value of 29.
SIFT AFFECT PROTEIN FUNCTION with a score of 0.00.
PolyPhen2 probably damaging
SNAP
MutationTaster disease causing
→ prediction = non-neutral

Prediction

SNP-Prediction
SNP Prediction Validation
Ala259Val
Arg123Ile non-neutral ?
Gln20Leu
Gly103Ser
His64Asn non-neutral ?
Ile421Thr non-neutral ?
Lys341Thr non-neutral correct
Phe392Ser non-neutral ?
Pro416Gln non-neutral correct
Thr266Ala non-neutral correct

References

<references/>

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