Gaucher Disease: Task 08 - Sequence-based mutation analysis

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Revision as of 23:16, 30 August 2013 by Gerkej (talk | contribs) (Mutation Analysis)

LabJournal

Mutation Set

<figtable id="sele">

Mutations
mRNA Protein
Reference Sequence Position Codon change Codon Number Amino Acid change One letter code
rs368786234 656 AGC ⇒ AGA 77 Ser ⇒ Arg S77R
rs374003673 847 AAT ⇒ AGT 141 Asn ⇒ Ser N141S
CM880035 - CGG ⇒ CAG 159 Arg ⇒ Gln R159Q
rs374591570 1062 CTC ⇒ TTC 213 Leu ⇒ Phe L213F
CM992894 - GGA ⇒ GAA 241 Gly ⇒ Glu G241E
rs371083513 1470 GTA ⇒ ATA 349 Val ⇒ Ile V349I
CM960697 - ACG ⇒ ATG 408 Thr ⇒ Met T408M
CM880036 - AAC ⇒ AGC 409 Asn ⇒ Ser N409S
CM870010 - CTG ⇒ CCG 483 Leu ⇒ Pro L483P
CM057072 - AAC ⇒ AGC 501 Asn ⇒ Ser N501S
Information about 10 randomly selected mutations for glucocerebrosidase taken from HGMD (CM...) and dbSNP (rs...).

</figtable>

Mutation Analysis

<figtable id="ana">

Mutation Analysis
Changes of Physiochemical Properties Structural Properties Conservation
Mutation From To Pymol Visualization Secondary Structure BLOSUM62 score BLOSUM score
S77R polar, neutral charge, sulfur-containing polar, positive, basic
Mutation of serine (blue) to arginine (orange) on position 77.
E -1 6
N141S polar, neutral charge, acidic polar, neutral, sulfur-containing
Mutation of asparagine (blue) to serine (orange) on position 141.
H 1 5
R159Q polar, positive charge, basic polar, neutral, acidic
Mutation of arginine (blue) to glutamine (orange) on position 159.
E 1 5
L213F nonpolar, neutral charge, aliphatic, hydrophobic nonpolar, neutral, aromatic, hydrophobic
Mutation of leucine (blue) to phenylalanine (orange) on position 213.
E 0 13
G241E nonpolar, neutral charge, aliphatic polar, negative, acidic
Mutation of glycine (blue) to glutamic acid (orange) on position 241.
C -2 9
V349I nonpolar, neutral charge, aliphatic, hydrophobic nonpolar, neutral, aliphatic, hydrophobic
Mutation of valine (blue) to isoleucine (orange) on position 349.
E 3 4
T408M polar, neutral charge, hydroxyl-containing nonpolar, neutral, sulfur-containing
Mutation of threonine (blue) to methionine (orange) on position 408.
H -1
N409S polar, neutral charge, acidic polar, neutral, sulfur-containing
Mutation of asparagine (blue) to serine (orange) on position 409.
H 1 5
L483P nonpolar, neutral charge, aliphatic, hydrophobic nonpolar, neutral, cyclic
Mutation of serine (blue) to arginine (orange) on position 483
E -3
N501S polar, neutral charge, acidic polar, neutral, sulfur-containing
Mutation of asparagine (blue) to serine (orange) on position 501.
E 1 5
Analysis of the chosen mutations of <xr id="sele"/> in the field of their properties, secondary structure and conservation. The secondary structure can be classified as helix (H), sheet (E) and loop (C). In case a mutations is the worst possible subsitution for this amino acid, the substitution matrix score is coloured red.

</figtable>

Substitution and Phenotype

blossom

PSSM

Multiple Sequence Alignment

Comparison of different approaches

SIFT, Polyphen, Mutationtaster, SNAP -> one table

References

http://en.wikipedia.org/wiki/Amino_acid

hgmd

[GENE%20AND%20%22human%22[ORGN]%20AND%20%22snp%22[SNP_CLASS]%20&cmd=DetailsSearch dbSNP]