Gaucher Disease: Task 08 - Sequence-based mutation analysis
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 |
</figtable>
Mutation Analysis
In our analysis we looked closer to the amino acid properties and their changing characteristics by mutation. We analysed the structural difference between wild type (WT) and mutation. We also considered their secondary structure and distinguished between helix (H), sheet (E) and loop (C). We also took two different substitution matrices into account, BLOSUM62 and PAM250. Point Accepted Mutation matrix has only positiv integer values as scores and is not symmetric. The score reflects the probability of a amino acid to mutate into another. In contrast the BLOcks SUbstitution Matrix has also negativ integers and is symmetric. A positive score indicates that a substitution occurs more than random. While a score of 0 shows that the substitution occurs randomly, a negative one points to a mutation less frequent than a random mutation. In case one of our selected mutations has the worst possible substitution score for this amino acids we highlighted the score red in <xr id="ana"/>. To consider also evolutionary information we created different PSSM matrices. These position specific scoring matrices are based on alignments. Just as BLOSUM, the PSSM has positive and negative integer values as scores. A positve value shows that the substitution occurs more often than expected. Critical functional residues, like active site residues, have high positive scores. One PSSM was created with a PsiBlast search. The other one is based on an alignment consisting of all mammalian homologous sequences.
<figtable id="ana">
Mutation Analysis | ||||||||||||
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Changes of Physiochemical Properties | Structural Properties | Conservation | Interpretation | |||||||||
Mutation | From | To | Pymol Visualization | Secondary Structure | BLOSUM62 score | PAM250 score | PSSM score | PSSM WT frequency | PSSM mutatant frequency | MSA WT frequency | MSA mutant frequency | |
S77R | polar, neutral charge, sulfur-containing | polar, positive, basic | E | -1 | 6 | 1 | 11% | 9% | 64% | 2% | ||
N141S | polar, neutral charge, acidic | polar, neutral, sulfur-containing | H | 1 | 5 | 0 | 10% | 7% | 55% | 3% | ||
R159Q | polar, positive charge, basic | polar, neutral, acidic | E | 1 | 5 | -4 | 83% | 0% | 86% | 0% | ||
L213F | nonpolar, neutral charge, aliphatic, hydrophobic | nonpolar, neutral, aromatic, hydrophobic | E | 0 | 13 | 3 | 22% | 13% | 100% | 0% | ||
G241E | nonpolar, neutral charge, aliphatic | polar, negative, acidic | C | -2 | 9 | -1 | 10% | 3% | 83% | 0% | ||
V349I | nonpolar, neutral charge, aliphatic, hydrophobic | nonpolar, neutral, aliphatic, hydrophobic | E | 3 | 4 | 0 | 14% | 5% | 97% | 3% | ||
T408M | polar, neutral charge, hydroxyl-containing | nonpolar, neutral, sulfur-containing | H | -1 | 5 | -1 | 4% | 2% | 82% | 0% | ||
N409S | polar, neutral charge, acidic | polar, neutral, sulfur-containing | H | 1 | 5 | 1 | 10% | 9% | 76% | 2% | ||
L483P | nonpolar, neutral charge, aliphatic, hydrophobic | nonpolar, neutral, cyclic | E | -3 | 5 | -3 | 29% | 1% | 100% | 0% | ||
N501S | polar, neutral charge, acidic | polar, neutral, sulfur-containing | E | 1 | 5 | -2 | 87% | 3% | 86% | 1% |
</figtable>
Comparison of different approaches
<figtable id="app">
Summary of different prediction approaches | ||||||
---|---|---|---|---|---|---|
Mutation | Analysis of <xr id="ana"/> | SIFT | Polyphen2 (HumDiv) | MutationTaster | SNAP | Validation |
S77R | 0.17 | |||||
N141S | Analysis of <xr id="ana"/> | SIFT | 0.01 | MutationTaster | SNAP | Validation |
R159Q | Analysis of <xr id="ana"/> | SIFT | 1 | MutationTaster | SNAP | Validation |
L213F | Analysis of <xr id="ana"/> | SIFT | 0.79 | MutationTaster | SNAP | Validation |
G241E | Analysis of <xr id="ana"/> | SIFT | 0.89 | MutationTaster | SNAP | Validation |
V349I | Analysis of <xr id="ana"/> | SIFT | 0.12 | MutationTaster | SNAP | Validation |
T408M | Analysis of <xr id="ana"/> | SIFT | 0.11 | MutationTaster | SNAP | Validation |
N409S | Analysis of <xr id="ana"/> | SIFT | 0.23 | MutationTaster | SNAP | Validation |
L483P | Analysis of <xr id="ana"/> | SIFT | 0.85 | MutationTaster | SNAP | Validation |
N501S | Analysis of <xr id="ana"/> | SIFT | 0.98 | MutationTaster | SNAP | Validation |
</figtable>
References
http://en.wikipedia.org/wiki/Amino_acid
[GENE%20AND%20%22human%22[ORGN]%20AND%20%22snp%22[SNP_CLASS]%20&cmd=DetailsSearch dbSNP]