Gaucher Disease: Task 08 - Sequence-based mutation analysis
From Bioinformatikpedia
Contents
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
<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 | E | -1 | |||
N141S | polar, neutral charge, acidic | polar, neutral, sulfur-containing | H | 1 | |||
R159Q | polar, positive charge, basic | polar, neutral, acidic | E | 1 | |||
L213F | nonpolar, neutral charge, aliphatic, hydrophobic | nonpolar, neutral, aromatic, hydrophobic | E | 0 | |||
G241E | nonpolar, neutral charge, aliphatic | polar, negative, acidic | C | -2 | |||
V349I | nonpolar, neutral charge, aliphatic, hydrophobic | nonpolar, neutral, aliphatic, hydrophobic | E | 3 | |||
T408M | polar, neutral charge, hydroxyl-containing | nonpolar, neutral, sulfur-containing | H | -1 | |||
N409S | polar, neutral charge, acidic | polar, neutral, sulfur-containing | H | 1 | |||
L483P | nonpolar, neutral charge, aliphatic, hydrophobic | nonpolar, neutral, cyclic | E | ||||
N501S | polar, neutral charge, acidic | polar, neutral, sulfur-containing | E | 1 | -3 |
</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
[GENE%20AND%20%22human%22[ORGN]%20AND%20%22snp%22[SNP_CLASS]%20&cmd=DetailsSearch dbSNP]