Sequence-based mutation analysis Gaucher Disease
From Bioinformatikpedia
The aim of this task was to carry out a thorough analysis of ten mutations and to classify them as disease-causing and non-disease causing. The mutations have been selected by another group from our [Researching SNPs Gaucher Disease|set of collected mutations] such that their impact had been unknown for us prior to this task. Technical details are reported in our protocol.
Contents
Mutations
<figtable id="tab:mutations">
| Nr | Position | From | To |
|---|---|---|---|
| 1 | 99 | H | R |
| 2 | 211 | V | I |
| 3 | 150 | E | K |
| 4 | 236 | L | P |
| 5 | 248 | W | R |
| 6 | 509 | L | P |
| 7 | 351 | W | C |
| 8 | 423 | A | D |
| 9 | 482 | D | N |
| 10 | 83 | R | S |
Randomly selected mutations from HGMD and dbSNP which were used for the sequence-based mutation analysis. </figtable>
Physicochemical properties
<figtable id="tab:props">
| Nr | Wildtype | Mutant | Severe change | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| AA | Charge | Polarity | Size | Aromatic | AA | Charge | Polarity | Size | Aromatic | ||
| 1 | H | negative | polar | large | no | R | negative | polar | large | no | no |
| 2 | V | neutral | unpolar | medium | no | I | neutral | unpolar | medium | no | no |
| 3 | E | positive | polar | large | no | K | negative | polar | large | no | yes |
| 4 | L | neutral | unpolar | medium | no | P | neutral | unpolar | medium | no | no |
| 5 | W | neutral | unpolar | large | yes | R | negative | polar | large | no | yes |
| 6 | L | neutral | unpolar | medium | no | P | neutral | unpolar | medium | no | no |
| 7 | W | neutral | unpolar | large | yes | C | neutral | polar | small | no | yes |
| 8 | A | neutral | unpolar | small | no | D | positive | polar | medium | no | yes |
| 9 | D | positive | polar | medium | no | N | neutral | polar | medium | no | no |
| 10 | R | negative | polar | large | no | S | neutral | polar | small | no | no |
Physicochemical properiets of the wildtype and mutatant amino acid which were used to classify the mutation as severe or non-severe. </figtable>
Structural analysis
<figtable id="tab:structure">
| Nr | Mutation | Accessibility | 2nd structure | Domain region | Mutation |
|---|---|---|---|---|---|
| 1 | H99R | exposed | C | no | 
|
| 2 | V211I | exposed | C | no | 
|
| 3 | E150K | exposed | C | no | 
|
| 4 | L236P | exposed | C | no | 
|
| 5 | W248R | buried | H | yes | 
|
| 6 | L509P | exposed | S | yes | 
|
| 7 | W351C | exposed | S | yes | 
|
| 8 | A423D | buried | C | yes | 
|
| 9 | D482N | exposed | C | yes | 
|
| 10 | R83S | exposed | C | yes | 
|
Location of mutations in 2nt0_A. Blue: wildtype; Red: mutant. </figtable>
<figure id="fig:structure_all">
</figure>
Substitution scores
BLOSUM62 scores
The scores were taken from the BLOSUM62 matrix.
<figtable id="tab:subst_blosum">
| Nr | Mutation | Score mutation | Score min | Score max |
|---|---|---|---|---|
| 1 | H99R | 0 | -3 | 8 |
| 2 | V211I | 3 | -3 | 4 |
| 3 | E150K | 1 | -4 | 5 |
| 4 | L236P | -3 | -4 | 4 |
| 5 | W248R | -3 | -4 | 11 |
| 6 | L509P | -3 | -4 | 4 |
| 7 | W351C | -2 | -4 | 11 |
| 8 | A423D | -2 | -3 | 4 |
| 9 | D482N | 1 | -4 | 6 |
| 10 | R83S | -1 | -3 | 5 |
BLOSUM62 scores of the selected mutations </figtable>
PSSM of all hits
PSSM.
<figtable id="tab:subst_pssm_all">
| Nr | Mutation | Score mutation | Score min | Score max | Conservation |
|---|---|---|---|---|---|
| 1 | H99R | 0 | -4 | 2 | |
| 2 | V211I | 4 | -4 | 4 | |
| 3 | E150K | 0 | -4 | 5 | |
| 4 | L236P | 0 | -3 | 1 | |
| 5 | W248R | -2 | -3 | 4 | |
| 6 | L509P | -6 | -6 | 4 | |
| 7 | W351C | -3 | -6 | 9 | |
| 8 | A423D | -3 | -3 | 3 | |
| 9 | D482N | 4 | -4 | 4 | |
| 10 | R83S | 0 | -3 | 2 | |
Position specific substitution scores derived from all significant hits after 5 rounds PSI-BLAST. </figtable>
Scoring Mutants
SIFT
The predicted results from SIFT Blink is shown here:
Substitution at pos 83 from R to S is predicted to be TOLERATED with a score of 0.17. Median sequence conservation: 2.12 Sequences represented at this position:77 Substitution at pos 99 from H to R is predicted to be TOLERATED with a score of 0.64. Median sequence conservation: 2.14 Sequences represented at this position:80 Substitution at pos 150 from E to K is predicted to be TOLERATED with a score of 0.76. Median sequence conservation: 2.10 Sequences represented at this position:86 Substitution at pos 211 from V to I is predicted to be TOLERATED with a score of 0.56. Median sequence conservation: 2.09 Sequences represented at this position:86 Substitution at pos 236 from L to P is predicted to AFFECT PROTEIN FUNCTION with a score of 0.02. Median sequence conservation: 2.09 Sequences represented at this position:86 Substitution at pos 248 from W to R is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 2.09 Sequences represented at this position:86 Substitution at pos 351 from W to C is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 2.10 Sequences represented at this position:87 Substitution at pos 423 from A to D is predicted to AFFECT PROTEIN FUNCTION with a score of 0.01. Median sequence conservation: 2.10 Sequences represented at this position:85 Substitution at pos 482 from D to N is predicted to be TOLERATED with a score of 0.69. Median sequence conservation: 2.18 Sequences represented at this position:66 Substitution at pos 509 from L to P is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 2.10 Sequences represented at this position:79
The predicted results from SIFT is shown here:
Substitution at pos 83 from R to S is predicted to AFFECT PROTEIN FUNCTION with a score of 0.05. Median sequence conservation: 3.10 Sequences represented at this position:15 Substitution at pos 99 from H to R is predicted to be TOLERATED with a score of 0.74. Median sequence conservation: 3.11 Sequences represented at this position:14 Substitution at pos 150 from E to K is predicted to be TOLERATED with a score of 0.44. Median sequence conservation: 3.10 Sequences represented at this position:16 Substitution at pos 211 from V to I is predicted to be TOLERATED with a score of 1.00. Median sequence conservation: 3.10 Sequences represented at this position:16 Substitution at pos 236 from L to P is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.10 Sequences represented at this position:16 Substitution at pos 248 from W to R is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.10 Sequences represented at this position:16 Substitution at pos 351 from W to C is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.10 Sequences represented at this position:16 Substitution at pos 423 from A to D is predicted to AFFECT PROTEIN FUNCTION with a score of 0.01. Median sequence conservation: 3.10 Sequences represented at this position:16 Substitution at pos 482 from D to N is predicted to be TOLERATED with a score of 0.77. Median sequence conservation: 3.10 Sequences represented at this position:16 Substitution at pos 509 from L to P is predicted to AFFECT PROTEIN FUNCTION with a score of 0.01. Median sequence conservation: 3.11 Sequences represented at this position:14
Polyphen2
H99R This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00) This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00) V211I This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00) This mutation is predicted to be benign with a score of 0.001 (sensitivity: 0.99; specificity: 0.09) E150K This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00) This mutation is predicted to be benign with a score of 0.001 (sensitivity: 0.99; specificity: 0.09) L236P This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) W248R This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) This mutation is predicted to be probably damaging with a score of 0.999 (sensitivity: 0.09; specificity: 0.99) L509P This mutation is predicted to be probably damaging with a score of 0.992 (sensitivity: 0.70; specificity: 0.97) This mutation is predicted to be probably damaging with a score of 0.988 (sensitivity: 0.53; specificity: 0.95) W351C This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) A423D This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.36; specificity: 0.97) D482N This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00) his mutation is predicted to be benign with a score of 0.002 (sensitivity: 0.99; specificity: 0.18) R83S This mutation is predicted to be benign with a score of 0.007 (sensitivity: 0.96; specificity: 0.75) This mutation is predicted to be benign with a score of 0.019 (sensitivity: 0.95; specificity: 0.55)
