Difference between revisions of "Lab Journal - Task 8 (PAH)"
From Bioinformatikpedia
(→PolyPhen2) |
(→PolyPhen2) |
||
| Line 96: | Line 96: | ||
==PolyPhen2== |
==PolyPhen2== |
||
*A259V |
*A259V |
||
| − | '''HumDiv''' |
+ | '''HumDiv''' |
| − | 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) |
| − | '''HumVar''' |
+ | '''HumVar''' |
| − | 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) |
*R123I |
*R123I |
||
| − | HumDiv |
+ | '''HumDiv''' |
This mutation is predicted to be possibly damaging with a score of 0.807 (sensitivity: 0.84; specificity: 0.93) |
This mutation is predicted to be possibly damaging with a score of 0.807 (sensitivity: 0.84; specificity: 0.93) |
||
| − | HumVar |
+ | '''HumVar''' |
This mutation is predicted to be possibly damaging with a score of 0.582 (sensitivity: 0.81; specificity: 0.83) |
This mutation is predicted to be possibly damaging with a score of 0.582 (sensitivity: 0.81; specificity: 0.83) |
||
*Q20L |
*Q20L |
||
| − | HumDiv |
+ | '''HumDiv''' |
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) |
||
| − | HumVar |
+ | '''HumVar''' |
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) |
||
*G103S |
*G103S |
||
| − | HumDiv |
+ | '''HumDiv''' |
This mutation is predicted to be benign with a score of 0.003 (sensitivity: 0.98; specificity: 0.44) |
This mutation is predicted to be benign with a score of 0.003 (sensitivity: 0.98; specificity: 0.44) |
||
| − | HumVar |
+ | '''HumVar''' |
This mutation is predicted to be benign with a score of 0.006 (sensitivity: 0.97; specificity: 0.45) |
This mutation is predicted to be benign with a score of 0.006 (sensitivity: 0.97; specificity: 0.45) |
||
*H64N |
*H64N |
||
| − | HumDiv |
+ | '''HumDiv''' |
This mutation is predicted to be probably damaging with a score of 0.993 (sensitivity: 0.70; specificity: 0.97) |
This mutation is predicted to be probably damaging with a score of 0.993 (sensitivity: 0.70; specificity: 0.97) |
||
| − | HumVar |
+ | '''HumVar''' |
This mutation is predicted to be probably damaging with a score of 0.962 (sensitivity: 0.62; specificity: 0.92) |
This mutation is predicted to be probably damaging with a score of 0.962 (sensitivity: 0.62; specificity: 0.92) |
||
*I421T |
*I421T |
||
| − | HumDiv |
+ | '''HumDiv''' |
This mutation is predicted to be possibly damaging with a score of 0.667 (sensitivity: 0.86; specificity: 0.91) |
This mutation is predicted to be possibly damaging with a score of 0.667 (sensitivity: 0.86; specificity: 0.91) |
||
| − | HumVar |
+ | '''HumVar''' |
This mutation is predicted to be probably damaging with a score of 0.913 (sensitivity: 0.69; specificity: 0.90) |
This mutation is predicted to be probably damaging with a score of 0.913 (sensitivity: 0.69; specificity: 0.90) |
||
*K341T |
*K341T |
||
| − | HumDiv |
+ | '''HumDiv''' |
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) |
||
| − | HumVar |
+ | '''HumVar''' |
This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.36; specificity: 0.97) |
This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.36; specificity: 0.97) |
||
*F392S |
*F392S |
||
| − | HumDiv |
+ | '''HumDiv''' |
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) |
||
| − | HumVar |
+ | '''HumVar''' |
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) |
||
*P416Q |
*P416Q |
||
| − | HumDiv |
+ | '''HumDiv''' |
This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.55; specificity: 0.98) |
This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.55; specificity: 0.98) |
||
| − | HumVar |
+ | '''HumVar''' |
This mutation is predicted to be probably damaging with a score of 0.985 (sensitivity: 0.55; specificity: 0.94) |
This mutation is predicted to be probably damaging with a score of 0.985 (sensitivity: 0.55; specificity: 0.94) |
||
*T266A |
*T266A |
||
| − | HumDiv |
+ | '''HumDiv''' |
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) |
||
| − | HumVar |
+ | '''HumVar''' |
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) |
||
Revision as of 10:22, 27 June 2013
Mutation dataset
For the generation of the mutation dataset the following five SNPs from the HGMD database were used (25th June 2013): <figtable id="mutds_hgmd">
| Missense mutations (SNPs) from HGMD | ||||||
|---|---|---|---|---|---|---|
| Accession Number | Codon change | Sequence position | Amino acid change | Codon number | Disease | Reference |
| CM000542 | CAG⇒CTG | 59 | Gln(Q)-Leu(L) | 20 | Hyperphenylalaninaemia | Hennermann (2000) Hum Mutat 15, 254 |
| CM045080 | GGT⇒AGT | 307 | Gly(G)-Ser(S) | 103 | Phenylketonuria | Lee (2004) J Hum Genet 49, 617 |
| CM910286 | GCC⇒GTC | 776 | Ala(A)-Val(V) | 259 | Phenylketonuria | Labrune (1991) Am J Hum Genet 48, 1115 |
| CM010981 | AAG⇒ACG | 1022 | Lys(K)-Thr(T) | 341 | Phenylketonuria | Tyfield (1997) Am J Hum Genet 60, 388 |
| CM090791 | CCA⇒CAA | 1247 | Pro(P)-Gln(Q) | 416 | Hyperphenylalaninaemia | Dobrowolski (2009) J Inherit Metab Dis 32, 10 |
</figtable>
Furthermore, the following five mutations from dbSNP were added (25th June 2013):
<figtable id="mutds_dbSNP">
| Missense mutations (SNPs) from dbSNP | |||||
|---|---|---|---|---|---|
| Reference SNP | Codon change | Sequence position | Amino acid change | Codon number | Disease |
| rs199475569 | CAC⇒AAC | 190 | His(H)-Asn(N) | 64 | ? |
| rs199475681 | AGA⇒ATA | 368 | Arg(R)-Ile(I) | 123 | ? |
| rs62508752 | ACA⇒CCA | 796 | Thr(T)-Ala(A) | 266 | Phenylketonuria |
| rs199475695 | TTT⇒TCT | 1175 | Phe(F)-Ser(S) | 392 | ? |
| rs199475696 | ATT⇒ACT | 1262 | Ile(I)-Thr(T) | 421 | ? |
</figtable>
SIFT
- A259V
Substitution at pos 20 from Q to L is predicted to be TOLERATED with a score of 0.16. Median sequence conservation: 3.20 Sequences represented at this position:42
- R123I
Substitution at pos 64 from H to N is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:77
- Q20L
Substitution at pos 103 from G to S is predicted to be TOLERATED with a score of 0.90. Median sequence conservation: 3.02 Sequences represented at this position:72
- G103S
Substitution at pos 123 from R to I is predicted to be TOLERATED with a score of 0.05. Median sequence conservation: 3.01 Sequences represented at this position:76
- H64N
Substitution at pos 259 from A to V is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:77
- I421T
Substitution at pos 266 from T to A is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:77
- K341T
Substitution at pos 341 from K to T is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:77
- F392S
Substitution at pos 392 from F to S is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.01 Sequences represented at this position:77
- P416Q
Substitution at pos 416 from P to Q is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.00 Sequences represented at this position:74
- T266A
Substitution at pos 421 from I to T is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00. Median sequence conservation: 3.00 Sequences represented at this position:74
PolyPhen2
- A259V
HumDiv This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) HumVar This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
- R123I
HumDiv This mutation is predicted to be possibly damaging with a score of 0.807 (sensitivity: 0.84; specificity: 0.93) HumVar This mutation is predicted to be possibly damaging with a score of 0.582 (sensitivity: 0.81; specificity: 0.83)
- Q20L
HumDiv This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00) HumVar This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00)
- G103S
HumDiv This mutation is predicted to be benign with a score of 0.003 (sensitivity: 0.98; specificity: 0.44) HumVar This mutation is predicted to be benign with a score of 0.006 (sensitivity: 0.97; specificity: 0.45)
- H64N
HumDiv This mutation is predicted to be probably damaging with a score of 0.993 (sensitivity: 0.70; specificity: 0.97) HumVar This mutation is predicted to be probably damaging with a score of 0.962 (sensitivity: 0.62; specificity: 0.92)
- I421T
HumDiv This mutation is predicted to be possibly damaging with a score of 0.667 (sensitivity: 0.86; specificity: 0.91) HumVar This mutation is predicted to be probably damaging with a score of 0.913 (sensitivity: 0.69; specificity: 0.90)
- K341T
HumDiv This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) HumVar This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.36; specificity: 0.97)
- F392S
HumDiv This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) HumVar This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
- P416Q
HumDiv This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.55; specificity: 0.98) HumVar This mutation is predicted to be probably damaging with a score of 0.985 (sensitivity: 0.55; specificity: 0.94)
- T266A
HumDiv This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00) HumVar This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
SNAP
- A259V
- R123I
- Q20L
- G103S
- H64N
- I421T
- K341T
- F392S
- P416Q
- T266A
MutationTaster
- A259V
- R123I
- Q20L
- G103S
- H64N
- I421T
- K341T
- F392S
- P416Q
- T266A
