Difference between revisions of "Lab Journal - Task 8 (PAH)"

From Bioinformatikpedia
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===Mutation dataset===
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==Mutation dataset==
 
For the generation of the mutation dataset the following five SNPs from the [http://www.hgmd.org/ HGMD] database were used (25th June 2013):
 
For the generation of the mutation dataset the following five SNPs from the [http://www.hgmd.org/ HGMD] database were used (25th June 2013):
 
<figtable id="mutds_hgmd">
  
<figtable id="mutds_hgmd">
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</figtable>
  
</figtable>
  +
  +
==SIFT==
  +
*A259V
  +
*R123I
  +
*Q20L
  +
*G103S
  +
*H64N
  +
*I421T
  +
*K341T
  +
*F392S
  +
*P416Q
  +
*T266A
  +
  +
==PolyPhen2==
  +
*A259V
  +
'''HumDiv'''<br>
  +
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)<br>
  +
'''HumVar'''<br>
  +
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
  +
*R123I
  +
*Q20L
  +
*G103S
  +
*H64N
  +
*I421T
  +
*K341T
  +
*F392S
  +
*P416Q
  +
*T266A
  +
==SNAP==
  +
*A259V
  +
*R123I
  +
*Q20L
  +
*G103S
  +
*H64N
  +
*I421T
  +
*K341T
  +
*F392S
  +
*P416Q
  +
*T266A
  +
==MutationTaster==
  +
*A259V
  +
*R123I
  +
*Q20L
  +
*G103S
  +
*H64N
  +
*I421T
  +
*K341T
  +
*F392S
  +
*P416Q
  +
*T266A

Revision as of 10:11, 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
  • R123I
  • Q20L
  • G103S
  • H64N
  • I421T
  • K341T
  • F392S
  • P416Q
  • T266A

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
  • Q20L
  • G103S
  • H64N
  • I421T
  • K341T
  • F392S
  • P416Q
  • T266A

SNAP

  • A259V
  • R123I
  • Q20L
  • G103S
  • H64N
  • I421T
  • K341T
  • F392S
  • P416Q
  • T266A

MutationTaster

  • A259V
  • R123I
  • Q20L
  • G103S
  • H64N
  • I421T
  • K341T
  • F392S
  • P416Q
  • T266A
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