Difference between revisions of "Task 5: Researching SNPs"

From Bioinformatikpedia
(SNPdbe)
(OMIM)
Line 22: Line 22:
 
= SNPedia =
 
= SNPedia =
 
= OMIM =
 
= OMIM =
  +
OMIM contains several entries for BCKDHA( obda_human ), all leading to MSUD
  +
<table border=1>
  +
<tr><td>OMIM - BCKDHA</td></tr>
  +
<tr><td>Mutation</td><td>Phenotype</td></tr>
  +
<tr><td>Y393ASN</td><td>MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA</td></tr>
  +
<tr><td>deletion(8) 887-894</td><td>MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA</td></tr>
  +
<tr><td>G245R</td><td>MAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA</td></tr>
  +
<tr><td>F364C</td><td>MAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA</td></tr>
  +
<tr><td>R220W</td><td>MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA</td></tr>
  +
<tr><td>G204S</td><td>MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA</td></tr>
  +
<tr><td>T265R</td><td>MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA</td></tr>
  +
<tr><td>C219W</td><td>MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA</td></tr>
  +
<tr><td>deletion(1) 117C</td><td>MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA</td></tr>
  +
</table>
   
 
= mutationmap =
 
= mutationmap =

Revision as of 17:05, 5 June 2012

In this task we are to research SNPs associated with our protein obda_human, in different databases.

HGMD

HGMD - Human Gene Mutation Database HGMD represents a collection of published mutations. This means HGMD contains only mutations leading to a disease. In our case publications between 1993-2008 are covered. The sequences and a list of all listed mutations can be found in the protocol-msud-task5 protocol

HGMD - BCKDHA (non-profit)
Mutation typenumber of entries
Missense/nonsense36
small deletions3
small insertions1
Gross deletions2
complex rearrangements1

dbSNP

SNPdbe

As SNPdbe contains predicted and experimental SNPs, we first have to parse the output of the database search. The list of all mutations can be found in the Protocol-msud-task5 protocol Unfortunately we only found not validated SNPs. Among those, 8 leading to MSUP.

SNPedia

OMIM

OMIM contains several entries for BCKDHA( obda_human ), all leading to MSUD

OMIM - BCKDHA
MutationPhenotype
Y393ASNMAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA
deletion(8) 887-894MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA
G245RMAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA
F364CMAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA
R220WMAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA
G204SMAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA
T265RMAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA
C219WMAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA
deletion(1) 117CMAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA

mutationmap