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 type | number of entries |
Missense/nonsense | 36 |
small deletions | 3 |
small insertions | 1 |
Gross deletions | 2 |
complex rearrangements | 1 |
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 | |
Mutation | Phenotype |
Y393ASN | MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA |
deletion(8) 887-894 | MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA |
G245R | MAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA |
F364C | MAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA |
R220W | MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA |
G204S | MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA |
T265R | MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA |
C219W | MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA |
deletion(1) 117C | MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA |