Difference between revisions of "Protocol-msud-task5 protocol"
From Bioinformatikpedia
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= SNPdbe = |
= SNPdbe = |
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<table border=1> |
<table border=1> |
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+ | <table border=1> |
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− | <tr><td>Mutation </td><td> Experimental evidence </td><td> Pssm wt </td></tr> |
||
− | <tr><td> |
+ | <tr><td>Mutation </td><td> Experimental evidence </td><td> Disease </td></tr> |
− | <tr><td> |
+ | <tr><td>V3G</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>L17F</td><td>Not validated</td><td> |
+ | <tr><td>L17F</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>L17F</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>G29E</td><td>Not validated</td><td> |
+ | <tr><td>G29E</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>G29E</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>S36A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>P39H</td><td>Not validated</td><td> |
+ | <tr><td>P39H</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>P39H</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>Q42R</td><td>Not validated</td><td> |
+ | <tr><td>Q42R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Q42R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>A59V</td><td>Not validated</td><td> |
+ | <tr><td>A59V</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>A59V</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>I62M</td><td>Not validated</td><td> |
+ | <tr><td>I62M</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>I62M</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>N71S</td><td>Not validated</td><td> |
+ | <tr><td>N71S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>N71S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>M82I</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>M82L</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>M82I</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>M82L</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>R117C</td><td>Not validated</td><td> |
+ | <tr><td>R117C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R117C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>R127W</td><td>Not validated</td><td> |
+ | <tr><td>R127W</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R127W</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>N150D</td><td>Not validated</td><td> |
+ | <tr><td>N150D</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>N150D</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>T151M</td><td>Not validated</td><td> |
+ | <tr><td>T151M</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>T151M</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Q157A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Y158A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R159W</td><td>Not validated</td><td>maple syrup urine disease type ia (SwissVar)</td></tr> |
− | <tr><td> |
+ | <tr><td>R159A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>P170S</td><td>Not validated</td><td> |
+ | <tr><td>P170S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>P170S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Q190K</td><td>Not validated</td><td>maple syrup urine disease type ia (SwissVar)</td></tr> |
− | <tr><td>R200C</td><td>Not validated</td><td> |
+ | <tr><td>R200C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R200C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>S207A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>L209A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>T211A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>T211M</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>A222T</td><td>Not validated</td><td> |
+ | <tr><td>A222T</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>A222T</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>E238A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>G244R</td><td>Not validated</td><td> |
+ | <tr><td>G244R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>G244R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>A248D</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>G249S</td><td>Not validated</td><td> |
+ | <tr><td>G249S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>G249S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>A253T</td><td>Not validated</td><td> |
+ | <tr><td>A253T</td><td>Not validated</td><td>maple syrup urine disease type ia (SwissVar)</td></tr> |
− | <tr><td> |
+ | <tr><td>A253T</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>A254D</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>C264W</td><td>Not validated</td><td> |
+ | <tr><td>C264W</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>C264W</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td>R265W</td><td>Not validated</td><td> |
+ | <tr><td>R265W</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R265W</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R265K</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R265A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>N267S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Y269A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>A285P</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>G289R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>G290R</td><td>Not validated</td><td>maple syrup urine disease type ia (SwissVar)</td></tr> |
− | <tr><td> |
+ | <tr><td>R296C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R297C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Y306H</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Y307H</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>T309R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>T310R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R313Q</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R314Q</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>I326T</td><td>Not validated</td><td>maple syrup urine disease type ia (SwissVar)</td></tr> |
− | <tr><td> |
+ | <tr><td>H336A</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>S337D</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>A343V</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>A344V</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R345C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>S346L</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R346C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>S347L</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>W354F</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Q356R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Q357R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>I360V</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>I361V</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>E397K</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>E398K</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R398Q</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R399Q</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>P402R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>P403R</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>N403S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>N404S</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>F408C</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>F409C</td><td>Not validated</td><td>maple syrup urine disease type ia (SwissVar)</td></tr> |
− | <tr><td> |
+ | <tr><td>Y413C</td><td>Not validated</td><td>maple syrup urine disease type ia (SwissVar)</td></tr> |
− | <tr><td> |
+ | <tr><td>Q423K</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Q424K</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R428H</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>R429H</td><td>Not validated</td><td>N/A</td></tr> |
− | <tr><td> |
+ | <tr><td>Y437N</td><td>Not validated</td><td>N/A</td></tr> |
+ | <tr><td>Y438N</td><td>Not validated</td><td>maple syrup urine disease type ia (SwissVar)</td></tr> |
||
</table> |
</table> |
Revision as of 16:49, 5 June 2012
HGMD
sequence used by HGMD can be found [here]
>gi|38372929|ref|NM_000709.2| Homo sapiens branched chain keto acid dehydrogenase E1, alpha polypeptide (BCKDHA), mRNA GCCGGACCGCTGAGTGGTTGTTAGCCAAGATGGCGGTAGCGATCGCTGCAGCGAGGGTCTGGCGGCTAAA CCGTGGTTTGAGCCAGGCTGCCCTCCTGCTGCTGCGGCAGCCTGGGGCTCGGGGACTGGCTAGATCTCAC CCCCCCAGGCAGCAGCAGCAGTTTTCATCTCTGGATGACAAGCCCCAGTTCCCAGGGGCCTCGGCGGAGT TTATAGATAAGTTGGAATTCATCCAGCCCAACGTCATCTCTGGAATCCCCATCTACCGCGTCATGGACCG GCAAGGCCAGATCATCAACCCCAGCGAGGACCCCCACCTGCCGAAGGAGAAGGTGCTGAAGCTCTACAAG AGCATGACACTGCTTAACACCATGGACCGCATCCTCTATGAGTCTCAGCGGCAGGGCCGGATCTCCTTCT ACATGACCAACTATGGTGAGGAGGGCACGCACGTGGGGAGTGCCGCCGCCCTGGACAACACGGACCTGGT GTTTGGCCAGTACCGGGAGGCAGGTGTGCTGATGTATCGGGACTACCCCCTGGAACTATTCATGGCCCAG TGCTATGGCAACATCAGTGACTTGGGCAAGGGGCGCCAGATGCCTGTCCACTACGGCTGCAAGGAACGCC ACTTCGTCACTATCTCCTCTCCACTGGCCACGCAGATCCCTCAGGCGGTGGGGGCGGCGTACGCAGCCAA GCGGGCCAATGCCAACAGGGTCGTCATCTGTTACTTCGGCGAGGGGGCAGCCAGTGAGGGGGACGCCCAT GCCGGCTTCAACTTCGCTGCCACACTTGAGTGCCCCATCATCTTCTTCTGCCGGAACAATGGCTACGCCA TCTCCACGCCCACCTCTGAGCAGTATCGCGGCGATGGCATTGCAGCACGAGGCCCCGGGTATGGCATCAT GTCAATCCGCGTGGATGGTAATGATGTGTTTGCCGTATACAACGCCACAAAGGAGGCCCGACGGCGGGCT GTGGCAGAGAACCAGCCCTTCCTCATCGAGGCCATGACCTACAGGATCGGGCACCACAGCACCAGTGACG ACAGTTCAGCGTACCGCTCGGTGGATGAGGTCAATTACTGGGATAAACAGGACCACCCCATCTCCCGGCT GCGGCACTATCTGCTGAGCCAAGGCTGGTGGGATGAGGAGCAGGAGAAGGCCTGGAGGAAGCAGTCCCGC AGGAAGGTGATGGAGGCCTTTGAGCAGGCCGAGCGGAAGCCCAAACCCAACCCCAACCTACTCTTCTCAG ACGTGTATCAGGAGATGCCCGCCCAGCTCCGCAAGCAGCAGGAGTCTCTGGCCCGCCACCTGCAGACCTA CGGGGAGCACTACCCACTGGATCACTTCGATAAGTGAGACCTGCTCAGCCCACCCCCACCCATCCTCAGC TACCCCGAGAGGTAGCCCCACTCTAAGGGGAGCAGGGGGACCTGACAGCACACCACTGTCTTCCCCAGTC AGCTCCCTCTAAAATACTCAGCGGCCAGGGCGGCTGCCACTCTTCACCCCTGCTCCTCCCGGCTGTTACA TTGTCAGGGGACAGCATCTGCAGCAGTTGCTGAGGCTCCGTCAGCCCCCTCTTCACCTGTTGTTACAGTG CCTTCTCCCAGGGGCTGGGTGAGGGCACATTCAGGACTAGAAGCCCCTCTGGGCATGGGGTGGACATGGC AGGTCAGCCTGTGGAACTTGCGCAGGTGCGAGTGGCCAGCAGAGGTCACGAATAAACTGCATCTCTGCGC CTGGCTCTCTACCAAAAAAAAAAAAAAAAAA
All Missense/Nonsense mutations listed in HGMD:
Q125E, T151M, D152N, R159W, Y166N, R167Q, Q190K, I213T, A216V, A220V, G249S, A253T, C258Y, C264W, R265W, N267S, G283D, A285P, R287TERM, G290R, R297C, R297H, G300S, D302A, T310R, R314TERM, I326T, E327K, A328T, R346H, R363W, F409C, V412M, Y413H, Y413C, Y438N,
SNPdbe
Mutation | Experimental evidence | Disease |
V3G | Not validated | N/A |
L17F | Not validated | N/A |
L17F | Not validated | N/A |
G29E | Not validated | N/A |
G29E | Not validated | N/A |
S36A | Not validated | N/A |
P39H | Not validated | N/A |
P39H | Not validated | N/A |
Q42R | Not validated | N/A |
Q42R | Not validated | N/A |
A59V | Not validated | N/A |
A59V | Not validated | N/A |
I62M | Not validated | N/A |
I62M | Not validated | N/A |
N71S | Not validated | N/A |
N71S | Not validated | N/A |
M82I | Not validated | N/A |
M82L | Not validated | N/A |
M82I | Not validated | N/A |
M82L | Not validated | N/A |
R117C | Not validated | N/A |
R117C | Not validated | N/A |
R127W | Not validated | N/A |
R127W | Not validated | N/A |
N150D | Not validated | N/A |
N150D | Not validated | N/A |
T151M | Not validated | N/A |
T151M | Not validated | N/A |
Q157A | Not validated | N/A |
Y158A | Not validated | N/A |
R159W | Not validated | maple syrup urine disease type ia (SwissVar) |
R159A | Not validated | N/A |
P170S | Not validated | N/A |
P170S | Not validated | N/A |
Q190K | Not validated | maple syrup urine disease type ia (SwissVar) |
R200C | Not validated | N/A |
R200C | Not validated | N/A |
S207A | Not validated | N/A |
L209A | Not validated | N/A |
T211A | Not validated | N/A |
T211M | Not validated | N/A |
A222T | Not validated | N/A |
A222T | Not validated | N/A |
E238A | Not validated | N/A |
G244R | Not validated | N/A |
G244R | Not validated | N/A |
A248D | Not validated | N/A |
G249S | Not validated | N/A |
G249S | Not validated | N/A |
A253T | Not validated | maple syrup urine disease type ia (SwissVar) |
A253T | Not validated | N/A |
A254D | Not validated | N/A |
C264W | Not validated | N/A |
C264W | Not validated | N/A |
R265W | Not validated | N/A |
R265W | Not validated | N/A |
R265K | Not validated | N/A |
R265A | Not validated | N/A |
N267S | Not validated | N/A |
Y269A | Not validated | N/A |
A285P | Not validated | N/A |
G289R | Not validated | N/A |
G290R | Not validated | maple syrup urine disease type ia (SwissVar) |
R296C | Not validated | N/A |
R297C | Not validated | N/A |
Y306H | Not validated | N/A |
Y307H | Not validated | N/A |
T309R | Not validated | N/A |
T310R | Not validated | N/A |
R313Q | Not validated | N/A |
R314Q | Not validated | N/A |
I326T | Not validated | maple syrup urine disease type ia (SwissVar) |
H336A | Not validated | N/A |
S337D | Not validated | N/A |
A343V | Not validated | N/A |
A344V | Not validated | N/A |
R345C | Not validated | N/A |
S346L | Not validated | N/A |
R346C | Not validated | N/A |
S347L | Not validated | N/A |
W354F | Not validated | N/A |
Q356R | Not validated | N/A |
Q357R | Not validated | N/A |
I360V | Not validated | N/A |
I361V | Not validated | N/A |
E397K | Not validated | N/A |
E398K | Not validated | N/A |
R398Q | Not validated | N/A |
R399Q | Not validated | N/A |
P402R | Not validated | N/A |
P403R | Not validated | N/A |
N403S | Not validated | N/A |
N404S | Not validated | N/A |
F408C | Not validated | N/A |
F409C | Not validated | maple syrup urine disease type ia (SwissVar) |
Y413C | Not validated | maple syrup urine disease type ia (SwissVar) |
Q423K | Not validated | N/A |
Q424K | Not validated | N/A |
R428H | Not validated | N/A |
R429H | Not validated | N/A |
Y437N | Not validated | N/A |
Y438N | Not validated | maple syrup urine disease type ia (SwissVar) |