Protocol-msud-task5 protocol

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	Pssm wt
V3G	Not validated	69
L17F	Not validated	29
L17F	Not validated	31
G29E	Not validated	34
G29E	Not validated	27
S36A	Not validated	36
P39H	Not validated	42
P39H	Not validated	40
Q42R	Not validated	23
Q42R	Not validated	26
A59V	Not validated	30
A59V	Not validated	32
I62M	Not validated	8
I62M	Not validated	7
N71S	Not validated	12
N71S	Not validated	12
M82I	Not validated	10
M82L	Not validated	10
M82I	Not validated	11
M82L	Not validated	10
R117C	Not validated	6
R117C	Not validated	6
R127W	Not validated	23
R127W	Not validated	21
N150D	Not validated	4
N150D	Not validated	4
T151M	Not validated	7
T151M	Not validated	7
Q157A	Not validated	5
Y158A	Not validated	6
R159W	Not validated	65
R159A	Not validated	65
P170S	Not validated	24
P170S	Not validated	24
Q190K	Not validated	19
R200C	Not validated	6
R200C	Not validated	6
S207A	Not validated	12
L209A	Not validated	6
T211A	Not validated	13
T211M	Not validated	13
A222T	Not validated	60
A222T	Not validated	60
E238A	Not validated	8
G244R	Not validated	72
G244R	Not validated	71
A248D	Not validated	5
G249S	Not validated	11
G249S	Not validated	11
A253T	Not validated	66
A253T	Not validated	70
A254D	Not validated	21
C264W	Not validated	11
C264W	Not validated	13
R265W	Not validated	6
R265W	Not validated	5
R265K	Not validated	5
R265A	Not validated	5
N267S	Not validated	62
Y269A	Not validated	21
A285P	Not validated	32
G289R	Not validated	25
G290R	Not validated	22
R296C	Not validated	15
R297C	Not validated	17
Y306H	Not validated	12
Y307H	Not validated	12
T309R	Not validated	9
T310R	Not validated	8
R313Q	Not validated	10
R314Q	Not validated	10
I326T	Not validated	26
H336A	Not validated	52
S337D	Not validated	27
A343V	Not validated	17
A344V	Not validated	16
R345C	Not validated	16
S346L	Not validated	5
R346C	Not validated	17
S347L	Not validated	5
W354F	Not validated	30
Q356R	Not validated	7
Q357R	Not validated	7
I360V	Not validated	32
I361V	Not validated	32
E397K	Not validated	26
E398K	Not validated	27
R398Q	Not validated	6
R399Q	Not validated	6
P402R	Not validated	53
P403R	Not validated	53
N403S	Not validated	5
N404S	Not validated	6
F408C	Not validated	40
F409C	Not validated	41
Y413C	Not validated	57
Q423K	Not validated	4
Q424K	Not validated	6
R428H	Not validated	13
R429H	Not validated	14
Y437N	Not validated	51
Y438N	Not validated	53