Difference between revisions of "Protocol-msud-task5 protocol"

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!Function

Revision as of 11:34, 6 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,

dbSNP

rs Cluster Id Function AA Pos Codon Pos From Nucleotide To Nucleotide From AA To AA
rs17173144 synonymous 5 3 C T, Ile [I] Ile [I],
rs34541442 synonymous 12 1 C A, Arg [R] Arg [R],
rs146823708 missense 17 3 G C, Leu [L] Phe [F],
rs140322984 synonymous 21 3 C T, Ala [A] Ala [A],
rs111855817 missense 29 2 G A, Gly [G] Glu [E],
rs62637712 synonymous 38 3 C G, T, Pro [P] Pro [P], Pro [P],
rs34589432 missense 39 2 C A, Pro [P] His [H],
rs80014754 synonymous 39 3 C A, Pro [P] Pro [P],
rs150177278 missense 42 2 A G, Gln [Q] Arg [R],
rs138373035 missense 59 2 C T, Ala [A] Val [V],
rs149251798 missense 62 3 A G, Ile [I] Met [M],
rs147370725 missense 71 2 A G, Asn [N] Ser [S],
rs138025447 synonymous 71 3 C T, Asn [N] Asn [N],
rs143167070 synonymous 80 3 C T, Arg [R] Arg [R],
rs11549938 missense 82 1 A C, Met [M] Leu [L],
rs147510183 missense 82 3 G A, Met [M] Ile [I],
rs148571328 synonymous 96 3 C T, His [H] His [H],
rs11549937 synonymous 97 3 G C, Leu [L] Leu [L],
rs142967869 synonymous 98 3 G A, Pro [P] Pro [P],
rs150700696 synonymous 112 3 T G, Leu [L] Leu [L],
rs188135164 missense 117 1 C T, Arg [R] Cys [C],
rs139678295 missense 127 1 C T, Arg [R] Trp [W],
rs143608852 synonymous 140 3 G A, Thr [T] Thr [T],
rs146804716 synonymous 141 3 C T, His [H] His [H],
rs140612545 missense 150 1 A G, Asn [N] Asp [D],
rs34442879 missense 151 2 C T, Thr [T] Met [M],
rs34956071 missense 170 1 C T, Pro [P] Ser [S],
rs190610188 missense 200 1 C T, Arg [R] Cys [C],
rs144995574 synonymous 206 3 C T, Ser [S] Ser [S],
rs10404506 synonymous 213 3 C T, Ile [I] Ile [I],
rs114716391 synonymous 216 3 G T, Ala [A] Ala [A],
rs151227241 synonymous 221 3 C T, Tyr [Y] Tyr [Y],
rs141086188 missense 222 1 G A, Ala [A] Thr [T],
rs146932786 synonymous 236 3 C T, Phe [F] Phe [F],
rs28940288 missense 244 1 G A, Gly [G] Arg [R],
rs137960127 synonymous 248 3 C T, Ala [A] Ala [A],
rs61737367 synonymous 280 3 C T, Arg [R] Arg [R],
rs145901144 missense 297 1 C T, Arg [R] Cys [C],
rs187669174 synonymous 297 3 C T, Arg [R] Arg [R],
rs138261404 missense 307 1 T C, Tyr [Y] His [H],
rs139390622 synonymous 308 3 C T, Asn [N] Asn [N],
rs144372407 missense 314 2 G A, Arg [R] Gln [Q],
rs190858285 synonymous 316 3 G T, Arg [R] Arg [R],
rs284652 synonymous 324 3 C T, Phe [F] Phe [F],
rs112312448 frame shift 325 1 C None, Leu [L] None,
rs55940366 synonymous 325 3 C T, Leu [L] Leu [L],
rs146300600 missense 344 2 C T, Ala [A] Val [V],
rs182923857 missense 346 1 C T, Arg [R] Cys [C],
rs139556493 missense 347 2 C T, Ser [S] Leu [L],
rs144276456 synonymous 347 3 G A, Ser [S] Ser [S],
rs185688419 missense 357 2 A G, Gln [Q] Arg [R],
rs61736656 missense 361 1 A G, Ile [I] Val [V],
rs190202447 synonymous 383 3 G A, Arg [R] Arg [R],
rs139553536 missense 399 2 G A, Arg [R] Gln [Q],
rs149722591 missense 403 2 C G, Pro [P] Arg [R],
rs145595627 synonymous 403 3 C T, Pro [P] Pro [P],
rs148090804 missense 404 2 A G, Asn [N] Ser [S],
rs4674 synonymous 407 3 A C, G, T, Leu [L] Leu [L], Leu [L], Leu [L],
rs147021347 synonymous 417 3 C T, Pro [P] Pro [P],
rs34492894 synonymous 420 3 C T, Leu [L] Leu [L],
rs141991700 missense 424 1 C A, Gln [Q] Lys [K],
rs143065803 missense 429 2 G A, Arg [R] His [H],
rs148224513 synonymous 443 3 C T, Phe [F] Phe [F],

SNPdbe

Mutation Experimental evidence Disease
V3GNot validatedN/A
L17FNot validatedN/A
L17FNot validatedN/A
G29ENot validatedN/A
G29ENot validatedN/A
S36ANot validatedN/A
P39HNot validatedN/A
P39HNot validatedN/A
Q42RNot validatedN/A
Q42RNot validatedN/A
A59VNot validatedN/A
A59VNot validatedN/A
I62MNot validatedN/A
I62MNot validatedN/A
N71SNot validatedN/A
N71SNot validatedN/A
M82INot validatedN/A
M82LNot validatedN/A
M82INot validatedN/A
M82LNot validatedN/A
R117CNot validatedN/A
R117CNot validatedN/A
R127WNot validatedN/A
R127WNot validatedN/A
N150DNot validatedN/A
N150DNot validatedN/A
T151MNot validatedN/A
T151MNot validatedN/A
Q157ANot validatedN/A
Y158ANot validatedN/A
R159WNot validatedmaple syrup urine disease type ia (SwissVar)
R159ANot validatedN/A
P170SNot validatedN/A
P170SNot validatedN/A
Q190KNot validatedmaple syrup urine disease type ia (SwissVar)
R200CNot validatedN/A
R200CNot validatedN/A
S207ANot validatedN/A
L209ANot validatedN/A
T211ANot validatedN/A
T211MNot validatedN/A
A222TNot validatedN/A
A222TNot validatedN/A
E238ANot validatedN/A
G244RNot validatedN/A
G244RNot validatedN/A
A248DNot validatedN/A
G249SNot validatedN/A
G249SNot validatedN/A
A253TNot validatedmaple syrup urine disease type ia (SwissVar)
A253TNot validatedN/A
A254DNot validatedN/A
C264WNot validatedN/A
C264WNot validatedN/A
R265WNot validatedN/A
R265WNot validatedN/A
R265KNot validatedN/A
R265ANot validatedN/A
N267SNot validatedN/A
Y269ANot validatedN/A
A285PNot validatedN/A
G289RNot validatedN/A
G290RNot validatedmaple syrup urine disease type ia (SwissVar)
R296CNot validatedN/A
R297CNot validatedN/A
Y306HNot validatedN/A
Y307HNot validatedN/A
T309RNot validatedN/A
T310RNot validatedN/A
R313QNot validatedN/A
R314QNot validatedN/A
I326TNot validatedmaple syrup urine disease type ia (SwissVar)
H336ANot validatedN/A
S337DNot validatedN/A
A343VNot validatedN/A
A344VNot validatedN/A
R345CNot validatedN/A
S346LNot validatedN/A
R346CNot validatedN/A
S347LNot validatedN/A
W354FNot validatedN/A
Q356RNot validatedN/A
Q357RNot validatedN/A
I360VNot validatedN/A
I361VNot validatedN/A
E397KNot validatedN/A
E398KNot validatedN/A
R398QNot validatedN/A
R399QNot validatedN/A
P402RNot validatedN/A
P403RNot validatedN/A
N403SNot validatedN/A
N404SNot validatedN/A
F408CNot validatedN/A
F409CNot validatedmaple syrup urine disease type ia (SwissVar)
Y413CNot validatedmaple syrup urine disease type ia (SwissVar)
Q423KNot validatedN/A
Q424KNot validatedN/A
R428HNot validatedN/A
R429HNot validatedN/A
Y437NNot validatedN/A
Y438NNot validatedmaple syrup urine disease type ia (SwissVar)

OMIM

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
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