Protocol-msud-task5 protocol

From Bioinformatikpedia
Revision as of 11:32, 6 June 2012 by Wagnerr (talk | contribs) (→‎dbSNP)

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

"{|class="wikitable" border="1" style="border-spacing:0;text-align: right;" !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
Retrieved from "https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Protocol-msud-task5_protocol&oldid=21778"