Task 5: Researching SNPs
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
Here is a list of the silent mutations we found in dbSNP. The complete list of all mutations from dbSNP (including missense and frameshift mutations) can be found in the protocol-msud-task5 protocol.
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] |
rs140322984 | synonymous | 21 | 3 | C | T | Ala [A] | Ala [A] |
rs62637712 | synonymous | 38 | 3 | C | G, T | Pro [P] | Pro [P], Pro [P] |
rs80014754 | synonymous | 39 | 3 | C | A | Pro [P] | Pro [P] |
rs138025447 | synonymous | 71 | 3 | C | T | Asn [N] | Asn [N] |
rs143167070 | synonymous | 80 | 3 | C | T | Arg [R] | Arg [R] |
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] |
rs143608852 | synonymous | 140 | 3 | G | A | Thr [T] | Thr [T] |
rs146804716 | synonymous | 141 | 3 | C | T | His [H] | His [H] |
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] |
rs146932786 | synonymous | 236 | 3 | C | T | Phe [F] | Phe [F] |
rs137960127 | synonymous | 248 | 3 | C | T | Ala [A] | Ala [A] |
rs61737367 | synonymous | 280 | 3 | C | T | Arg [R] | Arg [R] |
rs187669174 | synonymous | 297 | 3 | C | T | Arg [R] | Arg [R] |
rs139390622 | synonymous | 308 | 3 | C | T | Asn [N] | Asn [N] |
rs190858285 | synonymous | 316 | 3 | G | T | Arg [R] | Arg [R] |
rs284652 | synonymous | 324 | 3 | C | T | Phe [F] | Phe [F] |
rs55940366 | synonymous | 325 | 3 | C | T | Leu [L] | Leu [L] |
rs144276456 | synonymous | 347 | 3 | G | A | Ser [S] | Ser [S] |
rs190202447 | synonymous | 383 | 3 | G | A | Arg [R] | Arg [R] |
rs145595627 | synonymous | 403 | 3 | C | T | Pro [P] | Pro [P] |
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] |
rs148224513 | synonymous | 443 | 3 | C | T | Phe [F] | Phe [F] |
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 9 entries for BCKDHA( obda_human - 608348 ), all leading to MSUD. As reference sequence Uniprot is given.