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. Insertion or deletion of nucleotides can cause frameshifts. As the amino acid code is triplet based, inserting or deleting a single nucleotide from within the sequence will not only cause a amino acid to be changed, but will move all following codons out of frame, changing evry fololowing amino acid after die insertion or deletion. For a graphical representation please see figure 1. Insertions or deletions are less severe when they appear near the end of an exon, as this limits the number of amino acids changed.
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.