Task 5: Researching SNPs

In this task we are to research SNPs associated with our protein odba_human, in different databases.

HGMD( free version )

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 every 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.

Figure 1. Example of a frameshift mutation caused by an insertion.

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

In SNPedia wie found the folowing four SNPs for MSUD.

• rs12021720
• rs17856511
• rs28934895, also known as R183P (the most common SNP in Ashkenazi Jews); the risk genotype is CC
• rs28940288

of those the first two are merged into one in dbSNP and do not concern the BCKDHA protein. The same goes for the third entry and the fourth is already contained in dbSNP.

OMIM

OMIM contains 9 entries for BCKDHA( odba_human - 608348 ), all leading to MSUD. As reference sequence Uniprot is given.

Number	Phenotype	Mutation	dbSNP
.0001	MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA	BCKDHA, TYR393ASN	-
.0002	MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA	BCKDHA, 8-BP DEL, 887-894	-
.0003	MAPLE SYRUP URINE DISEASE,INTERMEDIATE, TYPE IA	BCKDHA, GLY245ARG	-
.0004	MAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA, INCLUDED	BCKDHA, PHE364CYS	-
.0005	MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA	BCKDHA, ARG220TRP	-
.0006	MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA	BCKDHA, GLY204SER	-
.0007	MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA	BCKDHA, THR265ARG	-
.0008	MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA	BCKDHA, CYS219TRP	-
.0009	MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IA	BCKDHA, 1-BP DEL, 117C	-

mutationmap

We first (with little sucess) tried to build a graphical per-nucleotide representation of the Sequence the result can be found in figure 2.

Figure 2. First experiment with a graphical representation of a mutation map. Nucleotide sequence is shown in red,green, blue and black. The scale is marked in 50 and 100 nucleotide discance. SNPs are markes red when missense and green when synonymous.

After that we decided to go for a structural representation using pymol. Two images of the colored representation can be found below in figures 3 and 4.

Figure 3. Green marked regions are synonymous mutations, red are missense and orande are positions where both synonymous and missense mutations were found.

Figure 4. Green marked regions are synonymous mutations, red are missense and orande are positions where both synonymous and missense mutations were found.

To actually take a look at the mapping we recommend directly loading it in pymol, for wich we provide the pymol session file here.

conclusion

will be added on tuesday...