Mapping SNPs BCKDHA

General

Maple syrup urine disease is an autosomal recessive disorder that affects the amino acid metabolism. The disease is caused by a defect in the branched-chain alpha-keto acid dehydrogenase complex which blocks oxidative decarboxylation. The result is a rising concentration of branched-chain amino acids. MSUD is caused by mutations in the gene coding for the alpha subunit of the branched-chain keto acid dehydrogenase(BCKDHA).

Reference Sequences: Reference_Sequence_BCKDHA

HGMD

Searching for "BCKDHA" a total of 39 mutations are reported, comprised of the following mutation types:

• missense/nonsense: 33 mutations
• small deletions: 3 mutations
• small insertions: 1 mutation
• gross deletions: 1 mutation
• complex rearrangements: 1 mutation

For us the missense/nonsense mutations are the most interesting ones, as a single nucleotide change can lead to the phenotype of Maple Syrup Urine Disease.

Codon change	Amino Acid change	Codon number
gCAG-GAG	Gln-Glu	80
ACG-ATG	THr-Met	106
cCGG-TGG	Arg-Trp	114
gTAT-AAAT	Tyr-Asn	121
CGG-CAG	Arg-Gln	122
cCAG-AAG	Gln-Lys	145
ATC-ACC	Ile-Thr	168
GCG-GTG	Ala-Val	171
GCG-GTG	Ala-Val	175
cGGC-AGC	Gly-Ser	204
cGCT-ACT	Ala-Thr	208
TGC-TAC	Cys-Thr	213
cCGG-TGG	Arg-Trp	220
AAT-AGT	Asn-Ser	222
GGC-GAC	Gly-Asp	238
tGCA-CCA	Ala-Pro	240
aCGA-TGA	Arg-Term	242
cGGG-AGG	Gly-Arg	245
cCGC-TGC	Arg-Cys	252
CGC-CAC	Arg-His	252
tGGT-AGT	Gly-Ser	255
GAT-GCT	Asp-Ala	257
ACA-AGA	Thr-Arg	265
cCGA-TGA	Arg-Term	269
ATC-ACC	Ile-Thr	281
cGAG-AAG	Glu-Lys	282
gGCC-ACC	Ala-Thr	283
CGC-CAC	Arg-His	301
cCGG-TGG	Arg-Trp	318
TTC-TGC	Phe-Cys	364
cGTG-ATG	Val-Met	367
TAT-TGT	Tyr-Cys	368
cTAC-AAC	Tyr-Asn	393

The mutations are given for a reference sequence, which can be found under the accession number NM_000709.3. This is a nucleotide sequence, which was translated using the Expasy Translate tool(<ref>http://expasy.org/tools/dna.html</ref>) into a protein sequence.

The following sequence shows the mutations annotatied in HGMD:

MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEF
IDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYE
SQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGN
ISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAA
SEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGN
DVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPI
SRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLR
KQQESLARHLQTYGEHYPLDHFDK

dbSNP

results for the SNPs search with BCKDHA:

-all: 742

-human: 371

SNPs in human

Missense Mutations annotated in dbSNP

RefSeq ID	SNP	Reference Sequence	Nucleotide Position	Nt old	Nt new	Codon Number	Reference AA	Mutated AA
rs10853751	TGGGCTCGGCGCGATGGAGGAGGAGA[C/T]GCATACTGACGCCAAAATCCGTGCT	NP_064543.3	14	C	T	5	Thr	Met
rs111855817	TGCCCTCCTGCTGCTGCGGCAGCCTG[A/G]GGCTCGGGGACTGGCTAGATCTGTG	NP_000700.1	86	G	A	29	Gly	Glu
rs34500671	TCTGGCCGCGACAGCAGGTTCTGTTC[C/G]CAGGCAAAGTGCCGGAGGCTGCAGC	NP_064543.3	99	C	G	33	Cys	Trp
rs34589432	CCTCTGCTCTCTTCCCCAGCACCCCC[A/C]CAGGCAGCAGCAGCAGTTTTCATCT	NP_000700.1	116	C	A	39	Pro	His
rs11549938	TCTCTGGAATCCCCATCTACCGCGTC[A/C]TGGACCGGCAAGGCCAGATCATCAA	NP_000700.1	244	A	C	82	Met	Leu
rs34442879	GGGGAGTGCCGCCGCCCTGGACAACA[C/T]GGACCTGGTGTTTGGCCAGTACCGG	NP_000700.1	452	C	T	151	Thr	Met
rs34956071	TAGGTGTGCTGATGTATCGGGACTAC[C/T]CCCTGGAACTATTCATGGCCCAGTG	NP_000700.1	508	C	T	170	Pro	Ser
rs28940288	ACTTCGGCGAGGGGGCAGCCAGTGAG[A/G]GGGACGCCCATGCCGGCTTCAACTT	NP_000700.1	730	G	A	244	Gly	Arg
rs137852874	CAGCCAGTGAGGGGGACGCCCATGCC[A/G]GCTTCAACTTCGCTGCCACACTTGA	NP_000700.1	745	G	A	249	Gly	Ser
rs137852876	CTTGAGTGCCCCATCATCTTCTTCTG[C/G]CGGAACAATGGCTACGCCATCTCCA	NP_000700.1	792	C	G	264	Cys	Trp
rs137852873	TTGAGTGCCCCATCATCTTCTTCTGC[C/T]GGAACAATGGCTACGCCATCTCCAC	NP_000700.1	793	C	T	265	Arg	Trp
rs137852871	GTGTCCCCACAGCAGCACGAGGCCCC[A/G]GGTATGGCATCATGTCAATCCGCGT	NP_000700.1	865	G	A	290	Gly	Arg
rs137852875	TGATGTGTTTGCCGTATACAACGCCA[C/G]AAAGGAGGCCCGACGGCGGGCTGTG	NP_000700.1	926	C	G	310	Thr	Arg
rs61736656	ATTACTGGGATAAACAGGACCACCCC[A/G]TCTCCCGGCTGCGGCACTATCTGCT	NP_000700.1	1078	A	G	361	Ile	Val
rs137852872	GCCCAAACCCAACCCCAACCTACTCT[G/T]CTCAGACGTGTATCAGGAGATGCCC	NP_000700.1	1223	T	G	409	Phe	Cys
rs137852870	GCCACCTGCAGACCTACGGGGAGCAC[A/T]ACCCACTGGATCACTTCGATAAGTG	NP_000700.1	1309	T	A	438	Tyr	Asn

The dbSNP mutation positions in the amino acid sequence are relative the RefSeq entry NP_000700.1 and NP_064543.3, respectively.

RefSeq ID	RefCodon	Mutated Codon	Reference Allele	Mutated Allele	Mutation Frame	Codon Number	Reference Residue	Mutated Residue
rs10853751	TGC	TTC	C	T	2	5	T	M
rs111855817	CGT	CAT	G	A	2	29	G	E
rs34500671	CAG	CAG	C	G	3	31	C	W
rs34589432	CTG	CAG	C	A	2	39	P	H
rs11549938	ATC	CTC	A	C	1	82	M	L
rs34442879	GAG	GTG	C	T	2	151	T	M
rs34956071	GGC	TGC	C	T	1	170	P	S
rs28940288	AGG	AGG	G	A	1	244	G	R
rs137852874	TAC	AAC	G	A	1	249	G	S
rs137852876	TTC	TTG	C	G	3	264	C	W
rs137852873	AAC	TAC	C	T	1	265	R	W
rs137852871	ACC	ACC	G	A	1	289	G	R
rs137852875	TCA	TGA	C	G	2	309	T	R
rs61736656	CGC	GGC	A	G	1	360	I	V
rs137852872	GAG	GGG	T	G	2	409	F	C
rs137852870	CAG	AAG	T	A	1	438	Y	N

MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEF
IDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYE
SQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGN
ISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAA
SEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGN
DVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPI
SRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLR
KQQESLARHLQTYGEHYPLDHFDK

Silent mutations annotated in dbSNP

RefSeq ID	RefCodon	Mutated Codon	Reference Allele	Mutated Allele	Mutation Frame	Codon Number	Reference Residue	Mutated Residue
rs17173144	TGC	TGT	C	T	3	5	I	I
rs34541442	TTA	ATA	C	A	1	12	R	R
rs75733136	ATC	ATA	C	A	3	19	S	S
rs34169026	AGC	AGT	C	T	3	32	A	A
rs62637712	CTG	CTT	C	T	3	38	P	P
rs80014754	CTG	CTA	C	A	3	39	P	P
rs11549937	GAC	GAC	G	C	3	97	L	L
rs10404506	GAA	GAT	C	T	3	213	I	I
rs114716391	TTC	TTT	G	T	3	216	A	A
rs61737367	AAC	AAT	C	T	3	280	R	R
rs284652	ACA	ACT	C	T	3	324	F	F
rs55940366	AAG	AAT	C	T	3	325	L	L
rs4674	GCC	GCG	A	G	3	407	L	L
rs34492894	CCC	CCT	C	T	3	419	L	L

Point mutations can have an influence on the amino acids or not depending on the kind of the point mutation. There are two different types: synonymous and non-synonymous mutations.

If a point mutation is synonymous it means that the change occurs only in the nucleotide sequence but not in the amino acid sequence. This is possible because of the fact that amino acids are encoded by three nucleotides (codons) and some of the amino acids are encoded by more than one possible arrangement of nucleotides. So it can happen that when there is a mutation in the nucleotide sequence there is also a change in the codon but both codons encode the same amino acid.

The other possibility is that a mutation is non-synonymous which means that the mutation has an influence on the amino acid sequence and the amino acid changes. This change can have more or less severe because amino acids have several properties. When an amino acid is replaced by an amino acid which has the same properties the change is not so grave as the change to an amino acid with completely different properties.

Mutation Map

Reference Sequence Alignments

To map the different mutations from different sources onto the same sequence, first the reference sequences needed to be compared. Herefore we performed pairwise alignments for the following sequences:

• NP_000700.1 and (source: Uniprot)

The alignment for these two sequences is perfect, the identity is 100%. This indicates that the reference sequence from dbSNP is the same one we were working with before.

• NP_000700.1 and NP_064543.3

The alignment for these two sequences showed only 9.9% identity and 17.3% similarity, whereas the 63.2% are gaps. As this alignment is not good enough to assume similar sequences, the SNPs found with reference sequence NP_064543.3 are ignored.

• NM_000709.3 and translated NP_000700.1

The alignment for the HGMD reference sequence and the translated dbSNP reference sequence shows 97.2% identity. The only difference in these sequences is a short oligopeptide at the beginning of the HGMD reference sequence. This oligo is 13 amino acids long. These 13 positions have to be taken into account when mapping the SNPs onto the same sequence. As we found out, the HGMD codon positions are relative to the start codon of the protein, so the signal peptide of 45 aa and the additional 13 aa have to be taken into account.

MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEF
IDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYE
SQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGN
ISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAA
SEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGN
DVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPI
SRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLR
KQQESLARHLQTYGEHYPLDHFDK

Colour code:

Mutations listed in both Databases

Mutations listed only in HGMD

Mutations listed only in dbSNP