Mapping SNPs BCKDHA
Contents
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.
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.
MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEF
IDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYE
SQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGN
ISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAA
SEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGN
DVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPI
SRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLR
KQQESLARHLQTYGEHYPLDHFDK
