Mapping SNPs BCKDHA
From Bioinformatikpedia
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).
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 |
dbSNP
results for SNPs in BCKDHA: -all: 742 -human: 371
SNPs in human
| ID | mutation in sequence | amino acid | position |
|---|---|---|---|
| rs137852876 | CTTGAGTGCCCCATCATCTTCTTCTG[C/G]CGGAACAATGGCTACGCCATCTCCA | Ser | pos=251 |
| rs137852875 | TGATGTGTTTGCCGTATACAACGCCA[C/G]AAAGGAGGCCCGACGGCGGGCTGTG | Ser | pos=251 |
| rs137852874 | CAGCCAGTGAGGGGGACGCCCATGCC[A/G]GCTTCAACTTCGCTGCCACACTTGA | Arg | pos=251 |
| rs137852873 | TTGAGTGCCCCATCATCTTCTTCTGC[C/T]GGAACAATGGCTACGCCATCTCCAC | Tyr | pos=251 |
| rs137852872 | GCCCAAACCCAACCCCAACCTACTCT[G/T]CTCAGACGTGTATCAGGAGATGCCC | Lys | pos=251 |
| rs137852871 | GTGTCCCCACAGCAGCACGAGGCCCC[A/G]GGTATGGCATCATGTCAATCCGCGT | Arg | pos=251 |
