BCAT1
protein-codingbranched chain amino acid transaminase 1
Gene summary
This gene encodes the cytosolic form of the enzyme branched-chain amino acid transaminase. This enzyme catalyzes the reversible transamination of branched-chain alpha-keto acids to branched-chain L-amino acids essential for cell growth. Two different clinical disorders have been attributed to a defect of branched-chain amino acid transamination: hypervalinemia and hyperleucine-isoleucinemia. As there is also a gene encoding a mitochondrial form of this enzyme, mutations in either gene may contribute to these disorders. Alternatively spliced transcript variants have been described. [provided by RefSeq, May 2010]
- BCT1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~139.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BCAT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005504.7. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 4 | 2 | 7 | ||
| missense | 56 | 2 | 58 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 58 | 6 | 2 | 66 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005495.2 | 11 | MANE Select | |
| Ensembl | ENSP00000261192.7 | 11 | MANE Select | |
| RefSeq | NP_001171562.1 | 10 | Standard | |
| RefSeq | NP_001171563.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pantothenate and CoA biosynthesis - Homo sapiens (human)
- Cysteine and methionine metabolism - Homo sapiens (human)
- Valine, leucine and isoleucine biosynthesis - Homo sapiens (human)
- Valine, leucine and isoleucine degradation - Homo sapiens (human)
- 3-Methylglutaconic Aciduria Type I
Biological Process
- G1/S transition of mitotic cell cycle
- cell population proliferation
- branched-chain amino acid biosynthetic process
- branched-chain amino acid catabolic process
- leucine biosynthetic process
Molecular Function
- branched-chain-amino-acid transaminase activity
- identical protein binding
- L-leucine transaminase activity
- L-valine transaminase activity
- L-isoleucine transaminase activity
Cellular Component
- mitochondrion
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000539282
- Coding exons
- 11
- Length
- 138099
- Individuals with no LoFs
- 124598
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 57
- Defined
- 124655
- p
- 0.000229
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.221 | 216 | 207 | 1.04 | 0.0000101 | 2547 |
| Missense (PolyPhen) | 73 | 80.001 | 0.91249 | 1003 | ||
| Synonymous | -0.288 | 79 | 75.8 | 1.04 | 0.00000381 | 781 |
| Loss of Function | 1.48 | 15 | 22.6 | 0.664 | 0.00000109 | 282 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.00021 | 0.00020 | rare |
| East Asian | 0.00045 | 0.00045 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00031 | 0.00030 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the first reaction in the catabolism of the essential branched chain amino acids leucine, isoleucine, and valine.;
Recessive Scores
- pRec
- 0.178
Intolerance Scores
- RVIS EVS
- 0.48
- RVIS percentile EVS
- 79.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.953
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |