KYAT1
protein-codingkynurenine aminotransferase 1
Gene summary
This gene encodes a cytosolic enzyme that is responsible for the metabolism of cysteine conjugates of certain halogenated alkenes and alkanes. This metabolism can form reactive metabolites leading to nephrotoxicity and neurotoxicity. Increased levels of this enzyme have been linked to schizophrenia. Multiple transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
- CCBL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.6 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 KYAT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004059.5. 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 | 1 | ||||
| missense | 9 | 1 | 10 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 11 | 1 | 0 | 12 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004050.3 | 12 | MANE Select | |
| Ensembl | ENSP00000302227.3 | 12 | MANE Select | |
| RefSeq | NP_001116143.1 | 12 | Standard | |
| RefSeq | NP_001116144.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tryptophan metabolism - Homo sapiens (human)
- Selenocompound metabolism - Homo sapiens (human)
- Chemical carcinogenesis - Homo sapiens (human)
- Tryptophan catabolism
- Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism
Biological Process
- L-phenylalanine catabolic process
- tryptophan catabolic process
- cellular modified amino acid metabolic process
- cellular amino acid biosynthetic process
- kynurenine metabolic process
Molecular Function
- protein binding
- transaminase activity
- kynurenine-oxoglutarate transaminase activity
- pyridoxal phosphate binding
- protein homodimerization activity
Cellular Component
- nucleoplasm
- cytoplasm
- mitochondrion
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000302586
- Coding exons
- 12
- Length
- 49553
- Individuals with no LoFs
- 124955
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 73
- Defined
- 125028
- p
- 0.000292
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.716 | 233 | 266 | 0.876 | 0.0000162 | 2809 |
| Missense (PolyPhen) | 77 | 85.235 | 0.90339 | 912 | ||
| Synonymous | -0.301 | 109 | 105 | 1.04 | 0.00000691 | 786 |
| Loss of Function | 0.640 | 20 | 23.3 | 0.857 | 0.00000108 | 251 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.00037 | 0.00037 | rare |
| European (Non-Finnish) | 0.00035 | 0.00035 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the irreversible transamination of the L- tryptophan metabolite L-kynurenine to form kynurenic acid (KA). Metabolizes the cysteine conjugates of certain halogenated alkenes and alkanes to form reactive metabolites. Catalyzes the beta- elimination of S-conjugates and Se-conjugates of L- (seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond. {ECO:0000269|PubMed:19338303}.;
Recessive Scores
- pRec
- 0.460
Intolerance Scores
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 34.82
Essentials
- Essential (gene trap)
- N