FAHD1
protein-codingfumarylacetoacetate hydrolase domain containing 1
Gene summary
Enables hydrolase activity, acting on carbon-carbon bonds, in ketonic substances; oxaloacetate decarboxylase activity; and oxaloacetate tautomerase activity. Involved in oxaloacetate metabolic process. Located in cytosol; mitochondrion; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- C16orf36
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.2 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 FAHD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031208.4. 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 | 0 | |||||
| missense | 44 | 44 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 0 | 0 | 45 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_112485.2 | 1 | MANE Select | |
| Ensembl | ENSP00000398053.3 | 1 | MANE Select | |
| RefSeq | NP_001018114.2 | 2 | Standard | |
| RefSeq | NP_001135870.2 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tyrosine metabolism - Homo sapiens (human)
- Citric acid cycle (TCA cycle)
- Pyruvate metabolism and Citric Acid (TCA) cycle
- The citric acid (TCA) cycle and respiratory electron transport
- Metabolism
Biological Process
- tricarboxylic acid cycle
Molecular Function
- oxaloacetate decarboxylase activity
- acetylpyruvate hydrolase activity
- fumarylpyruvate hydrolase activity
- metal ion binding
- acylpyruvate hydrolase activity
Cellular Component
- nucleoplasm
- mitochondrion
- mitochondrial matrix
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000382666
- Coding exons
- 2
- Length
- 13241
- Individuals with no LoFs
- 125621
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 108
- Defined
- 125729
- p
- 0.000430
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.84 | 198 | 137 | 1.44 | 0.00000630 | 1599 |
| Missense (PolyPhen) | 51 | 40.938 | 1.2458 | 469 | ||
| Synonymous | -1.71 | 76 | 59.3 | 1.28 | 0.00000293 | 509 |
| Loss of Function | -2.29 | 14 | 7.32 | 1.91 | 3.11e-7 | 96 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0019 | 0.0019 | notable |
| Latino/Admixed American | 0.00055 | 0.00055 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00027 | 0.00027 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable mitochondrial acylpyruvase which is able to hydrolyze acetylpyruvate and fumarylpyruvate in vitro (PubMed:15551868, PubMed:21878618). Also has oxaloacetate decarboxylase activity (PubMed:25575590). {ECO:0000269|PubMed:15551868, ECO:0000269|PubMed:21878618, ECO:0000269|PubMed:25575590}.;
Recessive Scores
- pRec
- 0.144
Intolerance Scores
- LoFtool
- 0.254
- RVIS EVS
- -0.29
- RVIS percentile EVS
- 33.2
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.879
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |