FAM162A
protein-codingfamily with sequence similarity 162 member A
Gene summary
Involved in cellular response to hypoxia; positive regulation of apoptotic process; and positive regulation of release of cytochrome c from mitochondria. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]
- C3orf28
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.2 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 FAM162A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014367.4. 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 | 20 | 2 | 22 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 22 | 2 | 0 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055182.3 | 5 | MANE Select | |
| Ensembl | ENSP00000419088.1 | 5 | MANE Select | |
| Ensembl | ENSP00000232125.5 | 5 | Standard | |
| Ensembl | ENSP00000419491.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- activation of cysteine-type endopeptidase activity involved in apoptotic process
- positive regulation of apoptotic process
- neuron apoptotic process
- cellular response to hypoxia
- positive regulation of release of cytochrome c from mitochondria
Molecular Function
- protein binding
Cellular Component
- mitochondrion
- cytosol
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000477892
- Coding exons
- 5
- Length
- 28159
- Individuals with no LoFs
- 124608
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 179
- Defined
- 124788
- p
- 0.000721
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.599 | 68 | 83.4 | 0.815 | 0.00000432 | 996 |
| Missense (PolyPhen) | 18 | 21.606 | 0.8331 | 266 | ||
| Synonymous | 0.782 | 23 | 28.3 | 0.813 | 0.00000156 | 276 |
| Loss of Function | 0.357 | 9 | 10.2 | 0.879 | 6.97e-7 | 110 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00021 | 0.00019 | rare |
| Latino/Admixed American | 0.00013 | 0.00012 | rare |
| Ashkenazi Jewish | 0.015 | 0.014 | notable |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00021 | 0.00020 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0.0015 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Proposed to be involved in regulation of apoptosis; the exact mechanism may differ between cell types/tissues. May be involved in hypoxia-induced cell death of transformed cells implicating cytochrome C release and caspase activation (such as CASP9) and inducing mitochondrial permeability transition. May be involved in hypoxia-induced cell death of neuronal cells probably by promoting release of AIFM1 from mitochondria to cytoplasm and its translocation to the nucleus; however, the involvement of caspases has been reported conflictingly. {ECO:0000269|PubMed:15082785}.;
Recessive Scores
- pRec
- 0.0640
Intolerance Scores
- LoFtool
- 0.762
- RVIS EVS
- 0.7
- RVIS percentile EVS
- 85.42
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0846
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |