FATE1
protein-codingfetal and adult testis expressed 1
Gene summary
This gene encodes a cancer-testis antigen that is highly expressed in hepatocellular carcinomas and other tumors and weakly expressed in normal tissues except testis. The protein is strongly expressed in spermatogonia, primary spermatocytes, and Sertoli cells in seminiferous tubules. This protein may have a role in the control of early testicular differentiation and cell proliferation. [provided by RefSeq, Jan 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~7.2 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 FATE1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033085.3. 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 | 2 | 1 | 3 | |||
| missense | 38 | 4 | 42 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 44 | 5 | 0 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_149076.1 | 5 | MANE Select | |
| Ensembl | ENSP00000359375.3 | 5 | MANE Select | |
| Ensembl | ENSP00000400493.1 | 3 | Standard | |
| Ensembl | ENSP00000610398.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- apoptotic process
- negative regulation of apoptotic process
- negative regulation of mitochondrial calcium ion concentration
Molecular Function
- protein binding
- ubiquitin protein ligase binding
Cellular Component
- mitochondrial outer membrane
- endoplasmic reticulum
- endoplasmic reticulum membrane
- integral component of membrane
- mitochondria-associated endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000370350
- Coding exons
- 5
- Length
- 7160
- Individuals with no LoFs
- 125641
- Homozygous LoFs
- 12
- Heterozygous LoFs
- 29
- Defined
- 125682
- p
- 0.000163
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.338 | 87 | 78.6 | 1.11 | 0.00000649 | 1184 |
| Missense (PolyPhen) | 24 | 17.235 | 1.3925 | 315 | ||
| Synonymous | 0.135 | 28 | 28.9 | 0.968 | 0.00000226 | 361 |
| Loss of Function | 0.950 | 4 | 6.64 | 0.602 | 5.56e-7 | 95 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.0014 | 0.0011 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000012 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00022 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the regulation of endoplasmic reticulum (ER)-mitochondria coupling. Negatively regulates the ER- mitochondria distance and Ca(2+) transfer from ER to mitochondria possibly implicating it in the regulation of apoptosis (PubMed:27402544). May collaborate with RNF183 to restrain BIK protein levels thus regulating apoptotic signaling (PubMed:26567849). {ECO:0000269|PubMed:27402544, ECO:0000305|PubMed:26567849}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.494
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.708
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |