FATE1

Chr X

fetal and adult testis expressed 1

Also known as: CT43, FATE

NCBI Gene: 89885ENSG00000147378UniProt: Q969F0

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]

0
Active trials
86
Pathogenic / LP
126
ClinVar variants
5
Pubs (1 yr)
-0.3
Missense Z
1.36
LOEUF
Clinical Summary— FATE1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
86 Pathogenic / Likely Pathogenic· 35 VUS of 126 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.36LOEUF
pLI 0.007
Z-score 0.95
OE 0.60 (0.29–1.36)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.34Z-score
OE missense 1.11 (0.93–1.32)
87 obs / 78.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.60 (0.29–1.36)
0≤0.351.4
Missense OE1.11 (0.93–1.32)
0≤0.61.4
Synonymous OE0.97
0≤1.21.6
LoF obs/exp: 4 / 6.6Missense obs/exp: 87 / 78.6Syn Z: 0.13
DN
DN
0.75top 25%
GOF
0.5563th %ile
LOF
0.3455th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

126 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic84
Likely Pathogenic2
VUS35
Likely Benign5
84
Pathogenic
2
Likely Pathogenic
35
VUS
5
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
84
0
84
Likely Pathogenic
0
0
2
0
2
VUS
0
31
4
0
35
Likely Benign
0
4
0
1
5
Benign
0
0
0
0
0
Total035901126

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

FATE1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 4 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients