FNDC3A

Chr 13

fibronectin type III domain containing 3A

Also known as: FNDC3, HUGO, bA203I16.1, bA203I16.5

NCBI Gene: 22862ENSG00000102531UniProt: Q9Y2H6

This protein mediates spermatid-Sertoli cell adhesion during spermatogenesis and has RNA binding activity. The gene is highly constrained against loss-of-function variants (pLI = 1.0, LOEUF = 0.22), but no human disease associations have been established in the provided data.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
2
Pubs (1 yr)
61
P/LP submissions
0%
P/LP missense
0.22
LOEUF· LoF intol.
LOF
Mechanism· predicted
Clinical Summary— FNDC3A
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
61 unique Pathogenic / Likely Pathogenic· 133 VUS of 237 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.22LOEUF
pLI 1.000
Z-score 6.58
OE 0.12 (0.07–0.22)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
1.53Z-score
OE missense 0.83 (0.77–0.89)
527 obs / 635.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.12 (0.07–0.22)
0≤0.351.4
Missense OE0.83 (0.77–0.89)
0≤0.61.4
Synonymous OE0.96
0≤1.21.6
LoF obs/exp: 8 / 65.4Missense obs/exp: 527 / 635.5Syn Z: 0.47
DN
0.3991th %ile
GOF
0.3392th %ile
LOF
0.73top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.22

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

237 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic59
Likely Pathogenic2
VUS133
Likely Benign10
Benign5
59
Pathogenic
2
Likely Pathogenic
133
VUS
10
Likely Benign
5
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
59
0
59
Likely Pathogenic
0
0
2
0
2
VUS
0
128
5
0
133
Likely Benign
0
4
2
4
10
Benign
0
2
0
3
5
Total0134687209

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

View in ClinVar →

Protein Context — Lollipop Plot

FNDC3A · 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
Open Research Assistant →
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 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
LncRNA SNHG14 Regulated by ZNF460 Promotes Gastric Cancer Progression and Metastasis by Targeting the miR-206/FNDC3A Axis.
Liu B et al.·J Cell Mol Med
2025Open Access
Silencing of fibronectin type III domain-containing protein 3A (FNDC3A) attenuates epithelial-to-mesenchymal transition (EMT), cancer invasion, and stemness in triple-negative breast cancer (TNBC).
Wada N et al.·Biochim Biophys Acta Mol Cell Res
2025
Exosomal or follicular FNDC3A decreases FOLR1 mRNA abundance and progesterone and lactate synthesis in bovine granulosa cells.
Daudon M et al.·Reproduction
2024
Microarray expression profiling of fndc3a zebrafish mutants.
Liedtke D et al.·MicroPubl Biol
2022Open AccessFunctional
FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy.
Manfrini N et al.·Cancer Res
2020
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