SPATA31A3

Chr 9

SPATA31 subfamily A member 3

Also known as: FAM75A3

NCBI Gene: 727830ENSG00000275969UniProt: Q5VYP0

The protein SPATA31A3 is predicted to be involved in cell differentiation and spermatogenesis and is located in cellular membranes. Limited information is available about disease associations with mutations in this gene. The gene shows relatively low constraint to loss-of-function variation, suggesting it may be more tolerant to certain types of genetic variants.

ResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.89
Clinical Summary— SPATA31A3
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.00) despite low pLI — interpret in context.
📋
ClinVar Variants
45 unique Pathogenic / Likely Pathogenic· 224 VUS of 301 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.89LOEUF
pLI 0.295
Z-score 0.34
OE 0.00 (0.00–1.89)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-1.28Z-score
OE missense 1.37 (1.19–1.58)
131 obs / 95.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.00 (0.00–1.89)
0≤0.351.4
Missense OE1.37 (1.19–1.58)
0≤0.61.4
Synonymous OE0.83
0≤1.21.6
LoF obs/exp: 0 / 0.1Missense obs/exp: 131 / 95.7Syn Z: 0.82
DN
0.75top 25%
GOF
0.84top 5%
LOF
0.3163th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
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

301 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic41
Likely Pathogenic4
VUS224
Likely Benign29
Benign1
Conflicting1
41
Pathogenic
4
Likely Pathogenic
224
VUS
29
Likely Benign
1
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
41
0
41
Likely Pathogenic
0
0
4
0
4
VUS
0
223
1
0
224
Likely Benign
0
26
0
3
29
Benign
0
0
1
0
1
Conflicting
—1
Total0249473300

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

View in ClinVar →

Protein Context — Lollipop Plot

SPATA31A3 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

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

No open access results found

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