SPATA31A7

Chr 9

SPATA31 subfamily A member 7

Also known as: AEP1, C9orf36, C9orf36A, FAM75A4, FAM75A7, SPATA31A4

NCBI Gene: 26165ENSG00000276040UniProt: Q8IWB4OMIM: 616584

The protein is predicted to be involved in cell differentiation and spermatogenesis and is located in cellular membranes. SPATA31A7 mutations have not been clearly established as a cause of human disease based on the available information. The inheritance pattern and clinical phenotypes associated with this gene remain to be determined.

OMIMResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.94
Clinical Summary— SPATA31A7
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
43 unique Pathogenic / Likely Pathogenic· 189 VUS of 255 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
1.94LOEUF
pLI 0.003
Z-score -0.99
OE 1.84 (0.63–1.94)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.56Z-score
OE missense 1.27 (0.99–1.64)
42 obs / 33.0 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.84 (0.63–1.94)
0≤0.351.4
Missense OE1.27 (0.99–1.64)
0≤0.61.4
Synonymous OE1.70
0≤1.21.6
LoF obs/exp: 3 / 1.6Missense obs/exp: 42 / 33.0Syn Z: -1.88
DN
0.76top 25%
GOF
0.85top 5%
LOF
0.3068th %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

255 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic40
Likely Pathogenic3
VUS189
Likely Benign22
Benign1
40
Pathogenic
3
Likely Pathogenic
189
VUS
22
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
40
0
40
Likely Pathogenic
0
0
3
0
3
VUS
0
166
23
0
189
Likely Benign
0
17
2
3
22
Benign
0
0
1
0
1
Total0183693255

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

View in ClinVar →

Protein Context — Lollipop Plot

SPATA31A7 · 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 2 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