SPATA31D4

Chr 9

SPATA31 subfamily D member 4

Also known as: FAM75D4

NCBI Gene: 389761ENSG00000189357UniProt: Q6ZUB0

The protein is predicted to be involved in cell differentiation and spermatogenesis and is located in cellular membranes. Clinical disease associations, inheritance patterns, and confirmed pathogenic mechanisms for SPATA31D4 mutations have not been established based on the available information.

ResearchSummary from RefSeq, UniProt, Mechanism
Multiplemechanism
Clinical Summary— SPATA31D4
📋
ClinVar Variants
29 unique Pathogenic / Likely Pathogenic· 55 VUS of 94 total submissions
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Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

DN
0.74top 25%
GOF
0.78top 25%
LOF
0.2971th %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

94 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic25
Likely Pathogenic4
VUS55
Likely Benign10
25
Pathogenic
4
Likely Pathogenic
55
VUS
10
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
25
0
25
Likely Pathogenic
0
0
4
0
4
VUS
0
53
2
0
55
Likely Benign
0
7
0
3
10
Benign
0
0
0
0
0
Total06031394

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

View in ClinVar →

Protein Context — Lollipop Plot

SPATA31D4 · 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 ↗
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