SPATA31A3

Chr 9

SPATA31 subfamily A member 3

Also known as: FAM75A3

NCBI Gene: 727830 ENSG00000275969 UniProt: 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

Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.89

LOEUF

Multiple*

Mechanism· predicted

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 OE?0.00 (0.00–1.89)

0≤0.351.4

Missense OE?1.37 (1.19–1.58)

0≤0.61.4

Synonymous OE?0.83

0≤1.21.6

LoF obs/exp: 0 / 0.1Missense obs/exp: 131 / 95.7Syn Z: 0.82

Background carrier burden — how many people carry a rare variant somewhere in SPATA31A3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 93

198 rare PASS variants

Rare truncating (LoF)

1 in 870

70 rare PASS variants

Rare synonymous (reference)

1 in 240

67 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SPATA31A3. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 180	1 in 470
South Asian	~43k	1 in 85	1 in 710
Remaining (unassigned)	~30k	1 in 80	1 in 2,700
European (Finnish)	~27k	1 in 260	1 in 2,700
Admixed American	~22k	1 in 71	1 in 460
African / African American	~21k	1 in 71	1 in 660
East Asian	~20k	1 in 81	1 in 1,800
Ashkenazi Jewish	~13k	1 in 190	≈ 1 in 13,000
Middle Eastern	~2,881	1 in 130	≈ 1 in 730

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 1 of 4 coding exons well covered in gnomAD exomes; exon 1 poorly covered; exons 3, 4 marginal. Genomes: 0 of 4 (exons 1, 2, 3, 4 below).? see exons ↓