SPATA31A6

Chr 9

SPATA31 subfamily A member 6

Also known as: FAM75A6

NCBI Gene: 389730 ENSG00000185775 UniProt: Q5VVP1

The protein is predicted to bind actin and function in spermatogenesis and cell differentiation, with localization to the acrosomal vesicle. Currently, no specific diseases have been definitively associated with mutations in this gene. The gene shows low constraint to loss-of-function variation (pLI < 0.1, LOEUF 1.92), suggesting it may be tolerant to genetic disruption.

ResearchSummary from RefSeq, UniProt

Predicted to enable actin binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.92

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.92LOEUF

pLI 0.000

Z-score -0.77

OE 1.40 (0.72–1.92)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-4.59Z-score

OE missense 1.66 (1.55–1.77)

637 obs / 384.0 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.40 (0.72–1.92)

0≤0.351.4

Missense OE?1.66 (1.55–1.77)

0≤0.61.4

Synonymous OE?1.61

0≤1.21.6

LoF obs/exp: 6 / 4.3Missense obs/exp: 637 / 384.0Syn Z: -5.99

Background carrier burden — how many people carry a rare variant somewhere in SPATA31A6?

gnomAD v4 · ~719k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 23

994 rare PASS variants

Rare truncating (LoF)

1 in 240

124 rare PASS variants

Rare synonymous (reference)

1 in 42

374 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SPATA31A6. 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)	~550k	1 in 36	1 in 240
South Asian	~42k	1 in 26	1 in 480
Remaining (unassigned)	~29k	1 in 23	1 in 380
European (Finnish)	~26k	1 in 63	1 in 320
Admixed American	~22k	1 in 21	1 in 430
East Asian	~19k	1 in 28	1 in 200
African / African American	~18k	1 in 20	1 in 150
Ashkenazi Jewish	~13k	1 in 110	1 in 1,600
Middle Eastern	~2,735	1 in 39	≈ 1 in 700

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