SPATA31A1

Chr 9

SPATA31 subfamily A member 1

Also known as: C9orf36, C9orf36A, FAM75A1, FAM75A2, SPATA31A2

NCBI Gene: 647060 ENSG00000204849 UniProt: Q5TZJ5 OMIM: 621335

SPATA31A1 encodes a protein predicted to be involved in cell differentiation and spermatogenesis and is located in cellular membranes. Currently, no established human diseases have been definitively associated with mutations in this gene. The inheritance pattern and clinical significance of SPATA31A1 variants remain to be determined.

OMIM 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]

OMIM 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

1.76

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.76LOEUF

pLI 0.378

Z-score 0.86

OE 0.00 (0.00–1.76)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.66Z-score

OE missense 1.26 (1.03–1.56)

62 obs / 49.1 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.00 (0.00–1.76)

0≤0.351.4

Missense OE?1.26 (1.03–1.56)

0≤0.61.4

Synonymous OE?0.89

0≤1.21.6

LoF obs/exp: 0 / 0.9Missense obs/exp: 62 / 49.1Syn Z: 0.39

Background carrier burden — how many people carry a rare variant somewhere in SPATA31A1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 50

699 rare PASS variants

Rare truncating (LoF)

1 in 1,200

79 rare PASS variants

Rare synonymous (reference)

1 in 78

254 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SPATA31A1. 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 79	1 in 1,300
South Asian	~43k	1 in 38	1 in 1,300
Remaining (unassigned)	~30k	1 in 45	1 in 420
European (Finnish)	~27k	1 in 100	≈ 1 in 19,000
Admixed American	~22k	1 in 44	1 in 780
African / African American	~21k	1 in 44	1 in 970
East Asian	~20k	1 in 35	1 in 930
Ashkenazi Jewish	~13k	1 in 150	none seen
Middle Eastern	~2,880	1 in 60	≈ 1 in 1,300

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; exon 1 poorly covered; exon 4 marginal. Genomes: 0 of 4 (exons 1, 2, 3, 4 below).? see exons ↓