MEIG1

Chr 10

meiosis/spermiogenesis associated 1

Also known as: SPATA39, bA2K17.3

NCBI Gene: 644890 ENSG00000197889 UniProt: Q5JSS6

The MEIG1 protein is essential for spermiogenesis, the process of sperm cell maturation during male fertility development. Mutations in this gene cause male infertility due to defects in sperm formation, following an autosomal recessive inheritance pattern. This gene shows low constraint against loss-of-function variants, consistent with its specialized role in male reproductive function.

ResearchSummary from RefSeq, UniProt

Predicted to be involved in cell differentiation. Predicted to act upstream of or within intracellular protein localization; manchette assembly; and sperm axoneme assembly. Predicted to be located in cytosol and manchette. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.84

LOEUF

—

Mechanism

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?

1.84LOEUF

pLI 0.000

Z-score -0.12

OE 1.06 (0.54–1.84)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.23Z-score

OE missense 1.09 (0.87–1.37)

53 obs / 48.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.06 (0.54–1.84)

0≤0.351.4

Missense OE?1.09 (0.87–1.37)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 5 / 4.7Missense obs/exp: 53 / 48.6Syn Z: 0.11

Background carrier burden — how many people carry a rare variant somewhere in MEIG1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 400

130 rare PASS variants

Rare truncating (LoF)

1 in 8,100

27 rare PASS variants

Rare synonymous (reference)

1 in 2,600

43 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MEIG1. 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 500	1 in 11,000
South Asian	~43k	1 in 910	1 in 8,600
Remaining (unassigned)	~30k	1 in 420	≈ 1 in 10,000
European (Finnish)	~27k	≈ 1 in 6,700	none seen
Admixed American	~22k	1 in 430	≈ 1 in 7,400
African / African American	~21k	1 in 230	1 in 2,500
East Asian	~20k	1 in 390	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 570	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 410	≈ 1 in 2,900

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): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓