SPATA22

Chr 17AR

spermatogenesis associated 22

Also known as: NYD-SP20, NYDSP20, POF25, SPGF96

NCBI Gene: 84690 ENSG00000141255 UniProt: Q8NHS9 OMIM: 617673

This meiosis-specific protein is required for homologous recombination during meiosis I. Mutations cause autosomal recessive spermatogenic failure in males and premature ovarian failure in females, affecting reproductive function. The gene shows low constraint against loss-of-function variants in the general population, consistent with its reproductive-specific phenotype that would not affect survival to reproductive age.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

Predicted to be involved in regulation of meiotic cell cycle. Predicted to act upstream of or within several processes, including fertilization; gamete generation; and meiosis I cell cycle process. Predicted to be located in chromosome. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

DNmechanismARLOEUF 0.772 OMIM phenotypes

Clinical Summary— SPATA22

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.77LOEUF

pLI 0.000

Z-score 2.35

OE 0.44 (0.26–0.77)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.29Z-score

OE missense 0.94 (0.83–1.07)

171 obs / 182.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.44 (0.26–0.77)

0≤0.351.4

Missense OE?0.94 (0.83–1.07)

0≤0.61.4

Synonymous OE?1.05

0≤1.21.6

LoF obs/exp: 9 / 20.5Missense obs/exp: 171 / 182.1Syn Z: -0.33

This gene — mechanism propensity

0.75top 25%

GOF

0.2895th %ile

LOF

0.3843th %ile

The highest-scoring mechanism for this gene is dominant-negative.

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.