SPATA2L

Chr 16

spermatogenesis associated 2 like

Also known as: C16orf76, tamo

NCBI Gene: 124044 ENSG00000158792 UniProt: Q8IUW3

SPATA2L encodes a protein predicted to be active in the cytoplasm, though its specific cellular function remains unclear. Mutations in this gene have not been definitively associated with any recognized pediatric neurological disorders in current medical literature. The gene shows tolerance to loss-of-function variants (pLI 0.04, LOEUF 0.85), suggesting that complete loss of function may not cause severe developmental phenotypes.

ResearchSummary from RefSeq

Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

LOEUF 0.85

Clinical Summary— SPATA2L

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Population Constraint (gnomAD)

Low constraint (pLI 0.04) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

76 VUS of 82 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.85LOEUF

pLI 0.041

Z-score 1.92

OE 0.37 (0.18–0.85)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.26Z-score

OE missense 1.05 (0.94–1.16)

265 obs / 253.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.37 (0.18–0.85)

0≤0.351.4

Missense OE?1.05 (0.94–1.16)

0≤0.61.4

Synonymous OE?1.38

0≤1.21.6

LoF obs/exp: 4 / 10.8Missense obs/exp: 265 / 253.5Syn Z: -3.26

ClinVar Variant Classifications

82 submitted variants in ClinVar

ClinVar

Classification Summary

VUS76

Likely Benign2

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	76	76
Likely Benign	2	2
Benign	0	0
Total	78	78

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

42 pathogenic / likely-pathogenic (of 77) ClinVar copy-number / structural variants overlap SPATA2L — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →