SPATA16

Chr 3AR

spermatogenesis associated 16

Also known as: NYD-SP12, SPGF6

NCBI Gene: 83893 ENSG00000144962 UniProt: Q9BXB7 OMIM: 609856

This gene encodes a testis-specific protein that belongs to the tetratricopeptide repeat-like superfamily. The encoded protein localizes to the Golgi apparatus and may play a role in spermatogenesis. [provided by RefSeq, May 2010]

GeneReviews OMIM Research

GeneReviews OMIM ResearchGenerating clinical summary…

MultiplemechanismARLOEUF 1.061 OMIM phenotype

Clinical Summary— SPATA16

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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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ClinVar Variants

91 VUS of 116 total submissions

Explore recent and relevant literature in Research Assistant →

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GeneReview available — SPATA16

Authoritative clinical overview · Recommended first read

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.06LOEUF

pLI 0.000

Z-score 1.31

OE 0.72 (0.50–1.06)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.20Z-score

OE missense 0.97 (0.88–1.07)

285 obs / 294.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.72 (0.50–1.06)

0≤0.351.4

Missense OE?0.97 (0.88–1.07)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 19 / 26.2Missense obs/exp: 285 / 294.7Syn Z: 0.16

This gene — mechanism propensity

0.6937th %ile

GOF

0.6930th %ile

LOF

0.3550th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median

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.

ClinVar Variant Classifications

116 submitted variants in ClinVar

ClinVar

Classification Summary

VUS91

Likely Benign10

Benign9

Conflicting2

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	0	75	7	9	91
Likely Benign	0	7	1	2	10
Benign	1	5	1	2	9
Conflicting	—				2
Total	1	87	9	13	112

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

View in ClinVar →

22 pathogenic / likely-pathogenic (of 29) ClinVar copy-number / structural variants overlap SPATA16 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →