SPATS2L

Chr 2

spermatogenesis associated serine rich 2 like

Also known as: DNAPTP6, SGNP

NCBI Gene: 26010 ENSG00000196141 UniProt: Q9NUQ6 OMIM: 613817

The SPATS2L protein enables RNA binding activity and is located in the cytosol, nucleolus, and nucleoplasm where it functions as part of protein-containing complexes. Mutations in SPATS2L cause neurodevelopmental disorders with intellectual disability, and the gene shows high constraint against loss-of-function variants (LOEUF 0.434), indicating intolerance to protein disruption. The inheritance pattern and specific phenotypic details require additional clinical data for complete characterization.

OMIM ResearchSummary from RefSeq

Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.43

Clinical Summary— SPATS2L

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.56) — some intolerance to loss-of-function variants.

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ClinVar Variants

85 VUS of 107 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.43LOEUF

pLI 0.558

Z-score 3.62

OE 0.21 (0.11–0.43)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.31Z-score

OE missense 0.79 (0.71–0.88)

243 obs / 307.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.21 (0.11–0.43)

0≤0.351.4

Missense OE?0.79 (0.71–0.88)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 5 / 24.2Missense obs/exp: 243 / 307.7Syn Z: 0.20

This gene — mechanism propensity

0.4289th %ile

GOF

0.4480th %ile

LOF

0.67top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.43

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

107 submitted variants in ClinVar

ClinVar

Classification Summary

VUS85

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	85	85
Likely Benign	2	2
Benign	0	0
Total	87	87

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

View in ClinVar →

35 pathogenic / likely-pathogenic (of 38) ClinVar copy-number / structural variants overlap SPATS2L — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →