NIPSNAP3A

Chr 9

nipsnap homolog 3A

Also known as: HSPC299, NIPSNAP4, TASSC

NCBI Gene: 25934ENSG00000136783UniProt: Q9UFN0OMIM: 608871

NIPSNAP3A encodes a protein involved in vesicular transport processes within cells. Mutations cause autosomal recessive developmental delays, intellectual disability, and seizures with onset in infancy or early childhood. The gene shows minimal constraint against loss-of-function variants, which is consistent with its recessive inheritance pattern.

OMIMResearchSummary from RefSeq
LOEUF 1.81
Clinical Summary— NIPSNAP3A
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
36 unique Pathogenic / Likely Pathogenic· 40 VUS of 89 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
1.81LOEUF
pLI 0.000
Z-score -0.83
OE 1.25 (0.84–1.81)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.29Z-score
OE missense 1.07 (0.94–1.23)
144 obs / 134.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.25 (0.84–1.81)
0≤0.351.4
Missense OE1.07 (0.94–1.23)
0≤0.61.4
Synonymous OE1.09
0≤1.21.6
LoF obs/exp: 16 / 12.8Missense obs/exp: 144 / 134.4Syn Z: -0.47

ClinVar Variant Classifications

89 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic34
Likely Pathogenic2
VUS40
34
Pathogenic
2
Likely Pathogenic
40
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
34
0
34
Likely Pathogenic
0
0
2
0
2
VUS
0
34
6
0
40
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total03442076

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

View in ClinVar →

Protein Context — Lollipop Plot

NIPSNAP3A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients