SNAPC3

Chr 9

small nuclear RNA activating complex polypeptide 3

Also known as: PTFbeta, SNAP50

The SNAPC3 protein is part of the SNAPc complex that binds to promoter sequences and is required for transcription of small nuclear RNA genes by both RNA polymerase II and III. Mutations cause autosomal recessive intellectual disability with seizures and macrocephaly, typically presenting in early childhood. This gene is not highly constrained against loss-of-function variants.

OMIMResearchSummary from RefSeq, UniProt
LOEUF 1.02
Clinical SummarySNAPC3
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
104 unique Pathogenic / Likely Pathogenic· 82 VUS of 200 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
1.02LOEUF
pLI 0.000
Z-score 1.50
OE 0.64 (0.421.02)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-1.03Z-score
OE missense 1.20 (1.081.34)
244 obs / 202.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.64 (0.421.02)
00.351.4
Missense OE1.20 (1.081.34)
00.61.4
Synonymous OE1.18
01.21.6
LoF obs/exp: 13 / 20.3Missense obs/exp: 244 / 202.7Syn Z: -1.22

ClinVar Variant Classifications

200 submitted variants in ClinVar

Classification Summary

Pathogenic97
Likely Pathogenic7
VUS82
Likely Benign3
97
Pathogenic
7
Likely Pathogenic
82
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
97
0
97
Likely Pathogenic
0
0
7
0
7
VUS
0
76
6
0
82
Likely Benign
0
3
0
0
3
Benign
0
0
0
0
0
Total0791100189

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

View in ClinVar →

Protein Context — Lollipop Plot

SNAPC3 · 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

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found