SNRPA1

Chr 15

small nuclear ribonucleoprotein polypeptide A'

Also known as: Lea1, U2A'

NCBI Gene: 6627ENSG00000131876UniProt: P09661OMIM: 603521

The SNRPA1 protein is a component of the U2 spliceosome that binds to U2 snRNA and is essential for pre-mRNA splicing. Mutations cause autosomal dominant connective tissue disease, and the gene is highly constrained against loss-of-function variants (pLI 0.99, LOEUF 0.22), indicating that such variants are likely pathogenic.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.22
Clinical Summary— SNRPA1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.22LOEUF
pLI 0.990
Z-score 3.44
OE 0.00 (0.00–0.22)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
1.87Z-score
OE missense 0.55 (0.46–0.67)
75 obs / 136.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.00–0.22)
0≤0.351.4
Missense OE0.55 (0.46–0.67)
0≤0.61.4
Synonymous OE1.12
0≤1.21.6
LoF obs/exp: 0 / 13.8Missense obs/exp: 75 / 136.5Syn Z: -0.68
DN
0.4686th %ile
GOF
0.4678th %ile
LOF
0.65top 25%

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

LOFprediction above median · LOEUF 0.22

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

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SNRPA1 · 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.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 3 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Identification of RNA-binding protein SNRPA1 for prognosis in prostate cancer.
Yuan P et al.·Aging (Albany NY)
2021
Elevated SNRPA1, as a Promising Predictor Reflecting Severe Clinical Outcome via Effecting Tumor Immunity for ccRCC, Is Related to Cell Invasion, Metastasis, and Sunitinib Sensitivity.
Jiang A et al.·Front Immunol
2022
mTOR up-regulation of SNRPA1 contributes to hepatocellular carcinoma development.
Feng J et al.·Biosci Rep
2020
TIGIT and SNRPA1 as novel diagnostic and predictive biomarkers in obstructive ventilatory dysfunction combined with pulmonary nontuberculous mycobacterial infection patients.
Zhang M et al.·Front Cell Infect Microbiol
2025Cohort
Multi-Omics analysis and in vitro validation reveal diagnostic and therapeutic roles of novel hub genes in ovarian cancer.
Wang J et al.·Hereditas
2025
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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