SNRPA1

Chr 15

small nuclear ribonucleoprotein polypeptide A'

Also known as: Lea1, U2A'

NCBI Gene: 6627ENSG00000131876UniProt: P09661

Enables RNA binding activity. Involved in mRNA splicing, via spliceosome and spermatogenesis. Located in nuclear speck. Part of U2-type catalytic step 2 spliceosome and U2-type precatalytic spliceosome. Implicated in connective tissue disease. [provided by Alliance of Genome Resources, Jul 2025]

126
ClinVar variants
77
Pathogenic / LP
0.99
pLI score· haploinsufficient
0
Active trials
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.
📋
ClinVar Variants
77 Pathogenic / Likely Pathogenic· 39 VUS of 126 total submissions
Some data sources returned errors (1)

pubmed: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.87Z-score
OE missense 0.55 (0.46–0.67)
75 obs / 136.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.00 (0.00–0.22)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.55 (0.46–0.67)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.12
0≤1.21.6
LoF obs/exp: 0 / 13.8Missense obs/exp: 75 / 136.5Syn Z: -0.68

ClinVar Variant Classifications

126 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic72
Likely Pathogenic5
VUS39
Likely Benign7
Benign3
72
Pathogenic
5
Likely Pathogenic
39
VUS
7
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
72
0
72
Likely Pathogenic
0
0
5
0
5
VUS
0
28
11
0
39
Likely Benign
0
0
7
0
7
Benign
0
0
3
0
3
Total028980126

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

View in 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.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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
2025🔓 Open AccessCohort
Long noncoding RNA ENST00000458139 promotes mitochondrial dysfunction and apoptosis of podocytes in diabetic kidney disease through binding with SNRPA1.
Yang M et al.·Int Immunopharmacol
2025
High SNRPA1 expression leads to poor prognosis in patients with lung adenocarcinoma.
Yang JJ et al.·Clin Respir J
2023🔓 Open AccessCohort
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🔓 Open Access
A prometastatic splicing program regulated by SNRPA1 interactions with structured RNA elements.
Fish L et al.·Science
2021
Top 5 resultsSearch Europe PMC ↗

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