SNRPN
Chr 15small nuclear ribonucleoprotein polypeptide N
Also known as: HCERN3, PWCR, RT-LI, SM-D, SMN, SNRNP-N, SNURF-SNRPN, sm-N
The protein functions as a component of the small nuclear ribonucleoprotein complex involved in pre-mRNA processing and may contribute to tissue-specific alternative splicing. Mutations or alterations in this paternally-expressed, imprinted gene located in the Prader-Willi syndrome critical region on chromosome 15 are associated with Prader-Willi syndrome and Angelman syndrome. The gene shows low constraint against loss-of-function variants (pLI 0.04, LOEUF 0.83), and these disorders typically present in infancy with distinct neurodevelopmental phenotypes depending on the parent of origin of the genetic alteration.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Moderately missense-constrained (top ~2.5%)
The highest-scoring mechanism for this gene is dominant-negative.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
423 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 1 | 0 | 302 | 0 | 303 |
Likely Pathogenic | 0 | 0 | 12 | 0 | 12 |
VUS | 3 | 52 | 22 | 0 | 77 |
Likely Benign | 0 | 0 | 12 | 10 | 22 |
Benign | 0 | 0 | 5 | 4 | 9 |
| Total | 4 | 52 | 353 | 14 | 423 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SNRPN · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
External Resources
Links to major genomics databases and tools