NSRP1

Chr 17AR

nuclear speckle splicing regulatory protein 1

Also known as: CCDC55, HSPC095, NEDSSBA, NSrp70

NCBI Gene: 84081ENSG00000126653UniProt: Q9H0G5OMIM: 616173

The NSRP1 protein is an RNA-binding protein that regulates alternative splicing of pre-mRNA and is localized to nuclear speckles as part of ribonucleoprotein complexes. Mutations cause autosomal recessive neurodevelopmental disorder with spasticity, seizures, and brain abnormalities. This condition primarily affects the central nervous system with early developmental onset.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.581 OMIM phenotype
Clinical Summary— NSRP1
🧬
Gene-Disease Validity (ClinGen)
neurodevelopmental disorder with spasticity, seizures, and brain abnormalities · ARModerate

Moderate evidence — consider for supplementary testing

⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.32) despite low pLI — interpret in context.
📋
ClinVar Variants
14 unique Pathogenic / Likely Pathogenic· 67 VUS of 96 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.58LOEUF
pLI 0.012
Z-score 3.16
OE 0.32 (0.19–0.58)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.15Z-score
OE missense 0.98 (0.88–1.08)
273 obs / 279.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.32 (0.19–0.58)
0≤0.351.4
Missense OE0.98 (0.88–1.08)
0≤0.61.4
Synonymous OE1.06
0≤1.21.6
LoF obs/exp: 8 / 25.1Missense obs/exp: 273 / 279.9Syn Z: -0.47
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongNSRP1-related developmental delay, epilepsy, and microcephalyLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.77top 25%
GOF
0.4184th %ile
LOF
0.3261th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

96 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
Likely Pathogenic3
VUS67
Likely Benign6
Benign1
11
Pathogenic
3
Likely Pathogenic
67
VUS
6
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
0
8
0
11
Likely Pathogenic
2
0
1
0
3
VUS
1
65
1
0
67
Likely Benign
0
5
0
1
6
Benign
0
0
1
0
1
Total67011188

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

View in ClinVar →

Protein Context — Lollipop Plot

NSRP1 · 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 →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 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