NCBP2
Chr 3nuclear cap binding protein subunit 2
Also known as: CBC2, CBP20, NIP1, PIG55
NCBP2 encodes a component of the nuclear cap-binding complex that binds to the 5' cap of pre-mRNAs and regulates pre-mRNA splicing, mRNA export from the nucleus, and nonsense-mediated mRNA decay. Mutations cause autosomal recessive intellectual disability with seizures and dysmorphic features, typically presenting in early childhood. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.675), suggesting some tolerance to complete protein loss.
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
127 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | — | — | — | — | 84 |
Likely Pathogenic | — | — | — | — | 3 |
VUS | — | — | — | — | 29 |
Likely Benign | — | — | — | — | 1 |
Benign | — | — | — | — | 0 |
Conflicting | — | 1 | |||
| Total | — | 118 | |||
Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
NCBP2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools