NAP1L3
Chr Xnucleosome assembly protein 1 like 3
Also known as: MB20, NPL3
This gene encodes a histone chaperone that facilitates nucleosome assembly and may contribute to cellular differentiation. Mutations cause X-linked intellectual disability with onset in early childhood. The gene follows X-linked inheritance and is located in a chromosomal region associated with multiple X-linked cognitive disability syndromes.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
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
117 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 | 0 | 0 | 56 | 0 | 56 |
Likely Pathogenic | 0 | 0 | 0 | 0 | 0 |
VUS | 0 | 45 | 13 | 0 | 58 |
Likely Benign | 0 | 0 | 1 | 1 | 2 |
Benign | 0 | 0 | 1 | 0 | 1 |
| Total | 0 | 45 | 71 | 1 | 117 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
NAP1L3 · 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