NOP2
Chr 12NOP2 nucleolar protein
Also known as: NOL1, NOP120, NSUN1, p120
NOP2 encodes a methyltransferase that methylates cytosine residues in 28S rRNA and is required for ribosome biogenesis and 60S ribosomal subunit assembly. The gene is highly constrained against loss-of-function variants (pLI=1.00, LOEUF=0.17), indicating that mutations are likely to cause severe developmental consequences. Pathogenic variants in NOP2 have not yet been definitively associated with a recognized human disease phenotype in the medical literature.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Mild missense constraint
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
204 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 | 42 | 0 | 42 |
Likely Pathogenic | 0 | 0 | 2 | 0 | 2 |
VUS | 0 | 117 | 8 | 0 | 125 |
Likely Benign | 0 | 7 | 0 | 3 | 10 |
Benign | 1 | 4 | 1 | 1 | 7 |
| Total | 1 | 128 | 53 | 4 | 186 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
NOP2 · 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