NSUN2 p.Pro760=
c.2280G>C · rs150472251 · VCV436071
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.357%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -4.2 |
| Overall | ||
| CADD | 0.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.357%
South Asian · 325/91,062 alleles
Filtering AF
0.325%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.312%
Overall
0.0208%
335/1,613,710 alleles · rare
exomes 319/1,461,342 · genomes 16/152,368 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.357% | 280 |
| Middle Eastern | 0.0173% | 5,790 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,925 |
| African / African-American | 0.00266% | 37,530 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NSUN2
- Protein
- p.Pro760=
- Coding
- c.2280G>C
- MANE Select
- NM_017755
- dbSNP
- rs150472251
- Type
- single nucleotide variant
- Location
- chr5:6599950 (GRCh38)
- Gene constraint
- LOEUF 0.965 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.09 · 11 PDB
- Residue 760
- the 'disordered' region
Similar variants
- NSUN2 p.Pro760Gln Benign/Likely benign ★★ same residue
- NSUN2 p.Pro760Leu Uncertain significance ★ ⚠ same residue
- NSUN2 c.1601+1G>A Likely pathogenic ★★ same type
- NSUN2 c.360-1G>C Pathogenic/Likely pathogenic ★★ same type
- NSUN2 p.Arg264Ter Pathogenic/Likely pathogenic ★★ same type
- NSUN2 p.Arg389Ter Pathogenic/Likely pathogenic ★★ same type
- NSUN2 p.Arg408Ter Pathogenic/Likely pathogenic ★★ same type
- NSUN2 p.Ser139Ter Pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nsun2-p-pro760 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown