NSUN2 p.Arg9=
c.25C>A · rs1200326805 · VCV1608127
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,495,648)
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 3.4 | GERP -0.99, phastCons 1 |
| Overall | ||
| CADD | 12.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,495,648). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- NSUN2
- Protein
- p.Arg9=
- Coding
- c.25C>A
- MANE Select
- NM_017755
- dbSNP
- rs1200326805
- Type
- single nucleotide variant
- Location
- chr5:6632955 (GRCh38)
- Gene constraint
- LOEUF 0.965 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.09 · 11 PDB
- Residue 9
- the 'disordered' region
Similar variants
- 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
- NSUN2 p.Trp377Ter Pathogenic ★★ same type
- NSUN2 c.1226+4A>T Uncertain significance ★★ 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-arg9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown