NONO p.Pro42=
c.126T>C · rs996588311 · VCV2028243
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.84 | GERP -4.1, phastCons 1 |
| Overall | ||
| CADD | 10.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- NONO
- Protein
- p.Pro42=
- Coding
- c.126T>C
- MANE Select
- NM_007363
- dbSNP
- rs996588311
- Type
- single nucleotide variant
- Location
- chrX:71290763 (GRCh38)
- Structure
- AlphaFold pLDDT 77.76 · 9 PDB
- Residue 42
- the 'disordered' region
Similar variants
- NONO c.651-1G>C Likely pathogenic ★★ same type
- NONO p.Ala377= Pathogenic ★★ same type
- NONO p.Arg184Ter Pathogenic ★★ same type
- NONO p.Ala453Pro Uncertain significance ★★ ⚠ same type
- NONO p.Arg202Trp Uncertain significance ★★ ⚠ same type
- NONO p.Arg456Ser Uncertain significance ★★ ⚠ same type
- NONO p.Asn161Asp Uncertain significance ★★ ⚠ same type
- NONO p.Gln380Arg 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/nono-p-pro42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown