NYX p.Arg246=
c.738C>T · VCV4798450
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000113%, nfe)
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 -4.5 | GERP -3.7 |
| Overall | ||
| CADD | 1.885 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000113%
European (non-Finnish) · 1/884,804 alleles
Overall
8.47e-05%
1/1,180,067 alleles · very rare
exomes 1/1,067,127 · genomes 0/112,940 · joint denominator
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
- NYX
- Protein
- p.Arg246=
- Coding
- c.738C>T
- MANE Select
- NM_001378477
- Type
- single nucleotide variant
- Location
- chrX:41474206 (GRCh38)
- Structure
- AlphaFold pLDDT 82.68
Similar variants
- NYX p.Arg246Cys Uncertain significance ★ ⚠ same residue
- NYX p.Asn211Ser Pathogenic/Likely pathogenic ★★ same type
- NYX p.Pro170Arg Pathogenic ★★ same type
- NYX p.Ser196Ter Pathogenic ★★ same type
- NYX p.Ser40Ter Pathogenic/Likely pathogenic ★★ same type
- NYX p.Ala113Thr Uncertain significance ★★ same type
- NYX p.Ala113Val Uncertain significance ★★ same type
- NYX p.Ala123Val 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/nyx-p-arg246 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown