NYX p.Pro170=
c.510G>C · rs779716726 · VCV1140925
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0227%, 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 -4.7 | GERP -3.3 |
| Overall | ||
| CADD | 4.207 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0227%
European (non-Finnish) · 190/835,791 alleles
Filtering AF
0.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0191%
Overall
0.0179%
193/1,077,274 alleles · ultra-rare
exomes 186/965,523 · genomes 7/111,751 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0227% | 4,399 |
| Remaining individualsnot grpmax-eligible | 0.00485% | 20,615 |
| African / African-American | 0.00197% | 50,871 |
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.Pro170=
- Coding
- c.510G>C
- MANE Select
- NM_001378477
- dbSNP
- rs779716726
- Type
- single nucleotide variant
- Location
- chrX:41473978 (GRCh38)
- Structure
- AlphaFold pLDDT 82.68
- Residue 170
- a UniProt-annotated variant site (in csnb1a)
Similar variants
- NYX p.Pro170Arg Pathogenic ★★ same residue
- NYX p.Pro170Leu Likely pathogenic ★ same residue
- NYX p.Pro170Ser Likely pathogenic ★ same residue
- NYX p.Pro170fs Pathogenic ★ same residue
- NYX p.Asn211Ser Pathogenic/Likely pathogenic ★★ same type
- NYX p.Ser196Ter Pathogenic ★★ same type
- NYX p.Ser40Ter Pathogenic/Likely pathogenic ★★ same type
- NYX p.Ala113Thr 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-pro170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown