NYX p.Phe373=
c.1119C>T · rs1438907414 · VCV2868321
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00907%, 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 -1.3 | GERP -3.8, phastCons 0.001 |
| Overall | ||
| CADD | 0.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00907%
South Asian · 5/55,128 alleles
Filtering AF
0.00349%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00222%
Overall
0.000668%
8/1,197,957 alleles · very rare
exomes 8/1,084,166 · genomes 0/113,791 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00907% | 11,026 |
| Remaining individualsnot grpmax-eligible | 0.00212% | 47,112 |
| European (non-Finnish) | 0.000225% | 444,626 |
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.Phe373=
- Coding
- c.1119C>T
- MANE Select
- NM_001378477
- dbSNP
- rs1438907414
- Type
- single nucleotide variant
- Location
- chrX:41474587 (GRCh38)
- Structure
- AlphaFold pLDDT 82.68
- Residue 373
- the lrrct domain
Similar variants
- 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
- NYX p.Ala151Thr 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-phe373 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown