NYX p.Ser369=
c.1107C>T · rs1380402119 · VCV1993102
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 1,198,181)
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 0.21 | GERP -3.8, phastCons 0.45 |
| Overall | ||
| CADD | 3.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,198,181). 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
- NYX
- Protein
- p.Ser369=
- Coding
- c.1107C>T
- MANE Select
- NM_001378477
- dbSNP
- rs1380402119
- Type
- single nucleotide variant
- Location
- chrX:41474575 (GRCh38)
- Structure
- AlphaFold pLDDT 82.68
- Residue 369
- 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-ser369 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown