NYX p.Ser362=
c.1086C>T · rs752006200 · VCV1635609
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0081%, 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 -13 | GERP -3.8 |
| Overall | ||
| CADD | 0.875 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0081%
European (non-Finnish) · 72/889,420 alleles
Filtering AF
0.00656%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00603%
Overall
0.00652%
78/1,196,255 alleles · very rare
exomes 72/1,084,114 · genomes 6/112,141 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0081% | 12,353 |
| Remaining individualsnot grpmax-eligible | 0.00636% | 15,712 |
| African / African-American | 0.00525% | 19,030 |
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.Ser362=
- Coding
- c.1086C>T
- MANE Select
- NM_001378477
- dbSNP
- rs752006200
- Type
- single nucleotide variant
- Location
- chrX:41474554 (GRCh38)
- Structure
- AlphaFold pLDDT 82.68
- Residue 362
- 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-ser362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown