Is NYX p.Pro170Ser (c.508C>T) pathogenic?

NYX p.Pro170Ser (c.508C>T) is classified Likely pathogenic in NYX (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-27). AlphaMissense: likely pathogenic (0.7138); No allele count reported in gnomAD v4.1 (AN 1,080,301); Associated with NYX-related disorder.

What condition is associated with NYX p.Pro170Ser (c.508C>T)?

NYX p.Pro170Ser (c.508C>T) is associated with NYX-related disorder (ClinVar).

How common is NYX p.Pro170Ser (c.508C>T) in the general population?

NYX p.Pro170Ser (c.508C>T) is no allele count reported in gnomAD v4.1 (AN 1,080,301) (gnomAD).

What do computational predictors say about NYX p.Pro170Ser (c.508C>T)?

AlphaMissense predicts likely pathogenic (score 0.7138) — an in-silico prediction, not a clinical call.

NYX p.Pro170Ser

c.508C>T · VCV4950020

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7138 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,080,301)

Conditions

NYX-related disorder

Computational evidence

Protein change
AlphaMissense	0.7138	likely pathogenic ✓ concordant with ClinVar
REVEL	0.494	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP -0.61, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 27 kb · p 0.84 · regional, not allelic
Overall
CADD	24.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P175S vs ClinVar P170S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,080,301). 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.Pro170Ser
Coding: c.508C>T
MANE Select: NM_001378477
Type: single nucleotide variant
Location: chrX:41473976 (GRCh38)
Structure: AlphaFold pLDDT 82.68

Full NYX gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

NYX-related disorder

Similar variants

NYX p.Pro170Arg Pathogenic ★★ same residue
NYX p.Pro170Leu Likely pathogenic ★ same residue
NYX p.Pro170= Likely benign ★ same residue
NYX p.Asn211Ser Pathogenic/Likely pathogenic ★★ same condition
NYX p.Ser196Ter Pathogenic ★★ same condition
NYX p.Ser40Ter Pathogenic/Likely pathogenic ★★ same condition
NYX c.23-1G>T Pathogenic ★ same condition
NYX p.Arg89Pro Likely pathogenic ★ same condition

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-pro170ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown