Is NYX p.Ser82Pro (c.244T>C) pathogenic?

NYX p.Ser82Pro (c.244T>C) is classified Uncertain significance in NYX (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-30). AlphaMissense: ambiguous (0.3677); No allele count reported in gnomAD v4.1 (AN 1,151,715).

How common is NYX p.Ser82Pro (c.244T>C) in the general population?

NYX p.Ser82Pro (c.244T>C) is no allele count reported in gnomAD v4.1 (AN 1,151,715) (gnomAD).

What do computational predictors say about NYX p.Ser82Pro (c.244T>C)?

AlphaMissense predicts ambiguous (score 0.3677) — an in-silico prediction, not a clinical call.

NYX p.Ser82Pro

c.244T>C · VCV4724488

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3677 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,151,715)

Computational evidence

Protein change
AlphaMissense	0.3677	ambiguous
REVEL	0.335	indeterminate
SaProt	—	withheld · numbering disagrees past residue 4 · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP -0.83, phastCons 0.96
Regional constraint	o/e 0.99	unconstrained · MANE · 27 kb · p 0.84 · regional, not allelic
Overall
CADD	23.6	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 S87P vs ClinVar S82P) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,151,715). 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.Ser82Pro
Coding: c.244T>C
MANE Select: NM_001378477
Type: single nucleotide variant
Location: chrX:41473712 (GRCh38)
Structure: AlphaFold pLDDT 82.68

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

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-ser82pro (accessed [today's date]).

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