Is ATRX p.Ser925Pro (c.2773T>C) pathogenic?

ATRX p.Ser925Pro (c.2773T>C) is classified Uncertain significance in ATRX (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-23). AlphaMissense: likely benign (0.0763); Absent from gnomAD v4.1.

How common is ATRX p.Ser925Pro (c.2773T>C) in the general population?

ATRX p.Ser925Pro (c.2773T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ATRX p.Ser925Pro (c.2773T>C)?

AlphaMissense predicts likely benign (score 0.0763) — an in-silico prediction, not a clinical call.

ATRX p.Ser925Pro

c.2773T>C · VCV4687788

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0763 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,209,733)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0763	likely benign
REVEL	0.14	moderately benign-leaning
SaProt	LLR -6.08	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.09	GERP 0.26
Regional constraint	o/e 1.31	unconstrained · MANE · 2,828 bp · p 3.3e-15 · regional, not allelic
Overall
CADD	11.17	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,209,733). 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: ATRX
Protein: p.Ser925Pro
Coding: c.2773T>C
MANE Select: NM_000489
Type: single nucleotide variant
Location: chrX:77682483 (GRCh38)
Structure: AlphaFold pLDDT 52.40 · 13 PDB
Residue 925: the 'disordered' region

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

Similar variants

ATRX p.Ser925= Likely benign ★★ same residue
ATRX c.134-2A>G Pathogenic/Likely pathogenic ★★ same type
ATRX c.5449-7A>G Likely pathogenic ★★ same type
ATRX p.Arg1022Ter Pathogenic/Likely pathogenic ★★ same type
ATRX p.Arg1661Cys Likely pathogenic ★★ ⚠ same type
ATRX p.Arg2085Cys Pathogenic/Likely pathogenic ★★ same type
ATRX p.Arg2085His Pathogenic/Likely pathogenic ★★ same type
ATRX p.Arg2131Gln Pathogenic/Likely pathogenic ★★ 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/atrx-p-ser925pro (accessed [today's date]).

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