Is WAS p.Arg431= (c.1293G>A) pathogenic?

WAS p.Arg431= (c.1293G>A) is classified Likely benign in WAS (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-19). Very rare (popmax 0.00173%, afr); Associated with thrombocytopenia 1.

What condition is associated with WAS p.Arg431= (c.1293G>A)?

WAS p.Arg431= (c.1293G>A) is associated with thrombocytopenia 1, X-linked severe congenital neutropenia, Wiskott-Aldrich syndrome (ClinVar).

How common is WAS p.Arg431= (c.1293G>A) in the general population?

WAS p.Arg431= (c.1293G>A) is very rare (popmax 0.00173%, afr) (gnomAD).

WAS p.Arg431=

c.1293G>A · rs782681903 · VCV2923415

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00173%, afr)

Conditions

thrombocytopenia 1

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 0.89	GERP 0.75, phastCons 1
Overall
CADD	8.481	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00173% African / African-American · 1/57,662 alleles

Overall 0.000166% 2/1,205,028 alleles · very rare exomes 2/1,091,757 · genomes 0/113,271 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00173%	57,662
European (non-Finnish)	0.000112%	893,943

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: WAS
Protein: p.Arg431=
Coding: c.1293G>A
MANE Select: NM_000377
dbSNP: rs782681903
Type: single nucleotide variant
Location: chrX:48689021 (GRCh38)
Structure: AlphaFold pLDDT 70.84 · 7 PDB
Residue 431: the wh2 domain; the 'disordered' region

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

Disease context

thrombocytopenia 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: X-linked severe congenital neutropenia Wiskott-Aldrich syndrome

Similar variants

WAS p.Arg431Trp Uncertain significance ★★ ⚠ same residue
WAS p.Arg431fs Pathogenic ★ same residue
WAS c.1339-2A>G Pathogenic/Likely pathogenic ★★ same condition
WAS c.1453+2T>C Pathogenic ★★ same condition
WAS c.273+1G>A Pathogenic ★★ same condition
WAS c.360+1G>A Pathogenic ★★ same condition
WAS c.559+5G>A Pathogenic ★★ same condition
WAS c.777+1G>A 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/was-p-arg431 (accessed [today's date]).

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