Is WAS p.Pro315= (c.945G>A) pathogenic?

WAS p.Pro315= (c.945G>A) is classified Benign in WAS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-21). Very rare (popmax 0.00708%, afr); Associated with thrombocytopenia 1.

What condition is associated with WAS p.Pro315= (c.945G>A)?

WAS p.Pro315= (c.945G>A) is associated with thrombocytopenia 1, X-linked severe congenital neutropenia, Wiskott-Aldrich syndrome (ClinVar).

How common is WAS p.Pro315= (c.945G>A) in the general population?

WAS p.Pro315= (c.945G>A) is very rare (popmax 0.00708%, afr) (gnomAD).

WAS p.Pro315=

c.945G>A · rs781866378 · VCV2924767

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00708%, afr)

Conditions

thrombocytopenia 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.23 · evaluated, not missing
Constraint at this position
Conservation	phyloP -4.5	GERP -2.5
Overall
CADD	0.133	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00708% African / African-American · 4/56,495 alleles

Filtering AF 0.00235% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00141%

Overall 0.001% 12/1,200,127 alleles · very rare exomes 10/1,089,565 · genomes 2/110,562 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00708%	14,124
Remaining individualsnot grpmax-eligible	0.00636%	15,726
East Asian	0.00595%	16,809
European (non-Finnish)	0.000337%	296,534

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.Pro315=
Coding: c.945G>A
MANE Select: NM_000377
dbSNP: rs781866378
Type: single nucleotide variant
Location: chrX:48688673 (GRCh38)
Structure: AlphaFold pLDDT 70.84 · 7 PDB
Residue 315: 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 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
WAS c.778-6G>A Pathogenic ★★ same condition
WAS p.Ala56Val 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-pro315 (accessed [today's date]).

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