Is WAS p.Pro402fs (c.1203del) pathogenic?

WAS p.Pro402fs (c.1203del) is classified Pathogenic in WAS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-24). No gnomAD frequency available for this variant; Associated with Wiskott-Aldrich syndrome.

What condition is associated with WAS p.Pro402fs (c.1203del)?

WAS p.Pro402fs (c.1203del) is associated with Wiskott-Aldrich syndrome, X-linked severe congenital neutropenia, thrombocytopenia 1 (ClinVar).

How common is WAS p.Pro402fs (c.1203del) in the general population?

WAS p.Pro402fs (c.1203del) is no gnomAD frequency available for this variant (gnomAD).

How is Wiskott-Aldrich syndrome inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

WAS p.Pro402fs

c.1203del · rs2519287822 · VCV2113185

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Wiskott-Aldrich syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 10 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.6	GERP 1.5, phastCons 1
Region caveats
Repeat context	tandem	(CCA)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: WAS
Protein: p.Pro402fs
Coding: c.1203del
MANE Select: NM_000377
dbSNP: rs2519287822
Type: Deletion
Location: chrX:48688931 (GRCh38)
Structure: AlphaFold pLDDT 70.84 · 7 PDB
Residue 402: the 'disordered' region

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

Disease context

Wiskott-Aldrich syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: X-linked severe congenital neutropenia thrombocytopenia 1

For Wiskott-Aldrich syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Not applicable
Onset: Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

WAS p.Pro402_Pro404dup Uncertain significance ★★ same residue
WAS p.Pro402Leu Uncertain significance ★★ ⚠ same residue
WAS p.Pro402_Pro404del Conflicting classifications of pathogenicity ★ same residue
WAS p.Pro402= Likely benign ★ same residue
WAS c.777+3_777+6del Pathogenic ★★ same condition
WAS p.Arg86fs Pathogenic/Likely pathogenic ★★ same condition
WAS p.Asn408fs Pathogenic ★★ same condition
WAS p.Gly334fs 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-pro402fs (accessed [today's date]).

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