Is WAS p.Phe293fs (c.879_882del) pathogenic?

WAS p.Phe293fs (c.879882del) is classified Pathogenic in WAS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-17). Associated with X-linked severe congenital neutropenia.

What condition is associated with WAS p.Phe293fs (c.879_882del)?

WAS p.Phe293fs (c.879_882del) is associated with X-linked severe congenital neutropenia, Wiskott-Aldrich syndrome, thrombocytopenia 1 (ClinVar).

How is X-linked severe congenital neutropenia inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

WAS p.Phe293fs

c.879_882del · VCV3758879

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

X-linked severe congenital neutropenia

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 9 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.22	GERP -1.6, phastCons 0.26

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

Variant & gene context

Gene: WAS
Protein: p.Phe293fs
Coding: c.879_882del
MANE Select: NM_000377
Type: Deletion
Location: chrX:48688399 (GRCh38)
Structure: AlphaFold pLDDT 70.84 · 7 PDB

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

Disease context

X-linked severe congenital neutropenia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Wiskott-Aldrich syndrome thrombocytopenia 1

For X-linked severe congenital neutropenia (Orphanet):

Inheritance: X-linked recessive
Onset: Infancy, Neonatal

Similar variants

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
WAS p.Pro353fs Pathogenic ★★ same condition
WAS p.Pro386fs Pathogenic/Likely pathogenic ★★ same condition
WAS p.Pro59fs Pathogenic ★★ same condition
WAS p.Ser242fs Pathogenic/Likely 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-phe293fs (accessed [today's date]).

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