Is WAS p.Pro59fs (c.176del) pathogenic?

WAS p.Pro59fs (c.176del) is classified Pathogenic in WAS (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-08-01). No gnomAD frequency available for this variant; Associated with thrombocytopenia 1.

What condition is associated with WAS p.Pro59fs (c.176del)?

WAS p.Pro59fs (c.176del) is associated with thrombocytopenia 1, X-linked severe congenital neutropenia, Wiskott-Aldrich syndrome (ClinVar).

How common is WAS p.Pro59fs (c.176del) in the general population?

WAS p.Pro59fs (c.176del) is no gnomAD frequency available for this variant (gnomAD).

WAS p.Pro59fs

c.176del · rs2147262809 · VCV1360224

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

thrombocytopenia 1

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 2 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.7	GERP -1.9, phastCons 1

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.Pro59fs
Coding: c.176del
MANE Select: NM_000377
dbSNP: rs2147262809
Type: Deletion
Location: chrX:48684322 (GRCh38)
Structure: AlphaFold pLDDT 70.84 · 7 PDB
Residue 59: the wh1 domain

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.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.Ser242fs Pathogenic/Likely pathogenic ★★ same condition
WAS c.-37_132+35del 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-pro59fs (accessed [today's date]).

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