Is WAS p.Pro402= (c.1206G>A) pathogenic?

WAS p.Pro402= (c.1206G>A) is classified Likely benign in WAS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-11). Very rare (popmax 0.00799%, sas); Associated with Wiskott-Aldrich syndrome.

What condition is associated with WAS p.Pro402= (c.1206G>A)?

WAS p.Pro402= (c.1206G>A) is associated with Wiskott-Aldrich syndrome, X-linked severe congenital neutropenia, thrombocytopenia 1 (ClinVar).

How common is WAS p.Pro402= (c.1206G>A) in the general population?

WAS p.Pro402= (c.1206G>A) is very rare (popmax 0.00799%, sas) (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.Pro402=

c.1206G>A · rs1557007285 · VCV2186743

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00799%, sas)

Conditions

Wiskott-Aldrich syndrome

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 -0.62	GERP -3
Overall
CADD	0.246	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00799% South Asian · 4/50,050 alleles

Filtering AF 0.00266% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00155%

Overall 0.000727% 8/1,100,511 alleles · very rare exomes 7/993,157 · genomes 1/107,354 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00799%	12,512
Remaining individualsnot grpmax-eligible	0.0024%	41,693
African / African-American	0.00188%	53,215
European (non-Finnish)	0.00024%	417,345

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.Pro402=
Coding: c.1206G>A
MANE Select: NM_000377
dbSNP: rs1557007285
Type: single nucleotide variant
Location: chrX:48688934 (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.Pro402Leu Uncertain significance ★★ ⚠ same residue
WAS p.Pro402_Pro404dup Uncertain significance ★★ same residue
WAS p.Pro402fs Pathogenic ★ same residue
WAS p.Pro402_Pro404del Conflicting classifications of pathogenicity ★ 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

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-pro402 (accessed [today's date]).

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