Is WAS p.Pro385Ala (c.1153C>G) pathogenic?

WAS p.Pro385Ala (c.1153C>G) is classified Uncertain significance in WAS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-09). AlphaMissense: likely benign (0.0607); No allele count reported in gnomAD v4.1 (AN 1,165,250); Associated with Inborn genetic diseases.

What condition is associated with WAS p.Pro385Ala (c.1153C>G)?

WAS p.Pro385Ala (c.1153C>G) is associated with Inborn genetic diseases (ClinVar).

How common is WAS p.Pro385Ala (c.1153C>G) in the general population?

WAS p.Pro385Ala (c.1153C>G) is no allele count reported in gnomAD v4.1 (AN 1,165,250) (gnomAD).

What do computational predictors say about WAS p.Pro385Ala (c.1153C>G)?

AlphaMissense predicts likely benign (score 0.0607) — an in-silico prediction, not a clinical call.

WAS p.Pro385Ala

c.1153C>G · VCV4200083

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0607 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,165,250)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0607	likely benign
REVEL	0.307	indeterminate
SaProt	LLR -11.26	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	Δ0.46	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 0.018	GERP 0.39
Regional constraint	o/e 0.90	unconstrained · MANE · 2,456 bp · p 0.22 · regional, not allelic
Overall
CADD	18.34	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,165,250). 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.Pro385Ala
Coding: c.1153C>G
MANE Select: NM_000377
Type: single nucleotide variant
Location: chrX:48688881 (GRCh38)
Structure: AlphaFold pLDDT 70.84 · 7 PDB
Residue 385: the 'disordered' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

WAS p.Pro385= Likely benign ★ same residue
WAS p.Arg328Gln Uncertain significance ★★ ⚠ same condition
WAS p.Arg377Cys Uncertain significance ★★ ⚠ same condition
WAS p.Arg94Gln Uncertain significance ★★ ⚠ same condition
WAS p.Asp489Gly Uncertain significance ★★ ⚠ same condition
WAS p.Pro386Ser Uncertain significance ★★ ⚠ same condition
WAS p.Thr282Ala Uncertain significance ★★ ⚠ same condition
WAS p.Arg157His Likely benign ★★ 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-pro385ala (accessed [today's date]).

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