Is WAS p.Pro383= (c.1149T>A) pathogenic?

WAS p.Pro383= (c.1149T>A) is classified Likely benign in WAS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-01). No allele count reported in gnomAD v4.1 (AN 909,153).

How common is WAS p.Pro383= (c.1149T>A) in the general population?

WAS p.Pro383= (c.1149T>A) is no allele count reported in gnomAD v4.1 (AN 909,153) (gnomAD).

WAS p.Pro383=

c.1149T>A · rs1602179487 · VCV3067325

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 909,153)

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 -0.21	GERP 0.49, phastCons 0.69
Overall
CADD	5.046	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 909,153). 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.Pro383=
Coding: c.1149T>A
MANE Select: NM_000377
dbSNP: rs1602179487
Type: single nucleotide variant
Location: chrX:48688877 (GRCh38)
Structure: AlphaFold pLDDT 70.84 · 7 PDB
Residue 383: the 'disordered' region

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

Similar variants

WAS p.Pro383Leu Uncertain significance ★ ⚠ same residue
WAS c.1339-2A>G Pathogenic/Likely pathogenic ★★ same type
WAS c.1453+2T>C Pathogenic ★★ same type
WAS c.273+1G>A Pathogenic ★★ same type
WAS c.360+1G>A Pathogenic ★★ same type
WAS c.360+1G>T Pathogenic/Likely pathogenic ★★ same type
WAS c.559+5G>A Pathogenic ★★ same type
WAS c.777+1G>A Pathogenic ★★ same type

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-pro383 (accessed [today's date]).

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