Is WAS p.Ser82Pro (c.244T>C) pathogenic?

WAS p.Ser82Pro (c.244T>C) is classified Likely pathogenic in WAS (ClinVar, Single submitter, 2 submitters; last evaluated 2019-12-04). AlphaMissense: likely pathogenic (0.9923); Absent from gnomAD v4.1.

How common is WAS p.Ser82Pro (c.244T>C) in the general population?

WAS p.Ser82Pro (c.244T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about WAS p.Ser82Pro (c.244T>C)?

AlphaMissense predicts likely pathogenic (score 0.9923) — an in-silico prediction, not a clinical call.

WAS p.Ser82Pro

c.244T>C · rs132630272 · VCV11122

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9923 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9923	likely pathogenic ✓ concordant with ClinVar · top 3% in WAS
REVEL	0.941	strongly pathogenic-leaning
SaProt	LLR -16.98	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.3, phastCons 1
Regional constraint	o/e 0.52	unconstrained · MANE · 1,973 bp · p 1.3e-07 · regional, not allelic
Overall
CADD	25.4	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: WAS
Protein: p.Ser82Pro
Coding: c.244T>C
MANE Select: NM_000377
dbSNP: rs132630272
Type: single nucleotide variant
Location: chrX:48684394 (GRCh38)
Structure: AlphaFold pLDDT 70.84 · 7 PDB
Residue 82: the wh1 domain; a UniProt-annotated variant site (in was; attenuated form)

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

Similar variants

WAS p.Ser82Phe Pathogenic 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-ser82pro (accessed [today's date]).

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