Is WT1 p.Pro381fs (c.1142del) pathogenic?

WT1 p.Pro381fs (c.1142del) is classified Likely pathogenic in WT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-10-15). No gnomAD frequency available for this variant; Associated with Wilms tumor 1.

What condition is associated with WT1 p.Pro381fs (c.1142del)?

WT1 p.Pro381fs (c.1142del) is associated with Wilms tumor 1 (ClinVar).

How common is WT1 p.Pro381fs (c.1142del) in the general population?

WT1 p.Pro381fs (c.1142del) is no gnomAD frequency available for this variant (gnomAD).

WT1 p.Pro381fs

c.1142del · rs1564972993 · VCV979072

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Wilms tumor 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 7 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -4.8	GERP -5.4

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: WT1
Protein: p.Pro381fs
Coding: c.1142del
MANE Select: NM_024426
dbSNP: rs1564972993
Type: Deletion
Location: chr11:32396379 (GRCh38)
Gene constraint: LOEUF 0.253 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 52.09 · 31 PDB
Residue 381: the 'important for interaction with target dna' region

Full WT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Wilms tumor 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

WT1 p.Pro381Leu Uncertain significance ★★ same residue
WT1 p.Pro381= Likely benign ★★ same residue
WT1 p.Pro381Ala Uncertain significance ★ same residue
WT1 p.Pro381Ser Conflicting classifications of pathogenicity ★ same residue
WT1 p.Pro137fs Pathogenic/Likely pathogenic ★★ same condition
WT1 c.882_887+3del Pathogenic ★ same condition
WT1 p.Arg476fs Likely pathogenic ★ same condition
WT1 p.Arg500fs Likely 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/wt1-p-pro381fs (accessed [today's date]).

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