Is WT1 p.Leu299fs (c.897del) pathogenic?

WT1 p.Leu299fs (c.897del) is classified Pathogenic in WT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-11-07). No gnomAD frequency available for this variant; Associated with Wilms tumor 1.

What condition is associated with WT1 p.Leu299fs (c.897del)?

WT1 p.Leu299fs (c.897del) is associated with Wilms tumor 1, Frasier syndrome, WAGR syndrome (ClinVar).

How common is WT1 p.Leu299fs (c.897del) in the general population?

WT1 p.Leu299fs (c.897del) is no gnomAD frequency available for this variant (gnomAD).

WT1 p.Leu299fs

c.897del · rs1852720329 · VCV958253

Pathogenic Single submitter

Classification

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 4 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.9, phastCons 1

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.Leu299fs
Coding: c.897del
MANE Select: NM_024426
dbSNP: rs1852720329
Type: Deletion
Location: chr11:32417645 (GRCh38)
Gene constraint: LOEUF 0.253 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 52.09 · 31 PDB

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

Also linked: Frasier syndrome WAGR syndrome Denys-Drash syndrome

Similar variants

WT1 p.Pro137fs Pathogenic/Likely pathogenic ★★ same condition
WT1 c.1354+4_1354+11del 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
WT1 p.Gln457_Cys458insTer Pathogenic ★ same condition
WT1 p.Glu423fs Pathogenic ★ same condition
WT1 p.His239fs 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-leu299fs (accessed [today's date]).

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