Is WT1 p.Phe487= (c.1461C>T) pathogenic?

WT1 p.Phe487= (c.1461C>T) is classified Likely benign in WT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-03). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with WT1 p.Phe487= (c.1461C>T)?

WT1 p.Phe487= (c.1461C>T) is associated with Inborn genetic diseases (ClinVar).

How common is WT1 p.Phe487= (c.1461C>T) in the general population?

WT1 p.Phe487= (c.1461C>T) is absent from gnomAD v4.1 (gnomAD).

WT1 p.Phe487=

c.1461C>T · VCV3982461

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

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
Pangolin	Δ0.21	loss · gain 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 12	GERP 1.6, phastCons 1
Overall
CADD	13.89	PHRED · no single calibrated threshold — expert panels disagree

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: WT1
Protein: p.Phe487=
Coding: c.1461C>T
MANE Select: NM_024426
Type: single nucleotide variant
Location: chr11:32389166 (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

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

Similar variants

WT1 c.1016+4A>C Uncertain significance ★★ same condition
WT1 c.1113+5G>A Uncertain significance ★★ same condition
WT1 c.1113+5G>C Uncertain significance ★★ same condition
WT1 c.1448-3C>T Uncertain significance ★★ same condition
WT1 c.888-1G>A Uncertain significance ★★ same condition
WT1 c.965+5G>A Uncertain significance ★★ same condition
WT1 p.Ala18Glu Uncertain significance ★★ same condition
WT1 p.Ala193Thr Uncertain significance ★★ 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-phe487 (accessed [today's date]).

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