Is WT1 p.Phe144= (c.432C>T) pathogenic?

WT1 p.Phe144= (c.432C>T) is classified Likely benign in WT1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-26). Ultra-rare (popmax 0.0255%, sas); Associated with Inborn genetic diseases.

What condition is associated with WT1 p.Phe144= (c.432C>T)?

WT1 p.Phe144= (c.432C>T) is associated with Inborn genetic diseases, Frasier syndrome, Wilms tumor 1 (ClinVar).

How common is WT1 p.Phe144= (c.432C>T) in the general population?

WT1 p.Phe144= (c.432C>T) is ultra-rare (popmax 0.0255%, sas) (gnomAD).

WT1 p.Phe144=

c.432C>T · rs754173303 · VCV705924

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0255%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.8	GERP 0.69, phastCons 1
Overall
CADD	14.14	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0255% South Asian · 23/90,174 alleles

Filtering AF 0.0173% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0147%

Overall 0.002% 32/1,602,700 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0255%	3,921
African / African-American	0.0107%	9,351
Remaining individualsnot grpmax-eligible	0.00161%	61,938

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: WT1
Protein: p.Phe144=
Coding: c.432C>T
MANE Select: NM_024426
dbSNP: rs754173303
Type: single nucleotide variant
Location: chr11:32434929 (GRCh38)

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

Also linked: Frasier syndrome Wilms tumor 1 WAGR syndrome Denys-Drash syndrome

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-phe144 (accessed [today's date]).

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