Is WDR1 p.Val263Phe (c.787G>T) pathogenic?

WDR1 p.Val263Phe (c.787G>T) is classified Uncertain significance in WDR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-25). AlphaMissense: likely benign (0.3081); No allele count reported in gnomAD v4.1 (AN 1,567,634); Associated with Inborn genetic diseases.

What condition is associated with WDR1 p.Val263Phe (c.787G>T)?

WDR1 p.Val263Phe (c.787G>T) is associated with Inborn genetic diseases (ClinVar).

How common is WDR1 p.Val263Phe (c.787G>T) in the general population?

WDR1 p.Val263Phe (c.787G>T) is no allele count reported in gnomAD v4.1 (AN 1,567,634) (gnomAD).

What do computational predictors say about WDR1 p.Val263Phe (c.787G>T)?

AlphaMissense predicts likely benign (score 0.3081) — an in-silico prediction, not a clinical call.

WDR1 p.Val263Phe

c.787G>T · VCV3815821

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3081 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,567,634)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3081	likely benign
REVEL	0.315	indeterminate
SaProt	LLR -10.61	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.56	GERP 1.7, phastCons 0.079
Regional constraint	o/e 0.84	unconstrained · MANE · 41 kb · p 7.6e-06 · regional, not allelic
Overall
CADD	20.2	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

No allele count reported in gnomAD v4.1 (AN 1,567,634). 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: WDR1
Protein: p.Val263Phe
Coding: c.787G>T
MANE Select: NM_017491
Type: single nucleotide variant
Location: chr4:10087871 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 96.57 · 2 PDB

Full WDR1 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

WDR1 p.Ala171Thr Uncertain significance ★★ ⚠ same condition
WDR1 p.Ala360Ser Uncertain significance ★★ ⚠ same condition
WDR1 p.Arg158Trp Uncertain significance ★★ ⚠ same condition
WDR1 p.Arg161Gln Uncertain significance ★★ ⚠ same condition
WDR1 p.Asn202Thr Uncertain significance ★★ ⚠ same condition
WDR1 p.Asp210Glu Uncertain significance ★★ ⚠ same condition
WDR1 p.Glu587Lys Uncertain significance ★★ ⚠ same condition
WDR1 p.Gly333Ser 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/wdr1-p-val263phe (accessed [today's date]).

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