Is WDR26 p.Phe313Val (c.937T>G) pathogenic?

WDR26 p.Phe313Val (c.937T>G) is classified Uncertain significance in WDR26 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-01). AlphaMissense: likely pathogenic (0.9956); Absent from gnomAD v4.1.

How common is WDR26 p.Phe313Val (c.937T>G) in the general population?

WDR26 p.Phe313Val (c.937T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about WDR26 p.Phe313Val (c.937T>G)?

AlphaMissense predicts likely pathogenic (score 0.9956) — an in-silico prediction, not a clinical call.

WDR26 p.Phe313Val

c.937T>G · rs2102919579 · VCV1699557

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9956 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9956	likely pathogenic
REVEL	0.693	pathogenic-leaning
SaProt	LLR -15.59	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.6, phastCons 1
Regional constraint	o/e 0.52	unconstrained · MANE · 44 kb · p 2.4e-35 · regional, not allelic
Overall
CADD	28.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM F213V vs ClinVar F313V) — verify the residue.

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: WDR26
Protein: p.Phe313Val
Coding: c.937T>G
MANE Select: NM_001379403
dbSNP: rs2102919579
Type: single nucleotide variant
Location: chr1:224424645 (GRCh38)
Gene constraint: LOEUF 0.144 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 81.30 · 4 PDB
Residue 313: a UniProt-annotated variant site (in skdeas); a UniProt-annotated variant site (in skdeas; uncertain significance); an α-helix

Full WDR26 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

WDR26 p.Asp735Gly Pathogenic/Likely pathogenic ★★ same type
WDR26 p.Ala137Val Uncertain significance ★★ ⚠ same type
WDR26 p.Ala154Pro Uncertain significance ★★ ⚠ same type
WDR26 p.Arg639Gln Uncertain significance ★★ same type
WDR26 p.Glu526Asp Uncertain significance ★★ ⚠ same type
WDR26 p.Ile481Met Uncertain significance ★★ same type
WDR26 p.Leu490Val Uncertain significance ★★ ⚠ same type
WDR26 p.Leu655Val Uncertain significance ★★ same type

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/wdr26-p-phe313val (accessed [today's date]).

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