Is WDR36 p.Ser807Phe (c.2420C>T) pathogenic?

WDR36 p.Ser807Phe (c.2420C>T) is classified Uncertain significance in WDR36 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-14). AlphaMissense: ambiguous (0.4218); Absent from gnomAD v4.1.

How common is WDR36 p.Ser807Phe (c.2420C>T) in the general population?

WDR36 p.Ser807Phe (c.2420C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about WDR36 p.Ser807Phe (c.2420C>T)?

AlphaMissense predicts ambiguous (score 0.4218) — an in-silico prediction, not a clinical call.

WDR36 p.Ser807Phe

c.2420C>T · VCV4604648

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4218 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.4218	ambiguous
REVEL	0.584	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 1.7, phastCons 1
Regional constraint	o/e 1.15	unconstrained · MANE · 34 kb · p 1.9e-06 · regional, not allelic
Overall
CADD	24.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S863F vs ClinVar S807F) — 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: WDR36
Protein: p.Ser807Phe
Coding: c.2420C>T
MANE Select: NM_139281
Type: single nucleotide variant
Location: chr5:111125677 (GRCh38)
Gene constraint: LOEUF 0.706 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.47 · 3 PDB

Full WDR36 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

WDR36 p.Ala297Ser Uncertain significance ★★ same type
WDR36 p.Ala75Thr Uncertain significance ★★ same type
WDR36 p.Arg374His Uncertain significance ★★ same type
WDR36 p.Arg473Gln Uncertain significance ★★ ⚠ same type
WDR36 p.Asn87Ser Uncertain significance ★★ ⚠ same type
WDR36 p.Asp571His Uncertain significance ★★ ⚠ same type
WDR36 p.Asp686Val Uncertain significance ★★ ⚠ same type
WDR36 p.Glu674Gly 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/wdr36-p-ser807phe (accessed [today's date]).

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