Is WDR72 p.Pro355Ser (c.1063C>T) pathogenic?

WDR72 p.Pro355Ser (c.1063C>T) is classified Uncertain significance in WDR72 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-21). AlphaMissense: ambiguous (0.5615); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with WDR72 p.Pro355Ser (c.1063C>T)?

WDR72 p.Pro355Ser (c.1063C>T) is associated with Inborn genetic diseases (ClinVar).

How common is WDR72 p.Pro355Ser (c.1063C>T) in the general population?

WDR72 p.Pro355Ser (c.1063C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about WDR72 p.Pro355Ser (c.1063C>T)?

AlphaMissense predicts ambiguous (score 0.5615) — an in-silico prediction, not a clinical call.

WDR72 p.Pro355Ser

c.1063C>T · rs2542092883 · VCV3190206

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5615 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.5615	ambiguous
REVEL	0.46	indeterminate
SaProt	LLR -9.83	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 215 kb · p 0.0025 · regional, not allelic
Overall
CADD	26.1	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

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: WDR72
Protein: p.Pro355Ser
Coding: c.1063C>T
MANE Select: NM_182758
dbSNP: rs2542092883
Type: single nucleotide variant
Location: chr15:53705966 (GRCh38)
Gene constraint: LOEUF 1.089 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.22

Full WDR72 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

WDR72 p.Ala373Val Uncertain significance ★★ ⚠ same condition
WDR72 p.Ala402Val Uncertain significance ★★ ⚠ same condition
WDR72 p.Ala795Thr Uncertain significance ★★ same condition
WDR72 p.Arg322Ser Uncertain significance ★★ ⚠ same condition
WDR72 p.Arg525Lys Uncertain significance ★★ ⚠ same condition
WDR72 p.Asp1071His Uncertain significance ★★ ⚠ same condition
WDR72 p.Asp393Asn Uncertain significance ★★ ⚠ same condition
WDR72 p.Asp495Val 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/wdr72-p-pro355ser (accessed [today's date]).

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