Is WDR19 p.Arg477= (c.1431T>C) pathogenic?

WDR19 p.Arg477= (c.1431T>C) is classified Likely benign in WDR19 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-19). Absent from gnomAD v4.1; Associated with asphyxiating thoracic dystrophy 5.

What condition is associated with WDR19 p.Arg477= (c.1431T>C)?

WDR19 p.Arg477= (c.1431T>C) is associated with asphyxiating thoracic dystrophy 5, Senior-Loken syndrome 8 (ClinVar).

How common is WDR19 p.Arg477= (c.1431T>C) in the general population?

WDR19 p.Arg477= (c.1431T>C) is absent from gnomAD v4.1 (gnomAD).

WDR19 p.Arg477=

c.1431T>C · rs2109332085 · VCV1546223

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

asphyxiating thoracic dystrophy 5

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.06	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.1	GERP -3.4, phastCons 0.001
Overall
CADD	5.933	PHRED · no single calibrated threshold — expert panels disagree

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: WDR19
Protein: p.Arg477=
Coding: c.1431T>C
MANE Select: NM_025132
dbSNP: rs2109332085
Type: single nucleotide variant
Location: chr4:39218057 (GRCh38)
Gene constraint: LOEUF 0.833 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.44 · 4 PDB

Full WDR19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

asphyxiating thoracic dystrophy 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Senior-Loken syndrome 8

Similar variants

WDR19 p.Arg477His Uncertain significance ★★ ⚠ same residue
WDR19 p.Arg477Cys Uncertain significance ★ ⚠ same residue
WDR19 p.Arg477Leu Likely pathogenic ★ ⚠ same residue
WDR19 c.1135-2A>G Likely pathogenic ★★ same condition
WDR19 c.1250-1G>A Pathogenic/Likely pathogenic ★★ same condition
WDR19 c.1778-1G>A Likely pathogenic ★★ same condition
WDR19 c.1982+2T>C Pathogenic/Likely pathogenic ★★ same condition
WDR19 c.2363+1G>A Pathogenic/Likely pathogenic ★★ 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/wdr19-p-arg477 (accessed [today's date]).

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