Is WDR19 p.Phe787= (c.2361C>T) pathogenic?

WDR19 p.Phe787= (c.2361C>T) is classified Conflicting classifications of pathogenicity in WDR19 (ClinVar, Conflicting submitters, 10 submitters; last evaluated 2026-01-26). Rare (popmax 0.259%, nfe); Associated with asphyxiating thoracic dystrophy 5.

What condition is associated with WDR19 p.Phe787= (c.2361C>T)?

WDR19 p.Phe787= (c.2361C>T) is associated with asphyxiating thoracic dystrophy 5, connective tissue disorder, cranioectodermal dysplasia 4 (ClinVar).

How common is WDR19 p.Phe787= (c.2361C>T) in the general population?

WDR19 p.Phe787= (c.2361C>T) is rare (popmax 0.259%, nfe) (gnomAD).

WDR19 p.Phe787=

c.2361C>T · rs200133722 · VCV287684

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

rare (popmax 0.259%, nfe)

Conditions

asphyxiating thoracic dystrophy 5

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP 0.7, phastCons 1
Overall
CADD	15.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.259% European (non-Finnish) · 2,969/1,145,242 alleles

Filtering AF 0.251% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.248%

Overall 0.219% 3,400/1,552,348 alleles · rare exomes 3,153/1,400,104 · genomes 247/152,244 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.492%	203
European (non-Finnish)grpmax	0.259%	386
Remaining individualsnot grpmax-eligible	0.219%	456
Admixed American	0.159%	629
Amishnot grpmax-eligible	0.11%	912
Middle Eastern	0.1%	997
Finnishnot grpmax-eligible	0.0364%	2,751
African / African-American	0.0327%	3,059
South Asian	0.0273%	3,660

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: WDR19
Protein: p.Phe787=
Coding: c.2361C>T
MANE Select: NM_025132
dbSNP: rs200133722
Type: single nucleotide variant
Location: chr4:39234873 (GRCh38)
Gene constraint: LOEUF 0.833 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.44 · 4 PDB
Residue 787: an α-helix

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: connective tissue disorder cranioectodermal dysplasia 4 Senior-Loken syndrome 8

Similar variants

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
WDR19 c.2364-2A>G Likely pathogenic ★★ same condition
WDR19 c.2646-2A>G Likely pathogenic ★★ same condition
WDR19 c.3184-2A>C 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-phe787 (accessed [today's date]).

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