WDR19 p.Pro514=
c.1542T>C · rs1162371392 · VCV1115333
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00722%, amr)
Conditions
2
asphyxiating thoracic dystrophy 5
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.46 | GERP -0.62, phastCons 1 |
| Overall | ||
| CADD | 8.556 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00722%
Admixed American · 4/55,434 alleles
Filtering AF
0.00238%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00143%
Overall
0.000253%
4/1,583,540 alleles · very rare
exomes 3/1,431,442 · genomes 1/152,098 · joint denominator
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.Pro514=
- Coding
- c.1542T>C
- MANE Select
- NM_025132
- dbSNP
- rs1162371392
- Type
- single nucleotide variant
- Location
- chr4:39224946 (GRCh38)
- Gene constraint
- LOEUF 0.833 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.44 · 4 PDB
Similar variants
- WDR19 p.Pro514His Uncertain significance ★ ⚠ 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
- WDR19 c.2364-2A>G Likely pathogenic ★★ same condition
- WDR19 c.2646-2A>G 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-pro514 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown