WNK4 p.Pro5=
c.15G>A · rs768740797 · VCV2193437
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0233%, amr)
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 -0.42 | GERP -2.9 |
| Overall | ||
| CADD | 2.789 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0233%
Admixed American · 14/59,960 alleles
Filtering AF
0.0141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.0018%
29/1,608,356 alleles · ultra-rare
exomes 23/1,456,328 · genomes 6/152,028 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0233% | 4,283 |
| Middle Eastern | 0.0171% | 5,834 |
| South Asian | 0.00439% | 22,755 |
| African / African-American | 0.00267% | 37,389 |
| East Asian | 0.00223% | 44,812 |
| European (non-Finnish) | 0.000593% | 168,500 |
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
- WNK4
- Protein
- p.Pro5=
- Coding
- c.15G>A
- MANE Select
- NM_032387
- dbSNP
- rs768740797
- Type
- single nucleotide variant
- Location
- chr17:42780713 (GRCh38)
- Gene constraint
- LOEUF 0.929 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.38 · 3 PDB
- Residue 5
- the 'disordered' region
Similar variants
- WNK4 p.Pro5Leu Uncertain significance ★★ ⚠ same residue
- WNK4 c.1477-12C>G Uncertain significance ★★ same type
- WNK4 p.Ala443Val Uncertain significance ★★ ⚠ same type
- WNK4 p.Ala50Thr Uncertain significance ★★ ⚠ same type
- WNK4 p.Ala574Ser Uncertain significance ★★ ⚠ same type
- WNK4 p.Arg1016Cys Uncertain significance ★★ ⚠ same type
- WNK4 p.Arg1075Cys Uncertain significance ★★ ⚠ same type
- WNK4 p.Arg1142Gln 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/wnk4-p-pro5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown