WNK4 p.Pro830=
c.2490C>T · rs1218774080 · VCV739547
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
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 -4.7 | GERP -3.9 |
| Overall | ||
| CADD | 0.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,856 alleles
Filtering AF
0.000554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000124%
2/1,612,660 alleles · very rare
exomes 2/1,461,516 · genomes 0/151,144 · 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
- WNK4
- Protein
- p.Pro830=
- Coding
- c.2490C>T
- MANE Select
- NM_032387
- dbSNP
- rs1218774080
- Type
- single nucleotide variant
- Location
- chr17:42794911 (GRCh38)
- Gene constraint
- LOEUF 0.929 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.38 · 3 PDB
- Residue 830
- the 'disordered' region
Similar variants
- 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
- WNK4 p.Arg1142Trp 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-pro830 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown