WNK2 p.Asp2=
c.6C>T · VCV3470688
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00405%, sas)
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 0.86, phastCons 1 |
| Overall | ||
| CADD | 14.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00405%
South Asian · 1/24,696 alleles
Filtering AF
0.000992%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000802%
Overall
0.00153%
18/1,176,406 alleles · very rare
exomes 13/1,025,916 · genomes 5/150,490 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00405% | 24,696 |
| Remaining individualsnot grpmax-eligible | 0.00244% | 41,052 |
| European (non-Finnish) | 0.00168% | 59,691 |
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
- WNK2
- Protein
- p.Asp2=
- Coding
- c.6C>T
- MANE Select
- NM_006648
- Type
- single nucleotide variant
- Location
- chr9:93184935 (GRCh38)
- Gene constraint
- LOEUF 0.508 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 44.29 · 2 PDB
- Residue 2
- the 'disordered' region
Similar variants
- WNK2 p.Pro1819Leu Uncertain significance ★★ ⚠ same type
- WNK2 c.2190+7G>A Benign ★★ same type
- WNK2 p.Ala2109= Benign/Likely benign ★★ same type
- WNK2 p.Ala808= Likely benign ★★ same type
- WNK2 p.Arg1849Trp Likely benign ★★ same type
- WNK2 p.Gly908Ala Benign ★★ same type
- WNK2 p.His758Asn Likely benign ★★ same type
- WNK2 p.Pro1046= Likely benign ★★ 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/wnk2-p-asp2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown