KANK2 p.Val682=
c.2046G>A · rs778713978 · VCV2724252
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0067%, 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 -0.33 | GERP -4.9, phastCons 0.088 |
| Overall | ||
| CADD | 2.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0067%
Admixed American · 4/59,684 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00062%
10/1,612,098 alleles · very rare
exomes 7/1,459,860 · genomes 3/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0067% | 14,921 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,805 |
| African / African-American | 0.00267% | 37,457 |
| East Asian | 0.00223% | 44,826 |
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
- KANK2
- Protein
- p.Val682=
- Coding
- c.2046G>A
- MANE Select
- NM_001136191
- dbSNP
- rs778713978
- Type
- single nucleotide variant
- Location
- chr19:11174495 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.58 · 3 PDB
- Residue 682
- the 'interaction with ncoa1' region; an α-helix
Similar variants
- KANK2 p.Val682Met Uncertain significance ★ ⚠ same residue
- KANK2 p.Ala182Val Uncertain significance ★★ ⚠ same type
- KANK2 p.Ala317Val Uncertain significance ★★ ⚠ same type
- KANK2 p.Ala347Thr Uncertain significance ★★ ⚠ same type
- KANK2 p.Ala351Thr Uncertain significance ★★ ⚠ same type
- KANK2 p.Ala393Gly Uncertain significance ★★ ⚠ same type
- KANK2 p.Ala653Val Uncertain significance ★★ ⚠ same type
- KANK2 p.Ala711Val 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/kank2-p-val682 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown