KANK2 p.Ala9=
c.27T>C · rs754529 · VCV1271100
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 10.8%, amr) — too common for a highly-penetrant pathogenic allele
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 0.94 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 13.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.8%
Admixed American · 6,480/59,964 alleles
Filtering AF
10.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.5%
Overall
8.04%
129,557/1,611,088 alleles · common
exomes 119,024/1,459,076 · genomes 10,533/152,012 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 10.8% | 9 |
| European (non-Finnish) | 8.86% | 11 |
| Remaining individualsnot grpmax-eligible | 7.51% | 13 |
| African / African-American | 6.05% | 17 |
| Amishnot grpmax-eligible | 5.6% | 18 |
| Finnishnot grpmax-eligible | 5.38% | 19 |
| Middle Eastern | 4.68% | 21 |
| Ashkenazi Jewishnot grpmax-eligible | 4.43% | 23 |
| South Asian | 3.98% | 25 |
| East Asian | 1.82% | 55 |
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.Ala9=
- Coding
- c.27T>C
- MANE Select
- NM_001136191
- dbSNP
- rs754529
- Type
- single nucleotide variant
- Location
- chr19:11194485 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.58 · 3 PDB
- Residue 9
- the 'interaction with aifm1' region; the 'disordered' region
Similar variants
- 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
- KANK2 p.Arg105His 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-ala9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown