KANK2 p.Pro324=
c.972G>A · rs115571447 · VCV1598676
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.05%, afr)
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 -5.2 | GERP -12 |
| Overall | ||
| CADD | 0.458 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.05%
African / African-American · 789/74,846 alleles
Filtering AF
0.993%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.969%
Overall
0.0618%
992/1,605,560 alleles · low-frequency
exomes 517/1,453,266 · genomes 475/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.05% | 95 |
| Admixed American | 0.079% | 1,266 |
| Remaining individualsnot grpmax-eligible | 0.0645% | 1,551 |
| Middle Eastern | 0.0333% | 3,005 |
| European (non-Finnish) | 0.00902% | 11,091 |
| East Asian | 0.00672% | 14,872 |
| South Asian | 0.00554% | 18,057 |
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.Pro324=
- Coding
- c.972G>A
- MANE Select
- NM_001136191
- dbSNP
- rs115571447
- Type
- single nucleotide variant
- Location
- chr19:11193108 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.58 · 3 PDB
- Residue 324
- the 'disordered' region
Similar variants
- KANK2 p.Pro324Leu Uncertain significance ★★ ⚠ same residue
- KANK2 p.Pro324Ala 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
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-pro324 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown