KANK2 p.Ala153=
c.459C>T · rs185317898 · VCV2173025
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.153%, eas)
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 -16 | GERP -13 |
| Overall | ||
| CADD | 0.564 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.153%
East Asian · 68/44,550 alleles
Filtering AF
0.123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.113%
Overall
0.00642%
102/1,587,952 alleles · rare
exomes 90/1,435,658 · genomes 12/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.153% | 655 |
| Remaining individualsnot grpmax-eligible | 0.00652% | 15,341 |
| Finnishnot grpmax-eligible | 0.00525% | 19,041 |
| African / African-American | 0.00402% | 24,846 |
| South Asian | 0.00338% | 29,571 |
| European (non-Finnish) | 0.0018% | 55,620 |
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.Ala153=
- Coding
- c.459C>T
- MANE Select
- NM_001136191
- dbSNP
- rs185317898
- Type
- single nucleotide variant
- Location
- chr19:11193621 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.58 · 3 PDB
- Residue 153
- 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-ala153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown