KANK1 p.Pro69=
c.207G>A · rs572271218 · VCV2171875
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -8.7 | GERP -5.6 |
| Overall | ||
| CADD | 3.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.0092%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00721%
Overall
0.00149%
24/1,614,166 alleles · ultra-rare
exomes 16/1,461,880 · genomes 8/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| African / African-American | 0.016% | 6,253 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,249 |
| European (non-Finnish) | 0.000763% | 131,113 |
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
- KANK1
- Protein
- p.Pro69=
- Coding
- c.207G>A
- MANE Select
- NM_015158
- dbSNP
- rs572271218
- Type
- single nucleotide variant
- Location
- chr9:710973 (GRCh38)
- Gene constraint
- LOEUF 1.149 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.50 · 5 PDB
- Residue 69
- the 'disordered' region
Similar variants
- KANK1 p.Pro69Leu Benign/Likely benign ★★ same residue
- KANK1 p.Pro69Arg Uncertain significance ★ ⚠ same residue
- KANK1 p.Pro69Ser Uncertain significance ★ ⚠ same residue
- KANK1 c.2896+2T>G Uncertain significance ★★ same type
- KANK1 p.Ala109Thr Uncertain significance ★★ ⚠ same type
- KANK1 p.Ala1184= Uncertain significance ★★ same type
- KANK1 p.Ala1203Val Uncertain significance ★★ ⚠ same type
- KANK1 p.Ala1255Asp 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/kank1-p-pro69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown