KANK1 p.Pro72=
c.216A>G · rs2539671145 · VCV2812956
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, 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 -0.088 | GERP -1.3 |
| Overall | ||
| CADD | 6.491 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,052 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.00031%
5/1,614,224 alleles · very rare
exomes 5/1,461,890 · genomes 0/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,052 |
| European (non-Finnish) | 0.000339% | 295,008 |
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.Pro72=
- Coding
- c.216A>G
- MANE Select
- NM_015158
- dbSNP
- rs2539671145
- Type
- single nucleotide variant
- Location
- chr9:710982 (GRCh38)
- Gene constraint
- LOEUF 1.149 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.50 · 5 PDB
- Residue 72
- the 'disordered' region
Similar variants
- 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
- KANK1 p.Ala228Gly Uncertain significance ★★ ⚠ same type
- KANK1 p.Ala718Gly Uncertain significance ★★ ⚠ same type
- KANK1 p.Ala961Thr 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-pro72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown