KANK1 p.Val413=
c.1239C>T · rs148387245 · VCV1597968
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
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 -7.9 | GERP -4.9 |
| Overall | ||
| CADD | 0.413 | 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
0.00814%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00735%
Overall
0.00861%
139/1,614,104 alleles · ultra-rare
exomes 115/1,461,886 · genomes 24/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| African / African-American | 0.0147% | 6,820 |
| Admixed American | 0.01% | 9,999 |
| European (non-Finnish) | 0.00932% | 10,728 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| East Asian | 0.00446% | 22,438 |
| South Asian | 0.00439% | 22,770 |
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.Val413=
- Coding
- c.1239C>T
- MANE Select
- NM_015158
- dbSNP
- rs148387245
- Type
- single nucleotide variant
- Location
- chr9:712005 (GRCh38)
- Gene constraint
- LOEUF 1.149 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.50 · 5 PDB
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-val413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown