KANK1 p.Ser421=
c.1263C>T · rs751062805 · VCV798004
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00525%, nfe)
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 -0.043 | GERP 1.1 |
| Overall | ||
| CADD | 8.251 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00525%
European (non-Finnish) · 62/1,180,048 alleles
Filtering AF
0.00418%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.00384%
62/1,613,980 alleles · very rare
exomes 57/1,461,886 · genomes 5/152,094 · joint denominator
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.Ser421=
- Coding
- c.1263C>T
- MANE Select
- NM_015158
- dbSNP
- rs751062805
- Type
- single nucleotide variant
- Location
- chr9:712029 (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-ser421 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown