KANK4 p.Arg219=
c.657A>C · rs779112819 · VCV2885145
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0423%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.18 | GERP 0.97 |
| Overall | ||
| CADD | 1.201 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0423%
East Asian · 19/44,884 alleles
Filtering AF
0.0277%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.023%
Overall
0.00118%
19/1,614,080 alleles · ultra-rare
exomes 15/1,461,876 · genomes 4/152,204 · 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
- KANK4
- Protein
- p.Arg219=
- Coding
- c.657A>C
- MANE Select
- NM_181712
- dbSNP
- rs779112819
- Type
- single nucleotide variant
- Location
- chr1:62274447 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.17
Similar variants
- KANK4 p.Arg219Gln Uncertain significance ★ ⚠ same residue
- KANK4 p.Arg219Ter Uncertain significance ★ same residue
- KANK4 p.Ala115Val Uncertain significance ★★ ⚠ same type
- KANK4 p.Ala987Thr Uncertain significance ★★ ⚠ same type
- KANK4 p.Arg336Met Uncertain significance ★★ ⚠ same type
- KANK4 p.Arg471Cys Uncertain significance ★★ ⚠ same type
- KANK4 p.Arg653Cys Uncertain significance ★★ ⚠ same type
- KANK4 p.Arg790Gln 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/kank4-p-arg219 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown