ANK2 p.Lys3464=
c.10392G>A · rs566264323 · VCV513543
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0802%, eas)
Conditions
3
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | donor loss, 5 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP -0.04, phastCons 1 |
| Overall | ||
| CADD | 4.453 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0802%
East Asian · 36/44,870 alleles
Filtering AF
0.0595%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0524%
Overall
0.00235%
38/1,614,108 alleles · ultra-rare
exomes 32/1,461,766 · genomes 6/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0802% | 1,246 |
| European (non-Finnish) | 0.000169% | 589,984 |
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
- ANK2
- Protein
- p.Lys3464=
- Coding
- c.10392G>A
- MANE Select
- NM_001148
- dbSNP
- rs566264323
- Type
- single nucleotide variant
- Location
- chr4:113359010 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- ANK2 p.Arg1007Ter Pathogenic/Likely pathogenic ★★ same condition
- ANK2 p.Arg1088Ter Pathogenic ★★ same condition
- ANK2 p.Arg3113Ter Pathogenic ★★ same condition
- ANK2 p.Arg895Ter Pathogenic/Likely pathogenic ★★ same condition
- ANK2 p.Arg977Ter Pathogenic ★★ same condition
- ANK2 c.11032+11G>T Uncertain significance ★★ same condition
- ANK2 c.11611-3T>A Uncertain significance ★★ same condition
- ANK2 c.1783-3C>T Uncertain significance ★★ same condition
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/ank2-p-lys3464 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown