ANK2 p.Thr1002=
c.3006G>A · VCV3540311
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.019 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -8.4 | GERP -4.9 |
| Overall | ||
| CADD | 0.718 | 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
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.000681%
11/1,614,214 alleles · very rare
exomes 9/1,461,866 · genomes 2/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,052 |
| European (non-Finnish) | 0.000847% | 118,004 |
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.Thr1002=
- Coding
- c.3006G>A
- MANE Select
- NM_001148
- Type
- single nucleotide variant
- Location
- chr4:113330351 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 1002
- a β-strand; the zu5 1 domain; the 'interaction with sptbn1' region
Similar variants
- ANK2 p.Thr1002Met Uncertain significance ★★ same residue
- ANK2 p.Arg3113Ter Pathogenic ★★ same condition
- ANK2 p.Arg895Ter Pathogenic/Likely pathogenic ★★ same condition
- ANK2 p.Arg977Ter Pathogenic ★★ same condition
- ANK2 c.11611-3T>A Uncertain significance ★★ same condition
- ANK2 c.1783-3C>T Uncertain significance ★★ same condition
- ANK2 c.2079+5T>G Uncertain significance ★★ same condition
- ANK2 p.Ala1152Val 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-thr1002 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown