Is ANK2 p.Arg1259= (c.3777A>G) pathogenic?

ANK2 p.Arg1259= (c.3777A>G) is classified Likely benign in ANK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-05). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with ANK2 p.Arg1259= (c.3777A>G)?

ANK2 p.Arg1259= (c.3777A>G) is associated with Cardiovascular phenotype (ClinVar).

How common is ANK2 p.Arg1259= (c.3777A>G) in the general population?

ANK2 p.Arg1259= (c.3777A>G) is absent from gnomAD v4.1 (gnomAD).

ANK2 p.Arg1259=

c.3777A>G · rs1588505996 · VCV1734802

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.417	indeterminate
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.61	GERP -2.4, phastCons 0.91
Overall
CADD	9.43	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ANK2
Protein: p.Arg1259=
Coding: c.3777A>G
MANE Select: NM_001148
dbSNP: rs1588505996
Type: single nucleotide variant
Location: chr4:113336762 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1259: the zu5 2 domain; a β-strand

Full ANK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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
ANK2 p.Ala1214Thr 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-arg1259 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown