Is ANK2 p.Arg463= (c.1389T>C) pathogenic?

ANK2 p.Arg463= (c.1389T>C) is classified Likely benign in ANK2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-13). Very rare (popmax 0.000434%, nfe); Associated with long QT syndrome.

What condition is associated with ANK2 p.Arg463= (c.1389T>C)?

ANK2 p.Arg463= (c.1389T>C) is associated with long QT syndrome (ClinVar).

How common is ANK2 p.Arg463= (c.1389T>C) in the general population?

ANK2 p.Arg463= (c.1389T>C) is very rare (popmax 0.000434%, nfe) (gnomAD).

ANK2 p.Arg463=

c.1389T>C · rs945947703 · VCV1115789

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000434%, nfe)

Conditions

long QT syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>G here scores Δ0.25 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.82	GERP -4.6, phastCons 0.013
Overall
CADD	8.527	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000434% European (non-Finnish) · 5/1,151,672 alleles

Filtering AF 0.000127% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.2e-05%

Overall 0.000355% 5/1,408,902 alleles · very rare

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.Arg463=
Coding: c.1389T>C
MANE Select: NM_001148
dbSNP: rs945947703
Type: single nucleotide variant
Location: chr4:113264899 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

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

Disease context

long QT syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ANK2 p.Arg463His Uncertain significance ★★ same residue
ANK2 p.Arg463Cys Uncertain significance ★ same residue
ANK2 p.Arg3113Ter 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 c.2278-3C>T Uncertain significance ★★ same condition
ANK2 c.3125+6G>A 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-arg463 (accessed [today's date]).

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