Is ANK2 p.Thr466= (c.1398G>A) pathogenic?

ANK2 p.Thr466= (c.1398G>A) is classified Likely benign in ANK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-14). Very rare (popmax 0.0019%, amr); Associated with long QT syndrome.

What condition is associated with ANK2 p.Thr466= (c.1398G>A)?

ANK2 p.Thr466= (c.1398G>A) is associated with long QT syndrome (ClinVar).

How common is ANK2 p.Thr466= (c.1398G>A) in the general population?

ANK2 p.Thr466= (c.1398G>A) is very rare (popmax 0.0019%, amr) (gnomAD).

ANK2 p.Thr466=

c.1398G>A · rs1430075101 · VCV2724760

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0019%, amr)

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	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -7.8	GERP -4.9
Overall
CADD	0.616	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0019% Admixed American · 1/52,524 alleles

Filtering AF 2.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000256% 4/1,563,932 alleles · very rare exomes 3/1,411,686 · genomes 1/152,246 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0019%	52,524
Remaining individualsnot grpmax-eligible	0.00165%	60,634
European (non-Finnish)	0.000173%	576,582

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.Thr466=
Coding: c.1398G>A
MANE Select: NM_001148
dbSNP: rs1430075101
Type: single nucleotide variant
Location: chr4:113264908 (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.Thr466Met 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
ANK2 c.693+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-thr466 (accessed [today's date]).

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