Is ANK2 p.Val2369Ala (c.7106T>C) pathogenic?

ANK2 p.Val2369Ala (c.7106T>C) is classified Benign/Likely benign in ANK2 (ClinVar, Multiple submitters, 13 submitters; last evaluated 2026-02-04). AlphaMissense: likely benign (0.0689); Common (popmax 17.9%, afr) — too common for a highly-penetrant pathogenic allele; Associated with cardiac rhythm disease.

What condition is associated with ANK2 p.Val2369Ala (c.7106T>C)?

ANK2 p.Val2369Ala (c.7106T>C) is associated with cardiac rhythm disease, long QT syndrome, cardiac arrhythmia, ankyrin-B-related (ClinVar).

What do computational predictors say about ANK2 p.Val2369Ala (c.7106T>C)?

AlphaMissense predicts likely benign (score 0.0689) — an in-silico prediction, not a clinical call.

ANK2 p.Val2369Ala

Q: How common is ANK2 p.Val2369Ala (c.7106T>C) in the general population?

ANK2 p.Val2369Ala (c.7106T>C) is common (popmax 17.9%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.7106T>C · rs28377576 · VCV35690

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 13 submitters

AlphaMissense

likely benign

0.0689 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 17.9%, afr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

cardiac rhythm disease

Computational evidence

Protein change
AlphaMissense	0.0689	likely benign
REVEL	0.055	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.25	GERP -3.9
Regional constraint	o/e 0.97	unconstrained · MANE · 28 kb · p 0.16 · regional, not allelic
Overall
CADD	0.593	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 17.9% African / African-American · 13,433/74,870 alleles

Filtering AF 17.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 17.6%

Overall 10.7% 172,872/1,613,532 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	17.9%	6
Middle Eastern	16.6%	6
Ashkenazi Jewishnot grpmax-eligible	11.8%	8
European (non-Finnish)	11.3%	9
Remaining individualsnot grpmax-eligible	10.9%	9
Finnishnot grpmax-eligible	10.6%	9
Admixed American	7.37%	14
Amishnot grpmax-eligible	5.16%	19
South Asian	3.61%	28
East Asian	0.0357%	2,803

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.Val2369Ala
Coding: c.7106T>C
MANE Select: NM_001148
dbSNP: rs28377576
Type: single nucleotide variant
Location: chr4:113355724 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2369: a UniProt-annotated variant site (in); the 'disordered' region

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

Disease context

cardiac rhythm disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: long QT syndrome cardiac arrhythmia, ankyrin-B-related

Similar variants

ANK2 p.Val2369Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
ANK2 p.Val2369Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
ANK2 p.Arg1007Ter Pathogenic/Likely pathogenic ★★ same condition
ANK2 p.Arg1088Ter Pathogenic ★★ same condition
ANK2 p.Arg3113Ter 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-val2369ala (accessed [today's date]).

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