Is ANK2 p.Ala799Val (c.2396C>T) pathogenic?

ANK2 p.Ala799Val (c.2396C>T) is classified Uncertain significance in ANK2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-01). AlphaMissense: likely pathogenic (0.6062); Very rare (popmax 0.0055%, sas); Associated with long QT syndrome.

What condition is associated with ANK2 p.Ala799Val (c.2396C>T)?

ANK2 p.Ala799Val (c.2396C>T) is associated with long QT syndrome (ClinVar).

How common is ANK2 p.Ala799Val (c.2396C>T) in the general population?

ANK2 p.Ala799Val (c.2396C>T) is very rare (popmax 0.0055%, sas) (gnomAD).

What do computational predictors say about ANK2 p.Ala799Val (c.2396C>T)?

AlphaMissense predicts likely pathogenic (score 0.6062) — an in-silico prediction, not a clinical call.

ANK2 p.Ala799Val

c.2396C>T · rs776957456 · VCV496108

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.6062 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0055%, sas)

Missense predictors

1/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

long QT syndrome

Computational evidence

Protein change
AlphaMissense	0.6062	likely pathogenic
REVEL	0.2	benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense calls this damaging; REVEL does not; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.5, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 98 kb · p 4.4e-21 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0055% South Asian · 5/90,974 alleles

Filtering AF 0.00211% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00137%

Overall 0.000744% 12/1,613,424 alleles · very rare exomes 11/1,461,412 · genomes 1/152,012 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0055%	18,195
European (non-Finnish)	0.000593%	168,567

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.Ala799Val
Coding: c.2396C>T
MANE Select: NM_001148
dbSNP: rs776957456
Type: single nucleotide variant
Location: chr4:113293459 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 799: an α-helix

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.Ala799= Likely benign ★ 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-ala799val (accessed [today's date]).

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