Is ANK2 p.Asn3955Ser (c.11864A>G) pathogenic?

ANK2 p.Asn3955Ser (c.11864A>G) is classified Benign/Likely benign in ANK2 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2025-11-25). AlphaMissense: likely benign (0.0876); Rare (popmax 0.585%, sas); Associated with cardiac arrhythmia, ankyrin-B-related.

What condition is associated with ANK2 p.Asn3955Ser (c.11864A>G)?

ANK2 p.Asn3955Ser (c.11864A>G) is associated with cardiac arrhythmia, ankyrin-B-related, long QT syndrome (ClinVar).

How common is ANK2 p.Asn3955Ser (c.11864A>G) in the general population?

ANK2 p.Asn3955Ser (c.11864A>G) is rare (popmax 0.585%, sas) (gnomAD).

How is Romano-Ward syndrome inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about ANK2 p.Asn3955Ser (c.11864A>G)?

AlphaMissense predicts likely benign (score 0.0876) — an in-silico prediction, not a clinical call.

ANK2 p.Asn3955Ser

c.11864A>G · rs201555985 · VCV377483

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.0876 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.585%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

cardiac arrhythmia, ankyrin-B-related

Computational evidence

Protein change
AlphaMissense	0.0876	likely benign
REVEL	0.231	benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	Δ0.64	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 7	GERP 1.5, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 28 kb · p 0.16 · regional, not allelic
Overall
CADD	19.72	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 0.585% South Asian · 533/91,082 alleles

Filtering AF 0.544% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.528%

Overall 0.0364% 587/1,614,168 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.585%	171
Remaining individualsnot grpmax-eligible	0.048%	2,084
Middle Eastern	0.0165%	6,060
African / African-American	0.00666%	15,010
European (non-Finnish)	0.00153%	65,557

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.Asn3955Ser
Coding: c.11864A>G
MANE Select: NM_001148
dbSNP: rs201555985
Type: single nucleotide variant
Location: chr4:113381461 (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

cardiac arrhythmia, ankyrin-B-related — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: long QT syndrome

For Romano-Ward syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: All ages
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

ANK2 p.Asn3955Asp Uncertain significance ★★ ⚠ 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
ANK2 c.2079+5T>G 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-asn3955ser (accessed [today's date]).

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