Is ANK2 p.Phe3055fs (c.9162del) pathogenic?

ANK2 p.Phe3055fs (c.9162del) is classified Pathogenic in ANK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-17). Absent from gnomAD; Associated with long QT syndrome.

What condition is associated with ANK2 p.Phe3055fs (c.9162del)?

ANK2 p.Phe3055fs (c.9162del) is associated with long QT syndrome (ClinVar).

How common is ANK2 p.Phe3055fs (c.9162del) in the general population?

ANK2 p.Phe3055fs (c.9162del) is absent from gnomAD (gnomAD).

ANK2 p.Phe3055fs

c.9162del · rs2505931124 · VCV2861152

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

long QT syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 38 of 46
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ANK2
Protein: p.Phe3055fs
Coding: c.9162del
MANE Select: NM_001148
dbSNP: rs2505931124
Type: Deletion
Location: chr4:113357779 (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 c.2901-3del Uncertain significance ★★ same condition
ANK2 p.Phe3055Val Uncertain significance ★★ ⚠ same residue
ANK2 c.11032+19_11032+20del Benign/Likely benign ★★ same condition
ANK2 p.Asp3081fs Pathogenic ★ same condition
ANK2 p.Glu1091fs Pathogenic ★ same condition
ANK2 p.Leu3108fs Pathogenic ★ same condition
ANK2 p.Ser3273fs Pathogenic ★ same condition
ANK2 p.Ser3495fs Pathogenic ★ 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-phe3055fs (accessed [today's date]).

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