Is ANK3 p.Thr4263fs (c.12788_12789del) pathogenic?

ANK3 p.Thr4263fs (c.1278812789del) is classified Likely pathogenic in ANK3 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-11-01). Absent from gnomAD.

How common is ANK3 p.Thr4263fs (c.12788_12789del) in the general population?

ANK3 p.Thr4263fs (c.12788_12789del) is absent from gnomAD (gnomAD).

ANK3 p.Thr4263fs

c.12788_12789del · rs2079078019 · VCV872692

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 LoF-intolerant gene
NMD	predicted	premature termination codon in exon 42 of 44
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 2.2, 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: ANK3
Protein: p.Thr4263fs
Coding: c.12788_12789del
MANE Select: NM_020987
dbSNP: rs2079078019
Type: Deletion
Location: chr10:60055934 (GRCh38)
Gene constraint: LOEUF 0.16 · pLI 1.00 (gnomAD)
Residue 4263: the 'disordered' region

Full ANK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANK3 p.Arg1456fs Pathogenic/Likely pathogenic ★★ same type
ANK3 p.Glu4256_Ile4257delinsVal Uncertain significance ★★ same type
ANK3 c.2614+6del Benign/Likely benign ★★ same type
ANK3 c.4351-10del Benign ★★ same type
ANK3 c.212_216+1del Likely pathogenic ★ same type
ANK3 p.Ala1197fs Pathogenic ★ same type
ANK3 p.Ala622fs Likely pathogenic ★ same type
ANK3 p.Asp1271fs Likely pathogenic ★ same type

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/ank3-p-thr4263fs (accessed [today's date]).

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