Is ABCC9 p.Arg366fs (c.1096_1111del) pathogenic?

ABCC9 p.Arg366fs (c.10961111del) is classified Uncertain significance in ABCC9 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-06). Associated with Cardiovascular phenotype.

What condition is associated with ABCC9 p.Arg366fs (c.1096_1111del)?

ABCC9 p.Arg366fs (c.1096_1111del) is associated with Cardiovascular phenotype (ClinVar).

ABCC9 p.Arg366fs

c.1096_1111del · VCV3305572

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 9 of 40
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1

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

Variant & gene context

Gene: ABCC9
Protein: p.Arg366fs
Coding: c.1096_1111del
MANE Select: NM_020297
Type: Deletion
Location: chr12:21910879 (GRCh38)
Gene constraint: LOEUF 0.557 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.72
Residue 366: the abc transmembrane type-1 1 domain

Full ABCC9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCC9 c.4450-5del Benign/Likely benign ★★ same condition
ABCC9 c.4512+745_4512+746del Likely benign ★★ same condition
ABCC9 c.389_406+6del Conflicting classifications of pathogenicity ★ same condition
ABCC9 p.Gln1032fs Uncertain significance ★ same condition
ABCC9 p.Ile338fs Uncertain significance ★ same condition
ABCC9 p.Leu410fs Uncertain significance ★ same condition
ABCC9 p.Lys201_Val202insTer Uncertain significance ★ same condition
ABCC9 p.Lys923fs Conflicting classifications of pathogenicity ★ 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/abcc9-p-arg366fs (accessed [today's date]).

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