ABCC9

Chr 12ADAR

ATP binding cassette subfamily C member 9

Also known as: ABC37, ATFB12, CANTU, CMD1O, IDMYS, SUR2

This protein forms ATP-sensitive potassium channels in cardiac, skeletal, and smooth muscle by serving as the regulatory subunit that enables channel activation, while partnering with other proteins that form the channel pore. Mutations cause a spectrum of conditions including Cantu syndrome (hypertrichotic osteochondrodysplasia with intellectual disability), dilated cardiomyopathy, and familial atrial fibrillation, with inheritance patterns that can be either autosomal dominant or autosomal recessive. The gene is highly constrained against loss-of-function variants, indicating that complete loss of protein function is likely incompatible with normal development.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
MultiplemechanismAD/ARLOEUF 0.484 OMIM phenotypes
Clinical SummaryABCC9
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Gene-Disease Validity (ClinGen)
hypertrichotic osteochondrodysplasia Cantu type · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

3 total gene-disease associations curated

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📖
GeneReview available — ABCC9
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Missense constrained — critical functional residues
LoF Constraint
0.48LOEUF
pLI 0.000
Z-score 5.49
OE 0.36 (0.270.48)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
4.97Z-score
OE missense 0.52 (0.480.56)
432 obs / 836.4 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.36 (0.270.48)
00.351.4
Missense OE0.52 (0.480.56)
00.61.4
Synonymous OE1.00
01.21.6
LoF obs/exp: 30 / 84.4Missense obs/exp: 432 / 836.4Syn Z: 0.01
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
moderateABCC9-related intellectual disability, myopathy and white matter abnormalitiesLOFAR
limitedABCC9-related dilated cardiomyopathyOTHERAD
definitiveABCC9-related Cantu SyndromeGOFAD
DN
0.75top 25%
GOF
0.78top 25%
LOF
0.2485th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median · 1 literature citation
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Literature Evidence

GOFCantu syndrome (CS) is a rare developmental disorder characterized by a coarse facial appearance, macrocephaly, hypertrichosis, skeletal and cardiovascular anomalies and caused by heterozygous gain-of-function variants in ABCC9 and KCNJ8, encoding subunits of heterooctameric ATP-sensitive potassium PMID:32622958

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

ABCC9 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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