GeneBe

ABCC2

ATP binding cassette subfamily C member 2, the group of ATP binding cassette subfamily C

Basic information

Region (hg38): 10:99782640-99852594

Previous symbols: [ "CMOAT" ]

Links

ENSG00000023839 ∙ NCBI:1244 ∙ OMIM:601107 ∙ HGNC:53 ∙ Uniprot:Q92887 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Dubin-Johnson syndrome (Supportive), mode of inheritance: AR
  • Dubin-Johnson syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Dubin-Johnson syndromeAD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingGastrointestinal13193360; 5926936; 5532959; 520367; 2035335; 8621134; 9425227; 16952291; 16863439; 16549534; 19881259; 21044052; 22955427; 23007012; 23069858; 23115734
Heterozygotes may display manifestations; The presence of variants may have pharmacogenomic implications

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCC2 gene.

  • not_provided (971 variants)
  • Dubin-Johnson_syndrome (196 variants)
  • ABCC2-related_disorder (172 variants)
  • Inborn_genetic_diseases (167 variants)
  • not_specified (20 variants)
  • Autosomal_recessive_inherited_pseudoxanthoma_elasticum (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000392.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
18
clinvar
330
clinvar
5
clinvar
 354
missense
5
clinvar
12
clinvar
301
clinvar
48
clinvar
4
clinvar
 370
nonsense
46
clinvar
11
clinvar
 57
start loss
1
 1
frameshift
61
clinvar
14
clinvar
3
clinvar
 78
splice donor/acceptor (+/-2bp)
6
clinvar
38
clinvar
1
clinvar
 45
Total 118 76 324 378 9

Highest pathogenic variant AF is 0.000542723

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ABCC2protein_codingprotein_codingENST00000370449 3269461
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
5.20e-476.44e-712519325531257480.00221
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.9958637851.100.000043310132
Missense in Polyphen317301.371.05183897
Synonymous-0.4063153061.030.00001703062
Loss of Function0.3817376.60.9530.00000430883

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002870.00287
Ashkenazi Jewish0.00009920.0000992
East Asian0.002990.00294
Finnish0.008640.00863
European (Non-Finnish)0.001150.00114
Middle Eastern0.002990.00294
South Asian0.003400.00337
Other0.001470.00147

dbNSFP

Source: dbNSFP

Function
FUNCTION: Mediates hepatobiliary excretion of numerous organic anions. May function as a cellular cisplatin transporter.;
Pathway
Methotrexate Pathway, Pharmacokinetics;Doxorubicin Pathway (Cancer Cell), Pharmacodynamics;Bile secretion - Homo sapiens (human);ABC transporters - Homo sapiens (human);Doxorubicin Pathway, Pharmacokinetics;Carbamazepine Pathway, Pharmacokinetics;Statin Pathway - Generalized, Pharmacokinetics;Atorvastatin/Lovastatin/Simvastatin Pathway, Pharmacokinetics;Pravastatin Pathway, Pharmacokinetics;Codeine and Morphine Pathway, Pharmacokinetics;Platinum Pathway, Pharmacokinetics/Pharmacodynamics;Vinka Alkaloid Pathway, Pharmacokinetics;Taxane Pathway, Pharmacokinetics;Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Tramadol Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics/Pharmacodynamics;Ibuprofen Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacodynamics;Doxorubicin Metabolism Pathway;Mycophenolic Acid Metabolism Pathway;Irinotecan Action Pathway;Docetaxel Action Pathway;Paclitaxel Action Pathway;Vincristine Action Pathway;Vinblastine Action Pathway;Vinorelbine Action Pathway;Vindesine Action Pathway;Tramadol Metabolism Pathway;Lamivudine Metabolism Pathway;Irinotecan Metabolism Pathway;Codeine and Morphine Metabolism;Drug Induction of Bile Acid Pathway;Irinotecan Pathway;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Nuclear Receptors in Lipid Metabolism and Toxicity;Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling;Liver steatosis AOP;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

pRec
0.239

Intolerance Scores

loftool
0.0978
rvis_EVS
0.96
rvis_percentile_EVS
90.09

Haploinsufficiency Scores

pHI
0.108
hipred
N
hipred_score
0.167
ghis
0.403

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.782

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Abcc2
Phenotype
renal/urinary system phenotype; homeostasis/metabolism phenotype; liver/biliary system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process
bilirubin transport;transmembrane transport;ATP hydrolysis coupled anion transmembrane transport
Cellular component
plasma membrane;integral component of plasma membrane;cell surface;membrane;apical plasma membrane
Molecular function
protein binding;ATP binding;organic anion transmembrane transporter activity;bilirubin transmembrane transporter activity;ATPase activity, coupled to transmembrane movement of substances;ATPase-coupled anion transmembrane transporter activity