ABCC1

ATP binding cassette subfamily C member 1, the group of ATP binding cassette subfamily C

Basic information

Region (hg38): 16:15949138-16143257

Previous symbols: [ "MRP", "MRP1" ]

Links

ENSG00000103222NCBI:4363OMIM:158343HGNC:51Uniprot:P33527AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hearing loss, autosomal dominant 77 (Moderate), mode of inheritance: AD
  • autosomal dominant nonsyndromic hearing loss (Supportive), mode of inheritance: AD
  • hearing loss, autosomal dominant 77 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Deafness, autosomal dominant 77ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic31273342

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCC1 gene.

  • not_specified (135 variants)
  • not_provided (45 variants)
  • ABCC1-related_disorder (12 variants)
  • Familial_cancer_of_breast (3 variants)
  • Autosomal_dominant_nonsyndromic_hearing_loss (2 variants)
  • Hearing_loss,_autosomal_dominant_77 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004996.4. 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
2
clinvar
17
clinvar
9
clinvar
28
missense
1
clinvar
134
clinvar
15
clinvar
6
clinvar
156
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 1 0 136 32 15

Highest pathogenic variant AF is 0.0000340739

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ABCC1protein_codingprotein_codingENST00000399410 31193498
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001170.9991248540561249100.000224
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.777829350.8370.00005949995
Missense in Polyphen230371.430.619233873
Synonymous-1.934574071.120.00002903053
Loss of Function5.852176.10.2760.00000392854

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005040.000500
Ashkenazi Jewish0.00009960.0000993
East Asian0.00005560.0000556
Finnish0.0003260.000325
European (Non-Finnish)0.0002930.000291
Middle Eastern0.00005560.0000556
South Asian0.00009820.0000980
Other0.0001650.000164

dbNSFP

Source: dbNSFP

Function
FUNCTION: Mediates export of organic anions and drugs from the cytoplasm. Mediates ATP-dependent transport of glutathione and glutathione conjugates, leukotriene C4, estradiol-17-beta-o- glucuronide, methotrexate, antiviral drugs and other xenobiotics. Confers resistance to anticancer drugs. Hydrolyzes ATP with low efficiency. {ECO:0000269|PubMed:10064732, ECO:0000269|PubMed:11114332, ECO:0000269|PubMed:16230346}.;
Pathway
Methotrexate Pathway (Brain Cell), Pharmacokinetics;Methotrexate Pathway, Pharmacokinetics;Doxorubicin Pathway (Cancer Cell), Pharmacodynamics;Vitamin digestion and absorption - Homo sapiens (human);ABC transporters - Homo sapiens (human);Doxorubicin Pathway, Pharmacokinetics;Sphingolipid signaling pathway - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Vinka Alkaloid Pathway, Pharmacokinetics;Taxane Pathway, Pharmacokinetics;Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacokinetics;Etoposide Pathway, Pharmacokinetics/Pharmacodynamics;Doxorubicin Metabolism Pathway;Irinotecan Action Pathway;Docetaxel Action Pathway;Paclitaxel Action Pathway;Vincristine Action Pathway;Vinblastine Action Pathway;Vinorelbine Action Pathway;Vindesine Action Pathway;Lamivudine Metabolism Pathway;Acetaminophen Metabolism Pathway;Irinotecan Metabolism Pathway;Irinotecan Pathway;multi-drug resistance factors;Metabolism of lipids;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Androgen and estrogen biosynthesis and metabolism;Cobalamin (Cbl, vitamin B12) transport and metabolism;Metabolism;Fatty acid metabolism;Transport of small molecules;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;ABC-family proteins mediated transport;Porphyrin metabolism;S1P1 pathway;Sphingosine 1-phosphate (S1P) pathway (Consensus)

Intolerance Scores

loftool
0.0802
rvis_EVS
-0.84
rvis_percentile_EVS
11.29

Haploinsufficiency Scores

pHI
0.234
hipred
Y
hipred_score
0.639
ghis
0.483

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.291

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Abcc1
Phenotype
homeostasis/metabolism phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process
leukotriene metabolic process;drug transmembrane transport;cobalamin metabolic process;cobalamin transport;glutathione transmembrane transport;response to drug;xenobiotic transport;phospholipid translocation;transmembrane transport;cell chemotaxis;sphingolipid translocation;ATP hydrolysis coupled anion transmembrane transport
Cellular component
vacuolar membrane;plasma membrane;integral component of plasma membrane;membrane;basolateral plasma membrane;extracellular exosome
Molecular function
phospholipid-translocating ATPase activity;transporter activity;ATP binding;xenobiotic transmembrane transporting ATPase activity;cobalamin-transporting ATPase activity;ATPase activity;glutathione transmembrane transporter activity;ATPase activity, coupled to transmembrane movement of substances;ATPase-coupled anion transmembrane transporter activity;sphingolipid-translocating ATPase activity