ABCC1
Basic information
Region (hg38): 16:15949138-16143257
Previous symbols: [ "MRP", "MRP1" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Deafness, autosomal dominant 77 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Audiologic/Otolaryngologic | 31273342 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 17 | 28 | ||||
missense | 134 | 15 | 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
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ABCC1 | protein_coding | protein_coding | ENST00000399410 | 31 | 193498 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00117 | 0.999 | 124854 | 0 | 56 | 124910 | 0.000224 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.77 | 782 | 935 | 0.837 | 0.0000594 | 9995 |
Missense in Polyphen | 230 | 371.43 | 0.61923 | 3873 | ||
Synonymous | -1.93 | 457 | 407 | 1.12 | 0.0000290 | 3053 |
Loss of Function | 5.85 | 21 | 76.1 | 0.276 | 0.00000392 | 854 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000504 | 0.000500 |
Ashkenazi Jewish | 0.0000996 | 0.0000993 |
East Asian | 0.0000556 | 0.0000556 |
Finnish | 0.000326 | 0.000325 |
European (Non-Finnish) | 0.000293 | 0.000291 |
Middle Eastern | 0.0000556 | 0.0000556 |
South Asian | 0.0000982 | 0.0000980 |
Other | 0.000165 | 0.000164 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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