ABCC3

ATP binding cassette subfamily C member 3, the group of ATP binding cassette subfamily C

Basic information

Region (hg38): 17:50634776-50692253

Links

ENSG00000108846 ∙ NCBI:8714 ∙ OMIM:604323 ∙ HGNC:54 ∙ Uniprot:O15438 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCC3 gene.

• Inborn genetic diseases (44 variants)
• not provided (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC3 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				7	1	8
missense			43	6	3	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	43	13	4

Variants in ABCC3

This is a list of pathogenic ClinVar variants found in the ABCC3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-50634975-G-C			Likely benign (Dec 01, 2022)
17-50655826-C-T			Likely benign (May 01, 2022)
17-50655877-T-G		not specified	Uncertain significance (Jan 26, 2022)
17-50655927-C-T			Likely benign (Sep 01, 2022)
17-50655934-C-T		not specified	Uncertain significance (Nov 03, 2022)
17-50655956-G-A		not specified	Uncertain significance (Mar 16, 2022)
17-50655968-G-A		not specified	Uncertain significance (Dec 19, 2022)
17-50655988-C-T			Benign (May 01, 2023)
17-50655992-T-C		not specified	Uncertain significance (Nov 09, 2023)
17-50656774-C-G		not specified	Uncertain significance (Dec 18, 2023)
17-50656775-G-A			Benign (May 09, 2018)
17-50656778-C-A		not specified	Uncertain significance (Aug 08, 2023)
17-50656819-G-T		not specified	Uncertain significance (Nov 18, 2022)
17-50657125-T-C			Uncertain significance (Aug 07, 2018)
17-50657132-G-A			Benign (Apr 10, 2018)
17-50658104-G-A		not specified	Uncertain significance (Dec 12, 2023)
17-50658133-C-G		not specified	Uncertain significance (Nov 10, 2022)
17-50658472-G-A		not specified	Uncertain significance (Mar 01, 2024)
17-50659353-A-G			Likely benign (-)
17-50660960-G-A		not specified	Likely benign (Jan 02, 2024)
17-50660970-A-G		not specified	Uncertain significance (Oct 31, 2022)
17-50661006-C-T		not specified	Uncertain significance (Feb 12, 2024)
17-50663837-C-G		not specified	Uncertain significance (Jan 23, 2024)
17-50664005-A-G		not specified	Uncertain significance (Dec 27, 2023)
17-50664016-G-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCC3	protein_coding	protein_coding	ENST00000285238	31	57476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.21e-26	0.507	125260	0	488	125748	0.00194

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.630	848	901	0.941	0.0000552	9849
Missense in Polyphen		288	321.22	0.89659		3591
Synonymous	1.59	346	386	0.897	0.0000239	3216
Loss of Function	2.29	52	73.1	0.711	0.00000358	799

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00378	0.00378
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00174	0.00174
Finnish	0.00116	0.00116
European (Non-Finnish)	0.00210	0.00209
Middle Eastern	0.00174	0.00174
South Asian	0.00232	0.00229
Other	0.00293	0.00294

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as an inducible transporter in the biliary and intestinal excretion of organic anions. Acts as an alternative route for the export of bile acids and glucuronides from cholestatic hepatocytes (By similarity). {ECO:0000250}.
• Pathway: Methotrexate Pathway, Pharmacokinetics;Bile secretion - Homo sapiens (human);ABC transporters - Homo sapiens (human);Codeine and Morphine Pathway, Pharmacokinetics;Fluoropyrimidine Pathway, Pharmacokinetics;Vinka Alkaloid Pathway, Pharmacokinetics;Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Etoposide Pathway, Pharmacokinetics/Pharmacodynamics;Vincristine Action Pathway;Vinblastine Action Pathway;Vinorelbine Action Pathway;Vindesine Action Pathway;Etoposide Action Pathway;Lamivudine Metabolism Pathway;Etoposide Metabolism Pathway;Fluoropyrimidine Activity;Codeine and Morphine Metabolism;Drug Induction of Bile Acid 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;multi-drug resistance factors;Metabolism of lipids;Androgen and estrogen biosynthesis and metabolism;Metabolism;Recycling of bile acids and salts;Bile acid and bile salt metabolism;Transport of small molecules;Metabolism of steroids;Bile acid biosynthesis;ABC-family proteins mediated transport (Consensus)

Recessive Scores

• pRec: 0.279

Intolerance Scores

• loftool: 0.0379
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.21

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.554
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Abcc3
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: bile acid and bile salt transport;canalicular bile acid transport;transmembrane transport;ATP hydrolysis coupled anion transmembrane transport
• Cellular component: vacuolar membrane;plasma membrane;integral component of plasma membrane;membrane
• Molecular function: ATP binding;organic anion transmembrane transporter activity;bile acid-exporting ATPase activity;ATPase activity, coupled to transmembrane movement of substances;ATPase-coupled anion transmembrane transporter activity