ABCG2

ATP binding cassette subfamily G member 2 (Junior blood group), the group of ATP binding cassette subfamily G|CD molecules|Blood group antigens

Basic information

Region (hg38): 4:88090149-88231628

Links

ENSG00000118777 ∙ NCBI:9429 ∙ OMIM:603756 ∙ HGNC:74 ∙ Uniprot:Q9UNQ0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, junior system	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	567888; 18522708; 20890084; 22246505; 22246507

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCG2 gene.

• Inborn genetic diseases (12 variants)
• not provided (8 variants)
• Blood group, Junior system (2 variants)
• rosuvastatin response - Metabolism/PK (1 variants)
• rosuvastatin response - Efficacy (1 variants)
• Uric acid concentration, serum, quantitative trait locus 1 (1 variants)
• not specified (1 variants)
• Gemcitabine response (1 variants)
• Neoplasm of ovary (1 variants)
• Uric acid concentration, serum, quantitative trait locus 1;Blood group, Junior system (1 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCG2 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				1	1	2
missense			12			12
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					4	4
Total	0	0	13	1	5

Variants in ABCG2

This is a list of pathogenic ClinVar variants found in the ABCG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-88092241-T-C		not specified	Uncertain significance (Jan 16, 2024)
4-88092254-A-G		not specified	Uncertain significance (Mar 12, 2024)
4-88092311-C-T		not specified	Uncertain significance (Oct 03, 2022)
4-88094620-G-A		not specified	Uncertain significance (Sep 06, 2022)
4-88097518-C-T		ABCG2-related disorder	Likely benign (Jul 12, 2022)
4-88097533-T-A		not specified	Uncertain significance (Dec 20, 2023)
4-88097559-A-G		not specified	Uncertain significance (Dec 20, 2022)
4-88097565-G-C		not specified	Uncertain significance (Nov 09, 2021)
4-88099363-G-T		not specified	Uncertain significance (Dec 26, 2023)
4-88101287-T-C		not specified	Uncertain significance (May 17, 2023)
4-88104957-C-T			Benign (Jan 09, 2019)
4-88105276-A-C			Benign (Jan 09, 2019)
4-88107206-C-A		not specified	Uncertain significance (Oct 25, 2022)
4-88107266-T-A		not specified	Uncertain significance (Dec 07, 2023)
4-88108100-A-C			Benign (Jan 09, 2019)
4-88113319-T-C		not specified	Uncertain significance (Feb 14, 2023)
4-88113362-A-G		not specified	Uncertain significance (Dec 14, 2021)
4-88113384-GGT-G		Blood group, Junior system	Affects (Jan 15, 2012)
4-88113437-C-T		ABCG2-related disorder	Likely benign (Feb 23, 2021)
4-88113525-C-A		not specified	Uncertain significance (Nov 17, 2023)
4-88114996-A-G		not specified	Uncertain significance (Jan 10, 2023)
4-88115031-G-C		not specified	Uncertain significance (Oct 04, 2022)
4-88115033-G-T		not specified	Uncertain significance (Jan 30, 2024)
4-88118106-T-C		ABCG2-related disorder	Likely benign (Sep 12, 2022)
4-88118148-C-T		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCG2	protein_coding	protein_coding	ENST00000237612	15	141059

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.10e-32	0.00000143	125263	4	481	125748	0.00193

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.881	400	353	1.13	0.0000181	4266
Missense in Polyphen		89	74.344	1.1971		903
Synonymous	0.690	123	133	0.924	0.00000735	1274
Loss of Function	-1.15	44	36.5	1.21	0.00000222	430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00255	0.00255
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.00753	0.00753
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00124	0.00124
Middle Eastern	0.00753	0.00753
South Asian	0.00370	0.00350
Other	0.00180	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High-capacity urate exporter functioning in both renal and extrarenal urate excretion. Plays a role in porphyrin homeostasis as it is able to mediates the export of protoporhyrin IX (PPIX) both from mitochondria to cytosol and from cytosol to extracellular space, and cellular export of hemin, and heme. Xenobiotic transporter that may play an important role in the exclusion of xenobiotics from the brain. Appears to play a major role in the multidrug resistance phenotype of several cancer cell lines. Implicated in the efflux of numerous drugs and xenobiotics: mitoxantrone, the photosensitizer pheophorbide, camptothecin, methotrexate, azidothymidine (AZT), and the anthracyclines daunorubicin and doxorubicin. {ECO:0000269|PubMed:12958161, ECO:0000269|PubMed:20705604, ECO:0000269|PubMed:22132962, ECO:0000269|PubMed:23189181}.
• Pathway: Methotrexate Pathway (Brain Cell), Pharmacokinetics;Methotrexate Pathway, Pharmacokinetics;Doxorubicin Pathway (Cancer Cell), Pharmacodynamics;Bile secretion - Homo sapiens (human);ABC transporters - Homo sapiens (human);Doxorubicin Pathway, Pharmacokinetics;Imatinib Pathway, Pharmacokinetics/Pharmacodynamics;Statin Pathway - Generalized, Pharmacokinetics;Pravastatin Pathway, Pharmacokinetics;Platinum Pathway, Pharmacokinetics/Pharmacodynamics;Fluoropyrimidine Pathway, Pharmacokinetics;Gefitinib Pathway, Pharmacokinetics;Taxane Pathway, Pharmacokinetics;Erlotinib Pathway, Pharmacokinetics;Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Mycophenolic acid Pathway, Pharmacokinetics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Uricosurics Pathway, Pharmacodynamics;Irinotecan Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacodynamics;Doxorubicin Metabolism Pathway;Mycophenolic Acid Metabolism Pathway;Irinotecan Action Pathway;Docetaxel Action Pathway;Paclitaxel Action Pathway;Erlotinib Action Pathway;Lamivudine Metabolism Pathway;Acetaminophen Metabolism Pathway;Irinotecan Metabolism Pathway;Fluoropyrimidine Activity;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Irinotecan Pathway;Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling;Imatinib and Chronic Myeloid Leukemia;HIF-2-alpha transcription factor network;Abacavir transmembrane transport;Abacavir transport and metabolism;Metabolism;Transport of small molecules;Iron uptake and transport;HIF-1-alpha transcription factor network (Consensus)

Recessive Scores

• pRec: 0.552

Intolerance Scores

• loftool: 0.454
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.17

Haploinsufficiency Scores

• pHI: 0.0710
• hipred: N
• hipred_score: 0.187
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.166

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcg2
• Phenotype: normal phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; renal/urinary system 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: drug transmembrane transport;cellular iron ion homeostasis;heme transport;response to drug;xenobiotic transport;urate metabolic process;transmembrane transport
• Cellular component: nucleus;plasma membrane;integral component of membrane;mitochondrial membrane
• Molecular function: transporter activity;protein binding;ATP binding;xenobiotic transmembrane transporting ATPase activity;heme transporter activity;ATPase activity, coupled to transmembrane movement of substances;identical protein binding;protein homodimerization activity