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): 4:88090150-88231628
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| 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
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 | 2 | |||||
| missense | 22 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | 2 | |||
| non coding | 5 | |||||
| Total | 0 | 0 | 23 | 4 | 6 |
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) | ||
| 4-88097455-T-A | not specified | Uncertain significance (Aug 20, 2024) | ||
| 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) | ||
| 4-88097563-G-C | not specified | Uncertain significance (Jul 15, 2024) | ||
| 4-88097565-G-C | not specified | Uncertain significance (Nov 09, 2021) | ||
| 4-88099363-G-T | not specified | Uncertain significance (Dec 26, 2023) | ||
| 4-88099374-A-T | not specified | Uncertain significance (Sep 04, 2024) | ||
| 4-88101251-A-G | not specified | Uncertain significance (Mar 15, 2024) | ||
| 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) | ||
| 4-88113382-G-T | not specified | Uncertain significance (May 24, 2024) | ||
| 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) |
GnomAD
Source:
| 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:
- 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