ABCG1

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

Basic information

Region (hg38): 21:42199688-42297244

Links

ENSG00000160179 ∙ NCBI:9619 ∙ OMIM:603076 ∙ HGNC:73 ∙ Uniprot:P45844 ∙ 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 ABCG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCG1 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				8	8	16
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding				1	6	7
Total	0	0	20	9	15

Variants in ABCG1

This is a list of pathogenic ClinVar variants found in the ABCG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-42201687-G-A		ABCG1-related disorder	Benign (Dec 06, 2019)
21-42201697-A-G		not specified	Uncertain significance (Oct 14, 2021)
21-42219222-CCCG-C		ABCG1-related disorder	Benign (Feb 19, 2019)
21-42219222-CCCGCCG-C		ABCG1-related disorder	Benign (May 24, 2019)
21-42219222-CCCGCCGCCGCCG-C		ABCG1-related disorder	Benign (Sep 05, 2019)
21-42219222-CCCGCCGCCGCCGCCG-C		ABCG1-related disorder	Likely benign (Apr 25, 2019)
21-42219222-C-CCCG		ABCG1-related disorder	Benign (May 22, 2019)
21-42219222-C-CCCGCCG		ABCG1-related disorder	Benign (Nov 21, 2019)
21-42219222-C-CCCGCCGCCGCCGCCG		ABCG1-related disorder	Benign (Jan 08, 2020)
21-42219271-T-C		ABCG1-related disorder	Benign (Feb 19, 2019)
21-42225699-C-T		not specified	Uncertain significance (Oct 02, 2023)
21-42225734-G-A		not specified	Uncertain significance (Mar 29, 2022)
21-42225765-C-T		not specified	Uncertain significance (Jul 27, 2022)
21-42225766-G-A		ABCG1-related disorder	Likely benign (May 30, 2019)
21-42225811-G-A		ABCG1-related disorder	Likely benign (Oct 07, 2019)
21-42225852-T-G		not specified	Uncertain significance (Apr 01, 2024)
21-42225918-G-A		ABCG1-related disorder	Benign (Mar 20, 2019)
21-42271122-G-A		ABCG1-related disorder	Benign (Aug 15, 2019)
21-42271132-A-C		not specified	Uncertain significance (Jan 24, 2024)
21-42273345-C-G		ABCG1-related disorder	Benign (Feb 20, 2019)
21-42273407-C-T		not specified	Uncertain significance (May 27, 2022)
21-42276889-C-T		ABCG1-related disorder	Benign (Jul 12, 2019)
21-42282294-G-A		ABCG1-related disorder	Likely benign (Feb 28, 2019)
21-42282349-C-T		not specified	Uncertain significance (Feb 15, 2023)
21-42282350-G-A		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCG1	protein_coding	protein_coding	ENST00000361802	15	97556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.112	0.888	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	309	434	0.712	0.0000278	4418
Missense in Polyphen		50	96.098	0.5203		982
Synonymous	0.423	189	197	0.962	0.0000144	1381
Loss of Function	3.86	8	31.3	0.256	0.00000143	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000977	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.0000986	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transporter involved in macrophage lipid homeostasis. Is an active component of the macrophage lipid export complex. Could also be involved in intracellular lipid transport processes. The role in cellular lipid homeostasis may not be limited to macrophages.
• Pathway: ABC transporters - Homo sapiens (human);Nuclear Receptors in Lipid Metabolism and Toxicity;HDL remodeling;ABC transporters in lipid homeostasis;Transport of small molecules;C21-steroid hormone biosynthesis and metabolism;ABC-family proteins mediated transport;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling (Consensus)

Recessive Scores

• pRec: 0.437

Intolerance Scores

• loftool: 0.410
• rvis_EVS: -1.37
• rvis_percentile_EVS: 4.43

Haploinsufficiency Scores

• pHI: 0.0964
• hipred: Y
• hipred_score: 0.623
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.517

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcg1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;cholesterol metabolic process;detection of hormone stimulus;response to organic substance;negative regulation of macrophage derived foam cell differentiation;regulation of cholesterol esterification;positive regulation of cholesterol efflux;negative regulation of cholesterol storage;intracellular cholesterol transport;cholesterol efflux;phospholipid efflux;response to lipid;low-density lipoprotein particle remodeling;high-density lipoprotein particle remodeling;glycoprotein transport;cholesterol homeostasis;amyloid precursor protein catabolic process;reverse cholesterol transport;positive regulation of cholesterol biosynthetic process;transmembrane transport;phospholipid homeostasis;cellular response to high density lipoprotein particle stimulus;toxin transport
• Cellular component: Golgi membrane;mitochondrion;endosome;endoplasmic reticulum membrane;Golgi apparatus;plasma membrane;external side of plasma membrane;integral component of membrane;recycling endosome
• Molecular function: ATP binding;phospholipid binding;phospholipid transporter activity;cholesterol binding;cholesterol transporter activity;toxin transmembrane transporter activity;sterol-transporting ATPase activity;glycoprotein transporter activity;ATPase activity, coupled to transmembrane movement of substances;protein homodimerization activity;ADP binding;protein heterodimerization activity;protein dimerization activity