ABCG1
ATP binding cassette subfamily G member 1, the group of ATP binding cassette subfamily G
Basic information
Region (hg38): 21:42199689-42304389
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (57 variants)
- ABCG1-related_disorder (16 variants)
- not_provided (6 variants)
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. These statistics are base on transcript: NM_000016818.3. 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 | 10 | 16 | ||||
| missense | 55 | 56 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 55 | 10 | 7 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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