ABCG5
protein-codingATP binding cassette subfamily G member 5, the group of ATP binding cassette subfamily G
Gene summary
The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the White subfamily. The protein encoded by this gene functions as a half-transporter to limit intestinal absorption and promote biliary excretion of sterols. It is expressed in a tissue-specific manner in the liver, colon, and intestine. This gene is tandemly arrayed on chromosome 2, in a head-to-head orientation with family member ABCG8. Mutations in this gene may contribute to sterol accumulation and atheroschlerosis, and have been observed in patients with sitosterolemia. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0020748
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0008863
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0020748
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0008863
Submitter: ClinGen
The relationship between ABCG5 and sitosterolemia, an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of January, 2019. ABCG5 was reported in relation to sitosterolemia as early as 2001 (Berge et al, PMID: 11099417; Lee et al, 2001, PMID: 11138003). At least 12 unique variants including nonsense, splice site, frameshift and missense variants have been reported in humans. ABCG5 encodes an ATP-binding cassette half-transporter and functions to limit intestinal absorption and promote biliary excretion of sterols. Sitosterolemia is characterized by increased intestinal absorption and decreased biliary excretion of plant sterols, leading to extremely high plasma levels of plant sterols. Patients with the disorder can develop tendon and tuberous xanthomas, accelerated atherosclerosis and premature coronary artery disease (PMID: 11099417). The hematological presentation of sitosterolemia has been previously described as Mediterranean stomatocytosis/macrothrombocytopenia. Stomatocytic hemolysis, large platelets, splenomegaly and abnormal bleeding can be associated features in about 30% of cases (PMID: 32546081); however, hematologic manifestations can sometimes be the only clinical sign of sitosterolemia (PMID: 16029460). While the mechanisms underlying the hematological features shown by some sitosterolemia patients remains unknown, it is proposed that the accumulation of circulating plant sterols into blood cell membranes results in their altered morphology and dysfunction (PMID: 32546081). Variants in both genes, ABCG5 and ABCG8, which share 28% homology, have been reported in relation to sitosterolemia (PMID: 11099417). Evidence supporting this gene-disease relationship includes case-level data and experimental data. Summary of Case Level Data: 12 Points Variants in this gene have been reported in at least 11 probands in 5 publications (PMID: 11138003, 28203044, 17976197, 16029460, 28521186). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts) has been reached. The mechanism for disease is biallelic loss of function (PMID: 11099417) Summary of Experimental Data: 6 Points This gene-disease association is supported by mouse model evidence and in vitro functional assays. ABCG5 is strongly expressed in the liver and small intestine (PMID: 11099417). ABCG5 functions similar to and interacts with ABCG8 to form a heterodimer for transportation to the cell surface (PMID: 12208867, 14504269, 19846887). ABCG5 knockout in mice recapitulates the sitosterolemia phenotype, including macrothrombocytopenia and affected mice were rescued by expression of the wild-type protein (PMID: 14699507, 19846887). In summary, ABCG5 is definitively associated with Autosomal Recessive Sitosterolemia. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Hemostasis/Thrombosis GCEP on July 10, 2020 (SOP Version 6).
Inheritance Pattern: AR
Disease ID:MONDO:0020747
Submitter: Laboratory for Molecular Medicine
This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.
Inheritance Pattern: AR
Disease ID:MONDO:0020747
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Hematologic
Intervention: Biochemical; Cardiovascular
Rationale: In some individuals, medical (eg, with bile acid resins/lipid-lowering agents) and dietary (eg, with cholesterol and plant fat restriction) treatment may be beneficial for some parameters, and may, along with preventive measures related to cardiovascular manifestations, reduce morbidity and mortality
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ABCG5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022436.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 9 | 195 | 3 | 207 | ||
| missense | 3 | 8 | 432 | 32 | 3 | 478 |
| nonsense | 14 | 13 | 27 | |||
| start loss | 2 | 2 | ||||
| frameshift | 12 | 10 | 2 | 24 | ||
| splice donor/acceptor (+/-2bp) | 7 | 20 | 2 | 29 | ||
| Total | 36 | 51 | 447 | 227 | 6 | 767 |
Highest pathogenic variant AF is 0.000110296896
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071881.1 | 13 | MANE Select | |
| Ensembl | ENSP00000384513.2 | 13 | MANE Select | |
| Ensembl | ENSP00000552173.1 | 11 | Standard | |
| Ensembl | ENSP00000552174.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fat digestion and absorption - Homo sapiens (human)
- Bile secretion - Homo sapiens (human)
- ABC transporters - Homo sapiens (human)
- Cholesterol metabolism - Homo sapiens (human)
- Statin Pathway, Pharmacodynamics
Biological Process
- drug transmembrane transport
- response to nutrient
- excretion
- response to ionizing radiation
- negative regulation of intestinal phytosterol absorption
Molecular Function
- protein binding
- ATP binding
- ATPase activity
- cholesterol transporter activity
- ATPase activity, coupled to transmembrane movement of substances
Cellular Component
- plasma membrane
- integral component of plasma membrane
- apical plasma membrane
- ATP-binding cassette (ABC) transporter complex
- receptor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000260645
- Coding exons
- 13
- Length
- 26394
- Individuals with no LoFs
- 125609
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 139
- Defined
- 125748
- p
- 0.000553
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.744 | 410 | 370 | 1.11 | 0.0000223 | 4218 |
| Missense (PolyPhen) | 136 | 121.35 | 1.1207 | 1451 | ||
| Synonymous | -1.48 | 179 | 156 | 1.15 | 0.0000102 | 1349 |
| Loss of Function | -0.133 | 31 | 30.2 | 1.03 | 0.00000176 | 333 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00043 | 0.00043 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0022 | 0.0022 | notable |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00037 | 0.00037 | rare |
| South Asian | 0.00098 | 0.00098 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: ABCG5 and ABCG8 form an obligate heterodimer that mediates Mg(2+)- and ATP-dependent sterol transport across the cell membrane (PubMed:27144356). Plays an essential role in the selective transport of dietary plant sterols and cholesterol in and out of the enterocytes and in the selective sterol excretion by the liver into bile (PubMed:11099417, PubMed:11138003, PubMed:27144356, PubMed:15054092). Required for normal sterol homeostasis (PubMed:11099417, PubMed:11138003, PubMed:15054092). The heterodimer with ABCG8 has ATPase activity (PubMed:16893193, PubMed:20210363, PubMed:27144356). {ECO:0000269|PubMed:11138003, ECO:0000269|PubMed:15054092, ECO:0000269|PubMed:16893193, ECO:0000269|PubMed:20210363, ECO:0000269|PubMed:27144356, ECO:0000303|PubMed:11590207, ECO:0000305|PubMed:11099417}.;
- Disease
- DISEASE: Sitosterolemia (STSL) [MIM:210250]: Rare autosomal recessive disorder characterized by increased intestinal absorption of all sterols including cholesterol, plant and shellfish sterols, and decreased biliary excretion of dietary sterols into bile. Sitosterolemia patients have hypercholesterolemia, very high levels of plant sterols in the plasma, and frequently develop tendon and tuberous xanthomas, accelerated atherosclerosis and premature coronary artery disease. {ECO:0000269|PubMed:11138003, ECO:0000269|PubMed:11452359, ECO:0000269|PubMed:11668628, ECO:0000269|PubMed:15054092}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.0867
Intolerance Scores
- LoFtool
- 0.359
- RVIS EVS
- 1.16
- RVIS percentile EVS
- 92.65
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.664
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |