ABCG5

protein-coding

ATP 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

NM_022436.3

Inheritance

AR

ClinVar variants

P:87U:447B:233

Top phenotype

Sitosterolemia 2

gnomAD constraint

pLI —, LoF o/e 1.03

Max pathogenic AF

—

Genomic locus

chr2:43,812,472-43,838,865

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~26.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

sitosterolemia 2DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0020748

Submitter: G2P

sitosterolemiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008863

Submitter: Orphanet

sitosterolemia 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0020748

Submitter: PanelApp Australia

sitosterolemiaDEFINITIVE

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).

sitosterolemia 1DEFINITIVE

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.

sitosterolemia 1STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0020747

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Sitosterolemia 2AR

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

Refs: 11099417; 11138003; 12840092; 16029460; 16472606; 17018391; 17785700; 17976197; 19111681; 20521169; 20543520; 20719861; 21576934; 24166850; 31901240Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCG5 variants in ClinVar

14 Conditions Cataloged
Cardiovascular phenotypeTotal: 507
SitosterolemiaTotal: 402
not providedTotal: 196
ABCG5-related disorderTotal: 143
Sitosterolemia 2Total: 132
not specifiedTotal: 87
Sitosterolemia 1Total: 62
ThrombocytopeniaTotal: 4

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.

EffectPLPVUSLBBSum
synonymous
9
clinvar
195
clinvar
3
clinvar
207
missense
3
clinvar
8
clinvar
432
clinvar
32
clinvar
3
clinvar
478
nonsense
14
clinvar
13
clinvar
27
start loss
2
clinvar
2
frameshift
12
clinvar
10
clinvar
2
clinvar
24
splice donor/acceptor (+/-2bp)
7
clinvar
20
clinvar
2
clinvar
29
Total36514472276767

Highest pathogenic variant AF is 0.000110296896

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_022436.3RefSeqNP_071881.113MANE Select
ENST00000405322.8EnsemblENSP00000384513.213MANE Select
ENST00000882114.1EnsemblENSP00000552173.111Standard
ENST00000882115.1EnsemblENSP00000552174.113Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.7444103701.110.00002234218
Missense (PolyPhen)136121.351.12071451
Synonymous-1.481791561.150.00001021349
Loss of Function-0.1333130.21.030.00000176333

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000370.00037rare
Latino/Admixed American0.000430.00043rare
Ashkenazi Jewish00.0absent
East Asian0.00220.0022notable
Finnish0.000140.00014rare
European (Non-Finnish)0.000370.00037rare
South Asian0.000980.00098rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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