ABCG1

protein-coding

ATP binding cassette subfamily G member 1, 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. It is involved in macrophage cholesterol and phospholipids transport, and may regulate cellular lipid homeostasis in other cell types. Six alternative splice variants have been identified. [provided by RefSeq, Jul 2008]

MANE transcript

NM_016818.3

Inheritance

—

ClinVar variants

U:67B:17

Top phenotype

ABCG1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr21:42,199,689-42,304,389

External References & Databases

Ensembl (ENSG00000160179)

Transcript & Mutation Effects

hg38 • Region Span ~104.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCG1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 63

ABCG1-related disorderTotal: 16

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016818.3. 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			2 clinvar	10 clinvar	6 clinvar	18
missense			62 clinvar		1 clinvar	63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	67	10	7	84

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016818.3	RefSeq	NP_058198.2	15	MANE Select
ENST00000398449.8	Ensembl	ENSP00000381467.3	15	MANE Select
NM_004915.4	RefSeq	NP_004906.3	15	Standard
NM_207174.1	RefSeq	NP_997057.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

ABC transporters - Homo sapiens (human)
Nuclear Receptors in Lipid Metabolism and Toxicity
HDL remodeling
ABC transporters in lipid homeostasis
Transport of small molecules

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

Molecular Function

ATP binding
phospholipid binding
phospholipid transporter activity
cholesterol binding
cholesterol transporter activity

Cellular Component

Golgi membrane
mitochondrion
endosome
endoplasmic reticulum membrane
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361802
Coding exons: 15
Length: 97556
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125748
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.13	309	434	0.712	0.0000278	4418
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0.000099	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.437

Intolerance Scores

LoFtool: 0.410
RVIS EVS: -1.37
RVIS percentile EVS: 4.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.517

Gene Damage Prediction

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