ABCG4

protein-coding

ATP binding cassette subfamily G member 4, the group of ATP binding cassette subfamily G

Gene summary

The protein encoded by this gene is a member of the ATP-binding cassette (ABC) transporter superfamily. 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). The encoded protein is a member of the White subfamily and plays an important role in cellular cholesterol homeostasis. This protein functions as either a homodimer or as a heterodimer with another ABC subfamily protein such as ABCG1. [provided by RefSeq, Jan 2017]

MANE transcript

NM_022169.5

Inheritance

—

ClinVar variants

U:58B:7

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr11:119,149,052-119,162,653

External References & Databases

Ensembl (ENSG00000172350)

Transcript & Mutation Effects

hg38 • Region Span ~13.6 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 ABCG4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 3

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022169.5. 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		2 clinvar	4
missense			56 clinvar	4 clinvar	1 clinvar	61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	4	3	65

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022169.5	RefSeq	NP_071452.2	14	MANE Select
ENST00000619701.5	Ensembl	ENSP00000481728.1	14	MANE Select
NM_001142505.1	RefSeq	NP_001135977.1	14	Standard
NM_001348191.2	RefSeq	NP_001335120.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

ABC transporters - Homo sapiens (human)
ABC transporters in lipid homeostasis
Transport of small molecules
ABC-family proteins mediated transport

Biological Process

cholesterol efflux
transmembrane transport
cellular response to leukemia inhibitory factor

Molecular Function

protein binding
ATP binding
cholesterol transporter activity
ATPase activity, coupled to transmembrane movement of substances
protein homodimerization activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000307417
Coding exons: 14
Length: 13639
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 125748
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.27	267	394	0.678	0.0000241	4196
Missense (PolyPhen)		56	94.149	0.5948		993
Synonymous	0.0833	167	168	0.992	0.0000109	1332
Loss of Function	2.30	15	28.2	0.532	0.00000138	337

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00030	0.00029	rare
South Asian	0.00020	0.00020	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in macrophage lipid homeostasis.;

Recessive Scores

pRec: 0.157

Intolerance Scores

RVIS EVS: -0.07
RVIS percentile EVS: 48.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.450

Gene Damage Prediction

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