ABCG4

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

Basic information

Region (hg38): 11:119149052-119162653

Links

ENSG00000172350 ∙ NCBI:64137 ∙ OMIM:607784 ∙ HGNC:13884 ∙ Uniprot:Q9H172 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCG4 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			15	3	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	3

Variants in ABCG4

This is a list of pathogenic ClinVar variants found in the ABCG4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-119149979-C-T		not specified	Uncertain significance (Jan 20, 2023)
11-119150033-C-A		not specified	Uncertain significance (May 03, 2023)
11-119150047-G-A		not specified	Uncertain significance (Sep 14, 2022)
11-119150202-G-T		Malignant tumor of prostate	Uncertain significance (-)
11-119154068-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-119154364-C-T		not specified	Uncertain significance (Dec 20, 2022)
11-119154569-G-A			Benign (Apr 16, 2018)
11-119156401-C-G		not specified	Uncertain significance (Jul 28, 2021)
11-119156652-C-G		not specified	Uncertain significance (Apr 20, 2024)
11-119156946-G-A		not specified	Likely benign (Apr 13, 2022)
11-119156981-C-T			Benign (Apr 16, 2018)
11-119156985-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-119157001-C-T			Benign (Apr 16, 2018)
11-119158331-C-T		not specified	Uncertain significance (Jul 20, 2021)
11-119158594-T-C		not specified	Uncertain significance (Oct 06, 2022)
11-119158632-G-A		not specified	Likely benign (Aug 09, 2021)
11-119158662-G-A		not specified	Uncertain significance (Dec 13, 2021)
11-119158846-G-A		not specified	Uncertain significance (Apr 25, 2023)
11-119160257-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-119160321-C-T		not specified	Uncertain significance (Feb 05, 2024)
11-119160964-G-A		not specified	Likely benign (Aug 22, 2023)
11-119161086-C-T		not specified	Uncertain significance (Nov 15, 2021)
11-119161087-G-A		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCG4	protein_coding	protein_coding	ENST00000307417	14	13639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.80e-7	0.988	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	267	394	0.678	0.0000241	4196
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000206
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000300	0.000290
Middle Eastern	0.000218	0.000217
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in macrophage lipid homeostasis.
• Pathway: ABC transporters - Homo sapiens (human);ABC transporters in lipid homeostasis;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.69

Haploinsufficiency Scores

• pHI: 0.187
• hipred: Y
• hipred_score: 0.671
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcg4
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: cholesterol efflux;transmembrane transport;cellular response to leukemia inhibitory factor
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;ATP binding;cholesterol transporter activity;ATPase activity, coupled to transmembrane movement of substances;protein homodimerization activity;protein heterodimerization activity