ABCC4

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

Basic information

Region (hg38): 13:95019835-95301475

Links

ENSG00000125257

∙ NCBI:10257 ∙ OMIM:605250 ∙ HGNC:55 ∙ Uniprot:O15439 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

qualitative platelet defect (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCC4 gene.

not_specified (107 variants)
not_provided (21 variants)
ABCC4-related_disorder (3 variants)
Prostate_cancer (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005845.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	2 clinvar	7
missense			111 clinvar	4 clinvar	4 clinvar	119
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	113	9	6

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCC4	protein_coding	protein_coding	ENST00000376887	31	281605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.07e-7	1.00	125606	0	142	125748	0.000565

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	591	719	0.821	0.0000397	8587
Missense in Polyphen		146	221.97	0.65773		2720
Synonymous	-0.746	294	278	1.06	0.0000169	2581
Loss of Function	5.12	26	73.3	0.355	0.00000355	913

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000655	0.000655
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000219	0.000163
Finnish	0.000280	0.000277
European (Non-Finnish)	0.000888	0.000862
Middle Eastern	0.000219	0.000163
South Asian	0.000330	0.000327
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: May be an organic anion pump relevant to cellular detoxification.;
Pathway: Methotrexate Pathway (Brain Cell), Pharmacokinetics;Bile secretion - Homo sapiens (human);ABC transporters - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Tenofovir/Adefovir Pathway, Pharmacodynamics;Tenofovir/Adefovir Pathway, Pharmacokinetics;Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Ibuprofen Pathway, Pharmacokinetics;Uricosurics Pathway, Pharmacodynamics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Thioguanine Action Pathway;Lamivudine Metabolism Pathway;Acetaminophen Metabolism Pathway;Mercaptopurine Metabolism Pathway;Fluoropyrimidine Activity;Androgen Receptor Network in Prostate Cancer;Drug Induction of Bile Acid Pathway;Ectoderm Differentiation;Pregnane X Receptor pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling;TYROBP Causal Network;Liver steatosis AOP;Prostaglandin Synthesis and Regulation;Androgen and estrogen biosynthesis and metabolism;Purine metabolism;Transport of small molecules;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Prostaglandin formation from arachidonate;ABC-family proteins mediated transport;Hemostasis (Consensus)

Recessive Scores

pRec: 0.370

Intolerance Scores

loftool: 0.0441
rvis_EVS: 0.21
rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

pHI: 0.179
hipred: Y
hipred_score: 0.538
ghis: 0.523

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.735

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Abcc4
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;

Zebrafish Information Network

Gene name: abcc4
Affected structure: post-vent region
Phenotype tag: abnormal
Phenotype quality: curved ventral

Gene ontology

Biological process: platelet degranulation;biological_process;response to organonitrogen compound;response to organic cyclic compound;prostaglandin secretion;response to drug;positive regulation of smooth muscle cell proliferation;transmembrane transport;oxidation-reduction process;cilium assembly;ATP hydrolysis coupled ion transmembrane transport;ATP hydrolysis coupled anion transmembrane transport
Cellular component: plasma membrane;membrane;integral component of membrane;basolateral plasma membrane;platelet dense granule membrane
Molecular function: ATP binding;ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism;15-hydroxyprostaglandin dehydrogenase (NAD+) activity;ATPase activity, coupled to transmembrane movement of substances;ATPase-coupled anion transmembrane transporter activity