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.

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.

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				5	2	7
missense			40	2	4	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					1	1
Total	0	0	40	7	7

Variants in ABCC4

This is a list of pathogenic ClinVar variants found in the ABCC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-95021583-C-T		not specified	Uncertain significance (Jan 02, 2024)
13-95021606-G-A		not specified	Uncertain significance (Dec 21, 2023)
13-95021609-G-A		not specified	Uncertain significance (Jun 28, 2023)
13-95021640-G-A		not specified	Uncertain significance (Jun 17, 2024)
13-95021657-T-C		not specified	Uncertain significance (Nov 07, 2023)
13-95021686-G-GA		ABCC4-related disorder	Likely benign (Feb 12, 2024)
13-95034631-C-T		not specified	Uncertain significance (May 24, 2024)
13-95034637-C-T		not specified	Uncertain significance (May 27, 2022)
13-95034700-A-C		not specified	Uncertain significance (Jun 02, 2024)
13-95043680-A-G			not provided (-)
13-95043696-T-C		not specified	Uncertain significance (Aug 27, 2024)
13-95043705-T-C		not specified	Uncertain significance (Oct 06, 2024)
13-95044300-T-C		not specified	Uncertain significance (Mar 18, 2024)
13-95044359-A-G		not specified	Uncertain significance (Nov 12, 2024)
13-95053117-T-C		not specified	Uncertain significance (Dec 04, 2024)
13-95053126-G-A			Benign (Jul 13, 2018)
13-95053184-C-T		not specified	Uncertain significance (Dec 01, 2022)
13-95062708-G-A		not specified	Uncertain significance (Apr 27, 2023)
13-95062787-C-T		not specified	Uncertain significance (Aug 13, 2021)
13-95062815-G-T			Benign (Jul 13, 2018)
13-95062838-C-T			Uncertain significance (Jan 11, 2024)
13-95062841-T-A		not specified	Uncertain significance (Oct 20, 2023)
13-95071817-G-C		not specified	Uncertain significance (Aug 13, 2021)
13-95073211-T-G		not specified	Uncertain significance (Oct 06, 2022)
13-95073226-T-G		not specified	Uncertain significance (Dec 14, 2022)

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