ABCC5

ATP binding cassette subfamily C member 5, the group of ATP binding cassette subfamily C

Basic information

Region (hg38): 3:183919933-184017939

Links

ENSG00000114770 ∙ NCBI:10057 ∙ OMIM:605251 ∙ HGNC:56 ∙ Uniprot:O15440 ∙ 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 ABCC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC5 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				1	2	3
missense			52	3		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	52	4	4

Variants in ABCC5

This is a list of pathogenic ClinVar variants found in the ABCC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-183921314-C-T		not specified	Uncertain significance (Aug 23, 2021)
3-183925620-T-A		not specified	Uncertain significance (Dec 17, 2021)
3-183927350-C-T		not specified	Uncertain significance (May 15, 2024)
3-183927373-C-T		not specified	Uncertain significance (Dec 17, 2021)
3-183928764-T-C		not specified	Uncertain significance (Jan 10, 2023)
3-183928775-G-C		not specified	Uncertain significance (Feb 07, 2023)
3-183937902-T-C		not specified	Uncertain significance (Mar 11, 2022)
3-183937913-C-A		not specified	Uncertain significance (Dec 26, 2023)
3-183938001-T-C		not specified	Uncertain significance (May 02, 2024)
3-183942757-T-G		not specified	Uncertain significance (Feb 10, 2022)
3-183942813-C-T		not specified	Likely benign (Jan 04, 2022)
3-183942876-G-A		not specified	Uncertain significance (May 09, 2023)
3-183942888-A-C		not specified	Uncertain significance (Jan 17, 2024)
3-183945935-G-A		not specified	Uncertain significance (Feb 13, 2024)
3-183949767-C-T			Benign (May 21, 2018)
3-183949777-T-C			Likely benign (Jan 01, 2024)
3-183949858-C-A		not specified	Uncertain significance (May 29, 2024)
3-183949871-G-A		not specified	Uncertain significance (Sep 25, 2023)
3-183949982-T-A		not specified	Uncertain significance (Jul 14, 2021)
3-183949999-A-G		not specified	Uncertain significance (Feb 10, 2023)
3-183950057-C-G		not specified	Uncertain significance (Dec 15, 2023)
3-183951488-G-T		not specified	Uncertain significance (Jul 19, 2023)
3-183951515-C-T		not specified	Uncertain significance (Jun 06, 2023)
3-183951971-C-T			Likely benign (May 01, 2022)
3-183953088-C-T		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCC5	protein_coding	protein_coding	ENST00000334444	29	98082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00415	0.996	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.60	537	829	0.648	0.0000482	9385
Missense in Polyphen		115	245.92	0.46763		2671
Synonymous	1.09	311	336	0.924	0.0000210	2899
Loss of Function	5.89	20	75.1	0.266	0.00000431	821

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000223	0.000217
South Asian	0.000131	0.000131
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a multispecific organic anion pump which can transport nucleotide analogs. {ECO:0000269|PubMed:10840050}.
• Pathway: ABC transporters - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Thioguanine Action Pathway;Acetaminophen Metabolism Pathway;Mercaptopurine Metabolism Pathway;Fluoropyrimidine Activity;Nuclear Receptors Meta-Pathway;NRF2 pathway;Hyaluronan biosynthesis and export;Hyaluronan metabolism;Metabolism of carbohydrates;Glycosaminoglycan metabolism;Purine metabolism;Metabolism;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

• pRec: 0.359

Intolerance Scores

• loftool: 0.146
• rvis_EVS: -1.97
• rvis_percentile_EVS: 1.82

Haploinsufficiency Scores

• pHI: 0.387
• hipred: Y
• hipred_score: 0.639
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.724

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcc5

Zebrafish Information Network

• Gene name: abcc5
• Affected structure: hematopoietic system
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: organic anion transport;hyaluronan biosynthetic process;transmembrane transport;ATP hydrolysis coupled anion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: ATP binding;organic anion transmembrane transporter activity;ATPase activity, coupled to transmembrane movement of substances;ATPase-coupled anion transmembrane transporter activity