ABCC10

ATP binding cassette subfamily C member 10, the group of ATP binding cassette subfamily C|MicroRNA protein coding host genes

Basic information

Region (hg38): 6:43427366-43450430

Links

ENSG00000124574 ∙ NCBI:89845 ∙ OMIM:612509 ∙ HGNC:52 ∙ Uniprot:Q5T3U5 ∙ 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 ABCC10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC10 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				3		3
missense			89	1	1	91
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	89	4	1

Variants in ABCC10

This is a list of pathogenic ClinVar variants found in the ABCC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43432142-G-C		not specified	Uncertain significance (Feb 26, 2024)
6-43432179-C-T		not specified	Uncertain significance (Aug 21, 2023)
6-43432257-G-T		not specified	Uncertain significance (Oct 13, 2023)
6-43432261-G-T		not specified	Uncertain significance (Jul 06, 2021)
6-43432321-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-43432335-C-G		not specified	Uncertain significance (Sep 14, 2022)
6-43432341-G-T		not specified	Uncertain significance (Mar 18, 2024)
6-43432372-G-A		not specified	Uncertain significance (Jul 09, 2021)
6-43432503-C-G		not specified	Uncertain significance (Mar 30, 2024)
6-43432579-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-43432587-C-G		not specified	Uncertain significance (Mar 28, 2023)
6-43432645-C-T		not specified	Uncertain significance (Dec 14, 2022)
6-43432668-G-C		not specified	Uncertain significance (Sep 22, 2023)
6-43432764-G-T		not specified	Uncertain significance (Mar 31, 2024)
6-43432834-A-G		not specified	Uncertain significance (Nov 12, 2021)
6-43432860-G-A		not specified	Uncertain significance (Sep 29, 2023)
6-43433022-G-A		not specified	Uncertain significance (Jul 08, 2022)
6-43433136-A-C		not specified	Uncertain significance (Apr 27, 2022)
6-43433148-C-G		not specified	Uncertain significance (Jan 25, 2023)
6-43433149-G-A		not specified	Uncertain significance (Jul 12, 2023)
6-43433268-G-C		not specified	Uncertain significance (Jul 14, 2021)
6-43433308-G-A		not specified	Uncertain significance (Apr 28, 2023)
6-43433320-G-A		not specified	Uncertain significance (Aug 08, 2022)
6-43433332-T-C		not specified	Uncertain significance (Nov 09, 2021)
6-43434648-C-T		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCC10	protein_coding	protein_coding	ENST00000372530	21	23065

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-26	0.175	125530	1	217	125748	0.000867

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.655	825	880	0.938	0.0000541	9374
Missense in Polyphen		340	344.3	0.98751		3708
Synonymous	0.0388	391	392	0.998	0.0000231	3423
Loss of Function	1.95	50	67.3	0.743	0.00000382	658

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00404	0.00403
Ashkenazi Jewish	0.00	0.00
East Asian	0.000545	0.000544
Finnish	0.00126	0.00120
European (Non-Finnish)	0.000707	0.000703
Middle Eastern	0.000545	0.000544
South Asian	0.000654	0.000653
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP-dependent transporter probably involved in cellular detoxification through lipophilic anion extrusion. {ECO:0000269|PubMed:12527806, ECO:0000269|PubMed:15256465}.
• Pathway: ABC transporters - Homo sapiens (human);Vinka Alkaloid Pathway, Pharmacokinetics;Tenofovir/Adefovir Pathway, Pharmacokinetics;Nevirapine Pathway, Pharmacokinetics;Vincristine Action Pathway;Vinblastine Action Pathway;Vinorelbine Action Pathway;Vindesine Action Pathway;Nevirapine Metabolism Pathway;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Intolerance Scores

• loftool: 0.0669
• rvis_EVS: -1.71
• rvis_percentile_EVS: 2.51

Haploinsufficiency Scores

• pHI: 0.0425
• hipred: N
• hipred_score: 0.216
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.154

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcc10
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; 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); growth/size/body region phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

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