ABCC10

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This ABC full-transporter is a member of the MRP subfamily which is involved in multi-drug resistance. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2010]

MANE transcript

NM_001198934.2

Inheritance

—

ClinVar variants

U:223B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr6:43,427,366-43,450,430

External References & Databases

Ensembl (ENSG00000124574)

Transcript & Mutation Effects

hg38 • Region Span ~23.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCC10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 215

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001198934.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			7 clinvar	5 clinvar		12
missense			210 clinvar	10 clinvar	1 clinvar	221
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	223	15	1	239

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001198934.2	RefSeq	NP_001185863.1	21	MANE Select
ENST00000372530.9	Ensembl	ENSP00000361608.4	21	MANE Select
NM_001350518.2	RefSeq	NP_001337447.1	20	Standard
NM_033450.3	RefSeq	NP_258261.2	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

ABC transporters - Homo sapiens (human)
Vinka Alkaloid Pathway, Pharmacokinetics
Tenofovir/Adefovir Pathway, Pharmacokinetics
Nevirapine Pathway, Pharmacokinetics
Vincristine Action Pathway

Biological Process

transmembrane transport
ATP hydrolysis coupled anion transmembrane transport

Molecular Function

ATP binding
ATPase activity, coupled to transmembrane movement of substances
ATPase-coupled anion transmembrane transporter activity

Cellular Component

lysosomal membrane
plasma membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372530
Coding exons: 21
Length: 23065
Individuals with no LoFs: 125530
Homozygous LoFs: 1
Heterozygous LoFs: 217
Defined: 125748
p: 0.000867

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.655	825	880	0.938	0.0000541	9374
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0034	0.0034	notable
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00054	0.00054	rare
Finnish	0.0013	0.0012	notable
European (Non-Finnish)	0.00071	0.00070	rare
South Asian	0.00065	0.00065	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: ATP-dependent transporter probably involved in cellular detoxification through lipophilic anion extrusion. {ECO:0000269|PubMed:12527806, ECO:0000269|PubMed:15256465}.;

Intolerance Scores

LoFtool: 0.0669
RVIS EVS: -1.71
RVIS percentile EVS: 2.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.154

Gene Damage Prediction

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