ABCC11

protein-coding

ATP binding cassette subfamily C member 11, the group of ATP binding cassette subfamily C

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, White). This ABC full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. The product of this gene participates in physiological processes involving bile acids, conjugated steroids, and cyclic nucleotides. In addition, a SNP in this gene is responsible for determination of human earwax type. This gene and family member ABCC12 are determined to be derived by duplication and are both localized to chromosome 16q12.1. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001370497.1

Inheritance

ClinVar variants

U:208B:42

Top phenotype

Apocrine gland secretion, variation in

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chr16:48,165,773-48,247,568

External References & Databases

Ensembl (ENSG00000121270)

Transcript & Mutation Effects

hg38 • Region Span ~81.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Apocrine gland secretion, variation inAD

Manifestation: Dermatologic

Intervention: General

Rationale: The clinical relevance is unclear

Refs: 16444273; 19710689

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCC11 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 237

not providedTotal: 18

APOCRINE GLAND SECRETION, VARIATION INTotal: 2

ABCC11-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370497.1. 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			1 clinvar	5 clinvar	4 clinvar	10
missense			203 clinvar	27 clinvar	5 clinvar	235
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	208	33	9	250

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370497.1	RefSeq	NP_001357426.1	29	MANE Select
ENST00000356608.7	Ensembl	ENSP00000349017.2	29	MANE Select
NM_001370496.1	RefSeq	NP_001357425.1	29	Standard
NM_032583.4	RefSeq	NP_115972.2	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

ABC transporters - Homo sapiens (human)
Androgen and estrogen biosynthesis and metabolism
Transport of small molecules
ABC-family proteins mediated transport

Biological Process

organic anion transport
purine nucleotide transport
transmembrane transport
ATP hydrolysis coupled anion transmembrane transport

Molecular Function

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

Cellular Component

vacuolar membrane
plasma membrane
integral component of plasma membrane
membrane
cytoplasmic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394747
Coding exons: 29
Length: 80659
Individuals with no LoFs: 122222
Homozygous LoFs: 21
Heterozygous LoFs: 3505
Defined: 125748
p: 0.0141

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.197	809	793	1.02	0.0000447	9012
Missense (PolyPhen)		223	238.74	0.93405		2902
Synonymous	-0.304	332	325	1.02	0.0000196	2761
Loss of Function	-0.0885	69	68.2	1.01	0.00000345	788

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0055	0.0054	notable
Latino/Admixed American	0.014	0.014	notable
Ashkenazi Jewish	0.019	0.019	notable
East Asian	0.0023	0.0023	notable
Finnish	0.012	0.012	notable
European (Non-Finnish)	0.020	0.020	notable
South Asian	0.0024	0.0024	notable
Other	0.017	0.017	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Participates in physiological processes involving bile acids, conjugated steroids and cyclic nucleotides (PubMed:12764137, PubMed:15537867). Enhances the cellular extrusion of cAMP and cGMP (PubMed:12764137, PubMed:15537867). Stimulates the ATP-dependent uptake of a range of physiological and synthetic lipophilic anions, including the glutathione S- conjugates leukotriene C4 and dinitrophenyl S-glutathione, steroid sulfates such as dehydroepiandrosterone 3-sulfate (DHEAS) and estrone 3-sulfate, glucuronides such as estradiol 17-beta-D- glucuronide (E(2)17betaG), the monoanionic bile acids glycocholate and taurocholate, and methotrexate (PubMed:15537867, PubMed:25896536). Probably functions to secrete earwax (PubMed:16444273, PubMed:19383836). Required for the secretion of components contributing to axillary odor formation (PubMed:19710689). {ECO:0000269|PubMed:12764137, ECO:0000269|PubMed:15537867, ECO:0000269|PubMed:16444273, ECO:0000269|PubMed:19383836, ECO:0000269|PubMed:19710689, ECO:0000269|PubMed:25896536}.;

Recessive Scores

pRec: 0.701

Intolerance Scores

LoFtool: 0.0152
RVIS EVS: 1.62
RVIS percentile EVS: 96.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.270

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High