ABCC11

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

Basic information

Region (hg38): 16:48165772-48247568

Links

ENSG00000121270 ∙ NCBI:85320 ∙ OMIM:607040 ∙ HGNC:14639 ∙ Uniprot:Q96J66 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Apocrine gland secretion, variation in	AD	General	The clinical relevance is unclear	Dermatologic	16444273; 19710689

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCC11 gene.

• Inborn genetic diseases (70 variants)
• not provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCC11 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	4	5
missense			60	12	5	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	0	0	61	13	9

Variants in ABCC11

This is a list of pathogenic ClinVar variants found in the ABCC11 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-48167353-T-G		not specified	Uncertain significance (Dec 01, 2022)
16-48167549-G-A		Apocrine gland secretion, variation in	Benign (Dec 31, 2023)
16-48167568-G-A			Benign (Jun 06, 2017)
16-48167586-TTCACGGATTGTGCGCTGGATCAGGGTG-T		Apocrine gland secretion, variation in	Affects (Mar 01, 2006)
16-48167590-C-T		not specified	Uncertain significance (Nov 07, 2022)
16-48167599-C-T		not specified	Likely benign (Jun 03, 2022)
16-48167600-G-A		not specified	Uncertain significance (May 25, 2022)
16-48167623-A-G		not specified	Likely benign (Dec 06, 2021)
16-48170149-T-C		not specified	Uncertain significance (Feb 15, 2023)
16-48170173-C-T		not specified	Uncertain significance (Jan 09, 2024)
16-48170185-C-A		not specified	Uncertain significance (Nov 09, 2021)
16-48170191-T-C		not specified	Likely benign (Oct 16, 2023)
16-48170192-A-T		not specified	Likely benign (Jul 25, 2023)
16-48170223-G-A			Likely benign (Nov 16, 2017)
16-48170905-G-A		not specified	Uncertain significance (Mar 29, 2022)
16-48170912-C-G		not specified	Uncertain significance (Nov 21, 2022)
16-48170944-C-T		not specified	Uncertain significance (Jun 21, 2023)
16-48170945-G-A		not specified	Likely benign (Dec 20, 2023)
16-48175303-A-T		not specified	Uncertain significance (Aug 16, 2021)
16-48175312-C-T		not specified	Uncertain significance (Jan 20, 2023)
16-48175348-C-T		not specified	Uncertain significance (Mar 29, 2023)
16-48175364-G-A		not specified	Uncertain significance (May 04, 2022)
16-48175388-G-A		not specified	Uncertain significance (May 11, 2022)
16-48176930-C-T		not specified	Uncertain significance (Dec 06, 2021)
16-48176965-C-T		not specified	Likely benign (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCC11	protein_coding	protein_coding	ENST00000394747	29	80659

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.99e-46	1.55e-7	122222	21	3505	125748	0.0141

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.197	809	793	1.02	0.0000447	9012
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0196	0.0196
Ashkenazi Jewish	0.0194	0.0191
East Asian	0.00231	0.00229
Finnish	0.0120	0.0120
European (Non-Finnish)	0.0203	0.0204
Middle Eastern	0.00231	0.00229
South Asian	0.00235	0.00235
Other	0.0168	0.0169

dbNSFP

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}.
• Pathway: ABC transporters - Homo sapiens (human);Androgen and estrogen biosynthesis and metabolism;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

• pRec: 0.701

Intolerance Scores

• loftool: 0.0152
• rvis_EVS: 1.62
• rvis_percentile_EVS: 96.04

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.270

Gene Damage Prediction

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

Gene ontology

• Biological process: organic anion transport;purine nucleotide transport;transmembrane transport;ATP hydrolysis coupled anion transmembrane transport
• Cellular component: vacuolar membrane;plasma membrane;integral component of plasma membrane;membrane;cytoplasmic vesicle membrane;extracellular exosome
• 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