ABCC12

protein-coding

ATP binding cassette subfamily C member 12, the group of ATP binding cassette subfamily C

Gene summary

This gene is a member of the superfamily of ATP-binding cassette (ABC) transporters and the encoded protein contains two ATP-binding domains and 12 transmembrane regions. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies: ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White. This gene is a member of the MRP subfamily which is involved in multi-drug resistance. This gene and another subfamily member are arranged head-to-tail on chromosome 16q12.1. Increased expression of this gene is associated with breast cancer. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001393797.1

Inheritance

—

ClinVar variants

U:208B:50

Top phenotype

ABCC12-related condition

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr16:48,080,882-48,156,018

External References & Databases

Ensembl (ENSG00000140798)

Transcript & Mutation Effects

hg38 • Region Span ~75.1 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 ABCC12 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 193

ABCC12-related conditionTotal: 67

not providedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001393797.1. 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				29 clinvar	2 clinvar	31
missense			195 clinvar	13 clinvar	2 clinvar	210
nonsense			6 clinvar	2 clinvar		8
start loss			1 clinvar			1
frameshift			5 clinvar	2 clinvar		7
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	208	46	4	258

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001393797.1	RefSeq	NP_001380726.1	29	MANE Select
ENST00000311303.8	Ensembl	ENSP00000311030.4	29	MANE Select
NM_001392028.1	RefSeq	NP_001378957.1	11	Standard
NM_001393798.1	RefSeq	NP_001380727.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

ABC transporters - Homo sapiens (human)

Biological Process

transmembrane transport

Molecular Function

ATP binding
ATPase activity, coupled to transmembrane movement of substances

Cellular Component

membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000311303
Coding exons: 29
Length: 73046
Individuals with no LoFs: 117133
Homozygous LoFs: 123
Heterozygous LoFs: 8492
Defined: 125748
p: 0.0349

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0921	779	772	1.01	0.0000438	8885
Missense (PolyPhen)		212	197.63	1.0727		2400
Synonymous	0.417	303	312	0.970	0.0000196	2694
Loss of Function	-0.364	72	68.7	1.05	0.00000360	794

Population LoF Frequency

Population	CAF	p-value	Status
African	0.065	0.064	notable
Latino/Admixed American	0.019	0.018	notable
Ashkenazi Jewish	0.015	0.015	notable
East Asian	0.014	0.014	notable
Finnish	0.020	0.019	notable
European (Non-Finnish)	0.043	0.042	notable
South Asian	0.042	0.041	notable
Other	0.032	0.032	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable transporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.0909

Intolerance Scores

LoFtool: 0.108
RVIS EVS: 1.11
RVIS percentile EVS: 92.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.464

Gene Damage Prediction

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