ABCA12 ATP binding cassette subfamily A member 12 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ABCA12provided by HGNC
Official Full Name: ATP binding cassette subfamily A member 12provided by HGNC
Primary source: HGNC:HGNC:14637
See related: Ensembl:ENSG00000144452 MIM:607800; AllianceGenome:HGNC:14637
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LI2; ICR2B; ARCI4A; ARCI4B
Summary: The membrane-associated 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 intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This encoded protein is a member of the ABC1 subfamily, which is the only major ABC subfamily found exclusively in multicellular eukaryotes. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
Expression: Biased expression in skin (RPKM 10.7) and colon (RPKM 0.6) See more
Orthologs: mouse all
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Genomic context

Location:: 2q35

Exon count:: 55

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (214931542..215138626, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (215416237..215623360, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (215796266..216003349, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Updated mutational spectrum and genotype-phenotype correlations in ichthyosis patients with ABCA12 pathogenic variants.
Title: Updated mutational spectrum and genotype-phenotype correlations in ichthyosis patients with ABCA12 pathogenic variants.
Erythrokeratodermia Variabilis-like Phenotype in Patients Carrying ABCA12 Mutations.
Title: Erythrokeratodermia Variabilis-like Phenotype in Patients Carrying ABCA12 Mutations.
Novel variants in ABCA12 cause erythrokeratodermia variabilis.
Title: Novel variants in ABCA12 cause erythrokeratodermia variabilis.
Patients with keratinization disorders due to ABCA12 variants showing pityriasis rubra pilaris phenotypes.
Title: Patients with keratinization disorders due to ABCA12 variants showing pityriasis rubra pilaris phenotypes.
Long-term survival of harlequin ichthyosis in two siblings with novel ABCA12 mutations.
Title: Long-term survival of harlequin ichthyosis in two siblings with novel ABCA12 mutations.
Partial Loss of Function ABCA12 Mutations Generate Reduced Deposition of Glucosyl-Ceramide, Leading to Patchy Ichthyosis and Erythrodermia Resembling Erythrokeratodermia Variabilis et Progressiva (EKVP).
Title: Partial Loss of Function ABCA12 Mutations Generate Reduced Deposition of Glucosyl-Ceramide, Leading to Patchy Ichthyosis and Erythrodermia Resembling Erythrokeratodermia Variabilis et Progressiva (EKVP).
Mutational Spectrum of the ABCA12 Gene and Genotype-Phenotype Correlation in a Cohort of 64 Patients with Autosomal Recessive Congenital Ichthyosis.
Title: Mutational Spectrum of the ABCA12 Gene and Genotype-Phenotype Correlation in a Cohort of 64 Patients with Autosomal Recessive Congenital Ichthyosis.
Novel mutations of the ABCA12, KRT1 and ST14 genes in three unrelated newborns showing congenital ichthyosis.
Title: Novel mutations of the ABCA12, KRT1 and ST14 genes in three unrelated newborns showing congenital ichthyosis.
Positive selection in Europeans and East-Asians at the ABCA12 gene.
Title: Positive selection in Europeans and East-Asians at the ABCA12 gene.
A novel pathogenic variant Val1927Leu was identified in a patient with severe harlequin ichthyosis.
Title: A novel ABCA12 pathologic variant identified in an Ecuadorian harlequin ichthyosis patient: A step forward in genotype-phenotype correlations.

Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive congenital ichthyosis 4A MedGen: C1832550 OMIM: 601277 GeneReviews: Autosomal Recessive Congenital Ichthyosis	Compare labs
Autosomal recessive congenital ichthyosis 4B MedGen: C0598226 OMIM: 242500 GeneReviews: Autosomal Recessive Congenital Ichthyosis	Compare labs

EBI GWAS Catalog

Description
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-86012 (e-PCR)
- UniSTS:170258

ABCA12_8176 (e-PCR)
- UniSTS:467541

REN28899 (e-PCR)
- UniSTS:353699

SHGC-105192 (e-PCR)
- UniSTS:169212

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ABC-type transporter activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	NAS Non-traceable Author Statement more info	PubMed
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATPase-coupled intramembrane lipid transporter activity	IEA Inferred from Electronic Annotation more info
enables ATPase-coupled lipid transmembrane transporter activity	IC Inferred by Curator more info	PubMed
enables ATPase-coupled transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables apolipoprotein A-I receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables apolipoprotein A-I receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables lipid transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables lipid transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables lipid transporter activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular homeostasis	NAS Non-traceable Author Statement more info	PubMed
involved_in ceramide metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ceramide metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in ceramide transport	IDA Inferred from Direct Assay more info	PubMed
involved_in ceramide transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ceramide transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in cholesterol efflux	IEA Inferred from Electronic Annotation more info
involved_in corneocyte desquamation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in corneocyte desquamation	ISS Inferred from Sequence or Structural Similarity more info
involved_in establishment of skin barrier	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in keratinization	IEA Inferred from Electronic Annotation more info
involved_in lipid homeostasis	IEA Inferred from Electronic Annotation more info
involved_in lipid translocation	IEA Inferred from Electronic Annotation more info
involved_in lipid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in lipid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in lipid transport	NAS Non-traceable Author Statement more info	PubMed
involved_in lipid transport	TAS Traceable Author Statement more info
involved_in lung alveolus development	IEA Inferred from Electronic Annotation more info
involved_in phospholipid efflux	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cholesterol efflux	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of intracellular lipid transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein localization to plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulated exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of keratinocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of keratinocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in secretion by cell	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in skin morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in surfactant homeostasis	IEA Inferred from Electronic Annotation more info
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in epidermal lamellar body	IDA Inferred from Direct Assay more info	PubMed
located_in epidermal lamellar body membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in transport vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: glucosylceramide transporter ABCA12

Names: ATP-binding cassette transporter 12; ATP-binding cassette, sub-family A (ABC1), member 12

NP_056472.2

EC 7.6.2.1

NP_775099.2

EC 7.6.2.1

XP_011509253.1

EC 7.6.2.1

XP_054197317.1

EC 7.6.2.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007074.2 RefSeqGene

Range

5000..212084

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_015657.4 → NP_056472.2 glucosylceramide transporter ABCA12 isoform b

See identical proteins and their annotated locations for NP_056472.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains a distinct 5' UTR and 5' coding region, compared to transcript variant 1. This results in a protein (isoform b) containing a shorter and distinct N-terminus, compared to isoform a.

Source sequence(s)

AC072062, AF418105, AK096597, AK123578, AY033486, AY219711

Consensus CDS

CCDS33373.1

UniProtKB/Swiss-Prot

Q86UK0

UniProtKB/TrEMBL

B3KVV3

Related

ENSP00000374312.4, ENST00000389661.4

Conserved Domains (4) summary

cd03263
Location:1936 → 2159

ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A

COG1121
Location:1028 → 1252

ZnuC; ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]

COG1131
Location:1941 → 2249

CcmA; ABC-type multidrug transport system, ATPase component [Defense mechanisms]

pfam12698
Location:1595 → 1856

ABC2_membrane_3; ABC-2 family transporter protein
NM_173076.3 → NP_775099.2 glucosylceramide transporter ABCA12 isoform a

See identical proteins and their annotated locations for NP_775099.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

AC072062, AF418105, AK096597, AK123578, AY219711, BC144073

Consensus CDS

CCDS33372.1

UniProtKB/Swiss-Prot

Q53QE2, Q53S55, Q86UK0, Q8IZW6, Q96JT3, Q9Y4M5

Related

ENSP00000272895.7, ENST00000272895.12

Conserved Domains (4) summary

cd03263
Location:2254 → 2477

ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A

COG1121
Location:1346 → 1570

ZnuC; ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]

COG1131
Location:2259 → 2567

CcmA; ABC-type multidrug transport system, ATPase component [Defense mechanisms]

pfam12698
Location:1913 → 2174

ABC2_membrane_3; ABC-2 family transporter protein

RNA

NR_103740.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) has two additional internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC072062, AK096597, AK123578, AY219711, BC144073

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

214931542..215138626 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011510951.3 → XP_011509253.1 glucosylceramide transporter ABCA12 isoform X1

Conserved Domains (4) summary

cd03263
Location:2257 → 2480

ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A

COG1121
Location:1349 → 1573

ZnuC; ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]

COG1131
Location:2262 → 2570

CcmA; ABC-type multidrug transport system, ATPase component [Defense mechanisms]

pfam12698
Location:1916 → 2177

ABC2_membrane_3; ABC-2 family transporter protein