ABCA12

gene
On this page

Also known as DKFZP434G232LI2

Summary

ABCA12 (ATP binding cassette subfamily A member 12, HGNC:14637) is a protein-coding gene on chromosome 2q35, encoding Glucosylceramide transporter ABCA12 (Q86UK0). Transports lipids such as glucosylceramides from the outer to the inner leaflet of lamellar granules (LGs) membrane, whereby the lipids are finally transported to the keratinocyte periphery via the trans-Golgi network and LGs and released to the apical surface of the granular ke….

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.

Source: NCBI Gene 26154 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): autosomal recessive congenital ichthyosis 4B (Definitive, GenCC) — +4 more curated relationships
  • Clinical variants (ClinVar): 1,807 total — 110 pathogenic, 89 likely-pathogenic
  • Phenotypes (HPO): 54
  • MANE Select transcript: NM_173076

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14637
Approved symbolABCA12
NameATP binding cassette subfamily A member 12
Location2q35
Locus typegene with protein product
StatusApproved
AliasesDKFZP434G232, LI2
Ensembl geneENSG00000144452
Ensembl biotypeprotein_coding
OMIM607800
Entrez26154

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000272895, ENST00000389661, ENST00000412081

RefSeq mRNA: 2 — MANE Select: NM_173076 NM_015657, NM_173076

CCDS: CCDS33372, CCDS33373

Canonical transcript exons

ENST00000272895 — 53 exons

ExonStartEnd
ENSE00000785453214934078214934215
ENSE00000785454214937510214937615
ENSE00000796793214942925214943017
ENSE00000965174215001558215001737
ENSE00000965175215000705215001020
ENSE00000965176214997695214997809
ENSE00000965185214989552214989621
ENSE00000965187214986542214986728
ENSE00000965188214982187214982383
ENSE00000965194214980483214980643
ENSE00000965195214978804214979040
ENSE00000965196214978316214978466
ENSE00000965197214975785214976037
ENSE00000965198214974778214974864
ENSE00000965199214973949214974042
ENSE00000965200214970273214970400
ENSE00000965201214968720214968807
ENSE00000965203214958277214958454
ENSE00000965204214956663214956778
ENSE00000965205214955202214955361
ENSE00000965206214953854214954107
ENSE00000965207214950879214951083
ENSE00000965208214949040214949149
ENSE00000965209214948596214948737
ENSE00000965969215026820215026938
ENSE00000965970215025673215025779
ENSE00001038423215004209215004299
ENSE00001038424215019540215019796
ENSE00001038465215019336215019448
ENSE00001038489214990702214991031
ENSE00001038505215018008215018132
ENSE00001147155214966848214966953
ENSE00001159716214987647214987793
ENSE00001159727214945001214945104
ENSE00001218062215010331215010470
ENSE00001218069215011439215011649
ENSE00001218123214947422214947556
ENSE00001218183214959024214959078
ENSE00001218264214989329214989463
ENSE00001218297215007727215007846
ENSE00001218314215011971215012135
ENSE00001218381215031821215031896
ENSE00001294976215036953215037065
ENSE00001319569215045837215046015
ENSE00001332834215049626215049811
ENSE00001332836215052487215052584
ENSE00001332837215054573215054664
ENSE00001332839215064066215064219
ENSE00001332840215111597215111690
ENSE00001332842215138140215138626
ENSE00001506513214983647214983865
ENSE00001506521215015490215015663
ENSE00001865752214931542214932741

Expression profiles

Bgee: expression breadth broad, 95 present calls, max score 91.76.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6735 / max 155.4044, expressed in 236 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
335580.8893195
335590.6234176
335600.115164
335610.045717

Top tissues by expression

258 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
penisUBERON:000098991.76gold quality
upper leg skinUBERON:000426289.78gold quality
upper arm skinUBERON:000426389.21gold quality
mammalian vulvaUBERON:000099788.50gold quality
skin of legUBERON:000151184.69gold quality
skin of abdomenUBERON:000141684.33gold quality
zone of skinUBERON:000001484.29gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047376.83gold quality
skin of hipUBERON:000155473.77gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099173.25gold quality
cervix epitheliumUBERON:000480167.98gold quality
lower esophagus mucosaUBERON:003583463.82gold quality
esophagus mucosaUBERON:000246961.30gold quality
vaginaUBERON:000099661.14gold quality
tongue squamous epitheliumUBERON:000691960.74gold quality
gingival epitheliumUBERON:000194960.47gold quality
gingivaUBERON:000182859.90gold quality
oviduct epitheliumUBERON:000480459.14silver quality
nippleUBERON:000203057.16gold quality
tonsilUBERON:000237254.98gold quality
ganglionic eminenceUBERON:000402354.73silver quality
cortical plateUBERON:000534354.13gold quality
uterine cervixUBERON:000000254.05gold quality
cervix squamous epitheliumUBERON:000692253.72silver quality
pigmented layer of retinaUBERON:000178252.27silver quality
olfactory segment of nasal mucosaUBERON:000538650.98gold quality
ventricular zoneUBERON:000305350.85silver quality
corpus epididymisUBERON:000435950.62gold quality
nasal cavity mucosaUBERON:000182649.89gold quality
bone marrow cellCL:000209249.61gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.88

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1H3, PPARA, PPARG, RARA, VDR

miRNA regulators (miRDB)

49 targeting ABCA12, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-8485100.0077.574731
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-366299.9973.825684
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-144-3P99.9473.982698
HSA-MIR-311999.9271.342390
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-129999.7771.242389
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-432099.7565.80793
HSA-MIR-6516-3P99.6568.571238
HSA-MIR-58799.6470.862611
HSA-MIR-875-3P99.6369.472548
HSA-MIR-613499.6365.681537
HSA-MIR-1212399.5271.792990
HSA-MIR-548G-3P99.4868.672159
HSA-MIR-4786-3P99.3668.351390
HSA-MIR-6853-3P99.3670.791558
HSA-MIR-130A-5P99.3370.262623

Literature-anchored findings (GeneRIF, showing 40)

  • Cloning, characterization and chromosome mapping of ABCA12. (PMID:12697999)
  • Mutations in the transporter ABCA12 are associated with lamellar ichthyosis type 2. (PMID:12915478)
  • Sequencing of the ABCA12 gene, which maps within the minimal region defined by homozygosity mapping, revealed disease-associated mutations, including large intragenic deletions and frameshift deletions in 11 of the 12 screened individuals with HI. (PMID:15756637)
  • 5 distinct ABCA12 mutations, either in a compound heterozygous or homozygous state, in patients from 4 harlequin ichthyosis families (PMID:16007253)
  • These mutation data establish ABCA12 as the major harlequin ichthyosis gene. (PMID:16902423)
  • study identified two novel ABCA12 mutations in two unrelated non-bullous congenital ichthyosiform erythroderma patients; both patients presented with multiple skin malignancies including malignant melanoma (PMID:17508018)
  • Our findings demonstrate that ABCA12 is highly expressed in fetal skin and suggest that ABCA12 may play an essential role under both the wet and dry conditions. (PMID:17591952)
  • PPAR and LXR activators regulate ABCA12 expression in human keratinocytes. (PMID:17611579)
  • ABCA12 plays an important role in lipid transport from the Golgi apparatus to lamellar granules in human granular layer keratinocytes. (PMID:17927575)
  • mutation analysis of twelve families demonstrated novel and recurring ABCA12 mutations (PMID:17986308)
  • ABCA12 is reduced in harlequin ichrhyosis and thus is a key molecule in regulating keratinocyte differentiation and transporting specific proteases associated with desquamation. (PMID:19179616)
  • ABCA12 is a major causative gene for non-bullous congenital ichthyosiform erythroderma. (PMID:19262603)
  • ceramide, an important lipid component of epidermis, up-regulates ABCA12 expression via the PPARdelta-mediated signaling pathway, providing a substrate-driven, feed-forward mechanism for regulating this key lipid transporter (PMID:19429679)
  • loss of ABCA12 function leads to a defective lipid barrier in the stratum corneum, resulting in an ichthyotic phenotype (Review) (PMID:20672373)
  • Our results clearly demonstrate that ABCA12 deficiency impairs glucosylceramide accumulation in lamellar bodies, thereby strongly indicating that ABCA12 transports glucosylceramide to the inner leaflet of lamellar bodies. (PMID:20869849)
  • Mutation analysis revealed that 52% of the survivors of harlequin ichthyosis had compound heterozygous mutations of ABCA12, whereas all deaths were associated with homozygous mutations of ABCA12. (PMID:21339420)
  • AKT signaling helps ABCA12 deficient keratinocytes survive during the keratinization process. (PMID:21633372)
  • The authors report on a 2282del4 mutation that may be associated with ichthyosis vulgaris in a Pakistani population. (PMID:21712002)
  • The researchers report on another fatal case of Harlequin ichthyosis that may be associated with mutations of the ABCA12 gene (PMID:21798141)
  • We show that homozygosity for a novel c.4676G>T transition in the ABCA12 gene, resulting in a p.G1559V substitution, causes non-bullous congenital ichthyosiform erythroderms in 5 members of an extended family. (PMID:22257947)
  • Report a consanguineous family of Arab Muslim origin with several members displaying a severe form of congenital ichthyosiform erythroderma. Identified a region of homozygosity shared by all patients on 2q34, in a region harbouring the ABCA12 gene. (PMID:23528209)
  • ABCA12 mutations result in defective lipid transport via lamellar granules in the keratinocytes, leading to ichthyosis phenotypes from malformation of the stratum corneum lipid barrier. (PMID:23954554)
  • Identification of the key promoter element of ABCA12 in this study may provide relevant information for genetic diagnosis of recessive congenital ichthyosis. (PMID:25338618)
  • Ssnger sequencing of the parents of neonates deceased patients with Harlequin ichthyosis identified novel mutations in ABCA12 gene. (PMID:25479012)
  • Autosomal recessive inheritance of mutations in the ATP-binding cassette, subfamily A, member 12 (ABCA12, OMIM*607800, chromosome 2q35) gene was found to be responsible for the disease. (PMID:25563821)
  • we identified three novel mutations and one reported mutation in the TGM1 and ABCA12 genes, respectively, in affected siblings of five Saudi unrelated families (PMID:27061915)
  • two missense ABCA12 mutations were uncovered in both of the affected brothers. (PMID:28236338)
  • Genes ABCC7, A3, A8, A12, and C8 prevailed among the most upregulated or downregulated ones. In conclusion, the results supported our theory about general adenosine triphosphate-binding cassette gene expression profiles and their importance for cancer on clinical as well as research levels. (PMID:28468577)
  • the present study has identified a novel homozygous deleterious intronic variant, which is associated with a severe phenotype of HI. (PMID:29377090)
  • Letter: describe ABCA12 mutations in patients with autosomal recessive congenital ichthyosis and report evidence of a founder effect of this mutation in the Spanish population. (PMID:29887490)
  • A novel heterozygous missense mutation was identified in ATP-binding cassette sub-family A member 12 (ABCA12) within a family afflicted with keratosis pilaris. In addition, upregulated ABCA12 expression levels in the sebaceous glands of patients with nevus comedonicus were investigated. (PMID:30066947)
  • Positive selection in Europeans and East-Asians at the ABCA12 gene. (PMID:30890716)
  • A novel pathogenic variant Val1927Leu was identified in a patient with severe harlequin ichthyosis. (PMID:30916489)
  • Novel mutations of the ABCA12, KRT1 and ST14 genes in three unrelated newborns showing congenital ichthyosis. (PMID:35964051)
  • Mutational Spectrum of the ABCA12 Gene and Genotype-Phenotype Correlation in a Cohort of 64 Patients with Autosomal Recessive Congenital Ichthyosis. (PMID:36980989)
  • Long-term survival of harlequin ichthyosis in two siblings with novel ABCA12 mutations. (PMID:37602715)
  • Patients with keratinization disorders due to ABCA12 variants showing pityriasis rubra pilaris phenotypes. (PMID:37752865)
  • Partial Loss of Function ABCA12 Mutations Generate Reduced Deposition of Glucosyl-Ceramide, Leading to Patchy Ichthyosis and Erythrodermia Resembling Erythrokeratodermia Variabilis et Progressiva (EKVP). (PMID:37762265)
  • Novel variants in ABCA12 cause erythrokeratodermia variabilis. (PMID:38085035)
  • Erythrokeratodermia Variabilis-like Phenotype in Patients Carrying ABCA12 Mutations. (PMID:38540347)

Cross-species orthologs

15 orthologs

OrganismSymbolGene ID
danio_rerioabca12ENSDARG00000074749
mus_musculusAbca12ENSMUSG00000050296
rattus_norvegicusAbca12ENSRNOG00000015248
drosophila_melanogasterEatoFBGN0028539
drosophila_melanogasterCG1494FBGN0031169
drosophila_melanogasterAbca3FBGN0031170
drosophila_melanogasterCG1801FBGN0031171
drosophila_melanogasterCG8908FBGN0034493
drosophila_melanogasterCG6052FBGN0036747
drosophila_melanogasterCG31213FBGN0051213
drosophila_melanogasterlddFBGN0083956
caenorhabditis_elegansWBGENE00000019
caenorhabditis_elegansabt-2WBGENE00000020
caenorhabditis_elegansWBGENE00000022
caenorhabditis_elegansabt-5WBGENE00000023

Paralogs (11): ABCA7 (ENSG00000064687), ABCA2 (ENSG00000107331), ABCA8 (ENSG00000141338), ABCA9 (ENSG00000154258), ABCA6 (ENSG00000154262), ABCA10 (ENSG00000154263), ABCA5 (ENSG00000154265), ABCA1 (ENSG00000165029), ABCA3 (ENSG00000167972), ABCA13 (ENSG00000179869), ABCA4 (ENSG00000198691)

Protein

Protein identifiers

Glucosylceramide transporter ABCA12Q86UK0 (reviewed: Q86UK0)

Alternative names: ATP-binding cassette sub-family A member 12, ATP-binding cassette transporter 12

All UniProt accessions (2): Q86UK0, E9PBK1

UniProt curated annotations — full annotation on UniProt →

Function. Transports lipids such as glucosylceramides from the outer to the inner leaflet of lamellar granules (LGs) membrane, whereby the lipids are finally transported to the keratinocyte periphery via the trans-Golgi network and LGs and released to the apical surface of the granular keratinocytes to form lipid lamellae in the stratum corneum of the epidermis, which is essential for skin barrier function. In the meantime, participates in the transport of the lamellar granules-associated proteolytic enzymes, in turn regulates desquamation and keratinocyte differentiation. Furthermore, is essential for the regulation of cellular cholesterol homeostasis by regulating ABCA1-dependent cholesterol efflux from macrophages through interaction with NR1H2 and ABCA1. Plays pleiotropic roles in regulating glucose stimulated insulin secretion from beta cells, regulating the morphology and fusion of insulin granules, lipid raft abundance and the actin cytoskeleton. Also involved in lung surfactant biogenesis.

Subunit / interactions. Interacts with NR1H2 and ABCA1; this interaction is required for ABCA1 localization to the cell surface and is necessary for its normal activity and stability.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle membrane. Golgi apparatus membrane.

Tissue specificity. Mainly expressed in the stomach, placenta, testis and fetal brain. Expressed in the upper epidermal layers, mainly the granular layers, of skin. Expressed throughout the normal interfollicular epidermis with prominent expression in the stratum granulosum. Expressed in alpha and beta cells of pancreatic islets.

Disease relevance. Ichthyosis, congenital, autosomal recessive 4A (ARCI4A) [MIM:601277] A form of autosomal recessive congenital ichthyosis, a disorder of keratinization with abnormal differentiation and desquamation of the epidermis, resulting in abnormal skin scaling over the whole body. The main skin phenotypes are lamellar ichthyosis (LI) and non-bullous congenital ichthyosiform erythroderma (NCIE), although phenotypic overlap within the same patient or among patients from the same family can occur. Lamellar ichthyosis is a condition often associated with an embedment in a collodion-like membrane at birth; skin scales later develop, covering the entire body surface. Non-bullous congenital ichthyosiform erythroderma characterized by fine whitish scaling on an erythrodermal background; larger brownish scales are present on the buttocks, neck and legs. The disease is caused by variants affecting the gene represented in this entry. Ichthyosis, congenital, autosomal recessive 4B (ARCI4B) [MIM:242500] A rare, very severe form of congenital ichthyosis, in which the neonate is born with a thick covering of armor-like scales. The skin dries out to form hard diamond-shaped plaques separated by fissures, resembling ‘armor plating’. The normal facial features are severely affected, with distortion of the lips (eclabion), eyelids (ectropion), ears, and nostrils. Affected babies are often born prematurely and rarely survive the perinatal period. Babies who survive into infancy and beyond develop skin changes resembling severe non-bullous congenital ichthyosiform erythroderma. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. Multifunctional polypeptide with two homologous halves, each containing a hydrophobic membrane-anchoring domain and an ATP binding cassette (ABC) domain.

Induction. Up-regulated during keratinization. Up-regulated after 15 weeks estimated gestational age (EGA). Highly up-regulated by PPARG activators such as ciglitazone, troglitazone, and the PPARD activator GW 0742 in time- and dose-dependent manner but independently of keratinocyte differentiation. In addition, modestly up-regulated by the NR1H3 and NR1H2 activator TO901317 in an keratinocyte differentiation-independent manner. Up-regulated by N-(hexanoyl)sphing-4-enine in a time- and dose-dependent manner or by glucosyltransferase inhibitors, ceramidase inhibitors and sphingomyelin synthase inhibitors that increase endogenous ceramide levels and induce ABCA12 expression via the PPARD signaling pathway. Up-regulated by N-acetylsphingosine in a time- and dose-dependent manner via the PPARD signaling pathway.

Similarity. Belongs to the ABC transporter superfamily. ABCA family.

Isoforms (2)

UniProt IDNamesCanonical?
Q86UK0-11yes
Q86UK0-22

RefSeq proteins (2): NP_056472, NP_775099* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003439ABC_transporter-like_ATP-bdDomain
IPR003593AAA+_ATPaseDomain
IPR013525ABC2_TMDomain
IPR017871ABC_transporter-like_CSConserved_site
IPR026082ABCAFamily
IPR027417P-loop_NTPaseHomologous_superfamily
IPR056264R2_ABCA1-4-likeDomain

Pfam: PF00005, PF12698, PF23321

Catalyzed reactions (Rhea), 1 shown:

  • a beta-D-glucosylceramide(in) + ATP + H2O = a beta-D-glucosylceramide(out) + ADP + phosphate + H(+) (RHEA:66660)

UniProt features (91 total): glycosylation site 35, sequence variant 29, transmembrane region 14, sequence conflict 4, domain 2, binding site 2, splice variant 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86UK0-F168.320.04

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (2): 1378–1385; 2290–2297

Glycosylation sites (35): 156, 174, 214, 275, 333, 367, 383, 412, 435, 528, 543, 577, 608, 623, 648, 752, 826, 920, 963, 1170 …

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-1369062ABC transporters in lipid homeostasis
R-HSA-5682294Defective ABCA12 causes ARCI4B
R-HSA-1643685Disease
R-HSA-382551Transport of small molecules
R-HSA-382556ABC-family protein mediated transport
R-HSA-5619084ABC transporter disorders
R-HSA-5619115Disorders of transmembrane transporters

MSigDB gene sets: 349 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, XU_GH1_AUTOCRINE_TARGETS_UP, GOBP_REGULATION_OF_EPIDERMIS_DEVELOPMENT, GOBP_EPITHELIAL_CELL_DEVELOPMENT, JAEGER_METASTASIS_DN, GOCC_SECRETORY_GRANULE, GOBP_INSULIN_SECRETION, GOZGIT_ESR1_TARGETS_DN, GOBP_CELLULAR_RESPONSE_TO_CARBOHYDRATE_STIMULUS, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_POSITIVE_REGULATION_OF_CHOLESTEROL_EFFLUX, GOBP_REGULATION_OF_CHOLESTEROL_EFFLUX, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION_TO_CELL_SURFACE, GOBP_REGULATION_OF_HORMONE_LEVELS

GO Biological Process (26): corneocyte desquamation (GO:0003336), ceramide metabolic process (GO:0006672), lipid transport (GO:0006869), intracellular protein transport (GO:0006886), positive regulation of cholesterol efflux (GO:0010875), cellular homeostasis (GO:0019725), keratinization (GO:0031424), positive regulation of intracellular lipid transport (GO:0032379), secretion by cell (GO:0032940), cholesterol efflux (GO:0033344), phospholipid efflux (GO:0033700), ceramide transport (GO:0035627), surfactant homeostasis (GO:0043129), regulated exocytosis (GO:0045055), regulation of keratinocyte differentiation (GO:0045616), lung alveolus development (GO:0048286), lipid homeostasis (GO:0055088), regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178), establishment of skin barrier (GO:0061436), protein localization to plasma membrane (GO:0072659), positive regulation of protein localization to cell surface (GO:2000010), keratinocyte differentiation (GO:0030216), positive regulation of cholesterol transport (GO:0032376), lipid translocation (GO:0034204), establishment of localization in cell (GO:0051649), transmembrane transport (GO:0055085)

GO Molecular Function (11): signaling receptor binding (GO:0005102), lipid carrier activity (GO:0005319), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), ATPase-coupled lipid transmembrane transporter activity (GO:0034040), apolipoprotein A-I receptor binding (GO:0034191), ATPase-coupled transmembrane transporter activity (GO:0042626), ATPase-coupled intramembrane lipid carrier activity (GO:0140326), ABC-type transporter activity (GO:0140359), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (11): Golgi membrane (GO:0000139), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020), transport vesicle membrane (GO:0030658), epidermal lamellar body (GO:0097209), epidermal lamellar body membrane (GO:0097234), Golgi apparatus (GO:0005794), secretory granule membrane (GO:0030667), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
ABC-family protein mediated transport1
ABC transporter disorders1
Transport of small molecules1
Disorders of transmembrane transporters1
Disease1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ATP-dependent activity3
bounding membrane of organelle3
cellular anatomical structure3
cytoplasm3
keratinocyte differentiation2
ATPase-coupled transmembrane transporter activity2
cytoplasmic vesicle membrane2
corneocyte development1
delamination1
sphingolipid metabolic process1
transport1
lipid localization1
intracellular protein localization1
protein transport1
intracellular transport1
regulation of cholesterol efflux1
positive regulation of cholesterol transport1
cholesterol efflux1
homeostatic process1
multicellular organismal process1
intracellular lipid transport1
positive regulation of lipid transport1
regulation of intracellular lipid transport1
positive regulation of intracellular transport1
secretion1
export from cell1
cholesterol transport1
phospholipid transport1
lipid transport1
nitrogen compound transport1
multicellular organismal-level chemical homeostasis1
exocytosis1
regulation of epidermal cell differentiation1
lung development1
anatomical structure development1
chemical homeostasis1
insulin secretion involved in cellular response to glucose stimulus1
regulation of insulin secretion1
regulation of cellular localization1
skin epidermis development1

Protein interactions and networks

STRING

1110 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ABCA12CYP4F22Q6NT55977
ABCA12TGM1P22735951
ABCA12NIPAL4Q0D2K0920
ABCA12LIPNQ5VXI9829
ABCA12CST6Q15828813
ABCA12ALOX12BO75342794
ABCA12ALOXE3Q9BYJ1794
ABCA12PNPLA1Q8N8W4784
ABCA12CERS3Q8IU89709
ABCA12LORICRINP23490658
ABCA12FLGP20930633
ABCA12SDR9C7Q8NEX9631
ABCA12FLG2Q5D862616
ABCA12TINCRA0A2R8Y7D0560
ABCA12ABCD4O14678554

IntAct

11 interactions, top by confidence:

ABTypeScore
ABCA1ABCA12psi-mi:“MI:0403”(colocalization)0.590
ABCA12ABCA1psi-mi:“MI:0915”(physical association)0.590
ABCA12ABCA1psi-mi:“MI:2364”(proximity)0.590
NR1H2ABCA1psi-mi:“MI:0914”(association)0.420
NEK4E2F8psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
BMI1MEIS3P1psi-mi:“MI:0914”(association)0.350
MBNL1A2ML1psi-mi:“MI:0914”(association)0.350
SMPD2A2ML1psi-mi:“MI:0914”(association)0.350

BioGRID (16): ABCA12 (Protein-RNA), ABCA12 (Affinity Capture-MS), ABCA12 (Affinity Capture-MS), ABCA12 (Affinity Capture-MS), ABCA12 (Affinity Capture-MS), ABCA12 (Synthetic Lethality), ABCA12 (Proximity Label-MS), ABCA12 (Proximity Label-MS), ABCA12 (Proximity Label-MS), GATAD2B (Cross-Linking-MS (XL-MS)), HDAC1 (Cross-Linking-MS (XL-MS)), EEA1 (Cross-Linking-MS (XL-MS)), ABCA12 (Affinity Capture-MS), ABCA12 (Proximity Label-MS), ABCA12 (Proximity Label-MS)

ESM2 similar proteins: A0JPP4, A6H7F9, A7WNB0, C0HMB7, C6KI89, E9Q355, E9Q876, F5HGK9, O36397, O75969, O77797, P01586, P03319, P04823, P06740, P14683, P25140, P28907, Q00997, Q02484, Q15846, Q2TAV2, Q2YDM0, Q3TBN1, Q3ZRW6, Q3ZRW7, Q3ZRW9, Q499E0, Q5BK38, Q5BKX0, Q5CCK0, Q5RBQ2, Q5RDR5, Q5RII3, Q5SSE9, Q5VAN0, Q68FB2, Q6AY76, Q6DFY8, Q6UWF9

Diamond homologs: A0A0G2K1Q8, C0SPB4, E9PU17, E9PX95, E9Q876, F1MWM0, O35600, O52618, O95477, P08720, P0A9U1, P0A9U2, P0DXG8, P0DXU5, P0DXU7, P19844, P22040, P23703, P26050, P30750, P32010, P36879, P37624, P41233, P41234, P44785, P50332, P54592, P55476, P63355, P63356, P70970, P72335, P78363, P94374, P94440, Q05067, Q0I5E9, Q0TLD2, Q13ZJ1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

1807 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic110
Likely pathogenic89
Uncertain significance422
Likely benign907
Benign105

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1385145NM_173076.3(ABCA12):c.1210C>T (p.Arg404Ter)Pathogenic
1526238NM_173076.3(ABCA12):c.4540C>T (p.Arg1514Cys)Pathogenic
152738GRCh38/hg38 2q32.3-35(chr2:192938826-215705052)x1Pathogenic
1686889NM_173076.3(ABCA12):c.3656C>T (p.Ala1219Val)Pathogenic
1693261NM_173076.3(ABCA12):c.7344-1G>CPathogenic
1997979NM_173076.3(ABCA12):c.2946del (p.Lys982fs)Pathogenic
2094179NM_173076.3(ABCA12):c.5963del (p.Ile1987_Leu1988insTer)Pathogenic
2096804NM_173076.3(ABCA12):c.6167dup (p.Lys2057fs)Pathogenic
2203257NM_173076.3(ABCA12):c.5848C>T (p.Arg1950Ter)Pathogenic
2203258NM_173076.3(ABCA12):c.3666C>A (p.Tyr1222Ter)Pathogenic
2427498NC_000002.11:g.(?215917191)(215919408_?)delPathogenic
2434711NM_173076.3(ABCA12):c.5641C>T (p.Arg1881Ter)Pathogenic
2505564NM_173076.3(ABCA12):c.5469_5472delPathogenic
2506520NM_173076.3(ABCA12):c.5046_5050del (p.Lys1682fs)Pathogenic
264997NM_173076.3(ABCA12):c.178C>T (p.Arg60Ter)Pathogenic
264999NM_173076.3(ABCA12):c.859C>T (p.Arg287Ter)Pathogenic
265000NM_173076.3(ABCA12):c.1300C>T (p.Arg434Ter)Pathogenic
265001NM_173076.3(ABCA12):c.2140C>T (p.Arg714Ter)Pathogenic
265004NM_173076.3(ABCA12):c.3256A>T (p.Lys1086Ter)Pathogenic
265005NM_173076.3(ABCA12):c.3889C>T (p.Arg1297Ter)Pathogenic
2699455NM_173076.3(ABCA12):c.5607C>G (p.Tyr1869Ter)Pathogenic
2703432NM_173076.3(ABCA12):c.4119del (p.Thr1374fs)Pathogenic
2703892NM_173076.3(ABCA12):c.5641del (p.Arg1881fs)Pathogenic
2705444NM_173076.3(ABCA12):c.6037C>T (p.Gln2013Ter)Pathogenic
2708066NM_173076.3(ABCA12):c.5446_5447del (p.Met1816fs)Pathogenic
2718324NM_173076.3(ABCA12):c.2394G>A (p.Trp798Ter)Pathogenic
2727250NM_173076.3(ABCA12):c.3908_3911dup (p.Lys1304fs)Pathogenic
2734375NM_173076.3(ABCA12):c.6858del (p.Phe2286fs)Pathogenic
2734376NM_173076.3(ABCA12):c.4543C>T (p.Arg1515Ter)Pathogenic
2734377NM_173076.3(ABCA12):c.3673C>T (p.Arg1225Ter)Pathogenic

SpliceAI

6964 predictions. Top by Δscore:

VariantEffectΔscore
2:214934073:CTTAC:Cdonor_loss1.0000
2:214934074:TTACC:Tdonor_loss1.0000
2:214934077:C:CAdonor_loss1.0000
2:214934077:CCT:Cdonor_gain1.0000
2:214934211:TGATC:Tacceptor_gain1.0000
2:214934212:GATC:Gacceptor_gain1.0000
2:214934212:GATCC:Gacceptor_gain1.0000
2:214934213:ATC:Aacceptor_gain1.0000
2:214934213:ATCCT:Aacceptor_gain1.0000
2:214934214:TC:Tacceptor_gain1.0000
2:214934214:TCCTG:Tacceptor_gain1.0000
2:214934215:CCTG:Cacceptor_gain1.0000
2:214934215:CCTGT:Cacceptor_gain1.0000
2:214934216:C:CAacceptor_loss1.0000
2:214934216:C:CCacceptor_gain1.0000
2:214934216:C:Tacceptor_gain1.0000
2:214934218:G:Cacceptor_gain1.0000
2:214934218:G:GCacceptor_gain1.0000
2:214934226:C:CTacceptor_gain1.0000
2:214934226:C:Tacceptor_gain1.0000
2:214934227:A:Tacceptor_gain1.0000
2:214937506:TTACT:Tdonor_loss1.0000
2:214937507:TAC:Tdonor_loss1.0000
2:214937508:A:ACdonor_gain1.0000
2:214937508:ACTTT:Adonor_loss1.0000
2:214937509:C:CTdonor_gain1.0000
2:214937611:CAAAC:Cacceptor_gain1.0000
2:214937613:AAC:Aacceptor_gain1.0000
2:214937614:AC:Aacceptor_gain1.0000
2:214937615:CC:Cacceptor_gain1.0000

AlphaMissense

17146 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:214937595:A:TV2486D1.000
2:214942930:C:AK2477N1.000
2:214942930:C:GK2477N1.000
2:214945059:A:GW2429R1.000
2:214945059:A:TW2429R1.000
2:214945061:A:GL2428P1.000
2:214945093:G:CS2417R1.000
2:214945093:G:TS2417R1.000
2:214945095:T:GS2417R1.000
2:214945097:G:CP2416R1.000
2:214945097:G:TP2416Q1.000
2:214945100:T:AE2415V1.000
2:214947473:T:AR2396S1.000
2:214947473:T:GR2396S1.000
2:214947474:C:GR2396T1.000
2:214947483:C:TG2393D1.000
2:214948686:C:AQ2338H1.000
2:214948686:C:GQ2338H1.000
2:214949126:A:CN2292K1.000
2:214949126:A:TN2292K1.000
2:214949133:C:TG2290E1.000
2:214949134:C:GG2290R1.000
2:214949134:C:TG2290R1.000
2:214949139:A:GL2288P1.000
2:214980502:A:GL1574P1.000
2:214980580:G:TA1548D1.000
2:214980586:C:GR1546P1.000
2:214980591:A:CS1544R1.000
2:214980591:A:TS1544R1.000
2:214980593:T:GS1544R1.000

dbSNP variants (sampled 300 via entrez): RS1000025382 (2:215132647 T>C), RS1000049903 (2:215011248 C>T), RS1000056770 (2:215132333 G>A,T), RS1000068243 (2:215000946 C>T), RS1000078845 (2:214952492 A>G), RS1000086849 (2:215000323 G>C), RS1000102250 (2:214965520 CTTAAA>C), RS1000125835 (2:215103507 T>C), RS1000142296 (2:215048595 C>A,T), RS1000158051 (2:215054851 T>C), RS1000159410 (2:214958092 C>T), RS1000161150 (2:214979613 C>T), RS1000176241 (2:215055753 A>C), RS1000179206 (2:215041551 C>A), RS1000225019 (2:215066904 G>C)

Disease associations

OMIM: gene MIM:607800 | disease phenotypes: MIM:601277, MIM:242500, MIM:114480

GenCC curated gene-disease

DiseaseClassificationInheritance
autosomal recessive congenital ichthyosis 4BDefinitiveAutosomal recessive
autosomal recessive congenital ichthyosis 4AStrongAutosomal recessive
autosomal recessive congenital ichthyosisStrongAutosomal recessive
lamellar ichthyosisSupportiveAutosomal recessive
congenital non-bullous ichthyosiform erythrodermaSupportiveAutosomal recessive

Mondo (8): autosomal recessive congenital ichthyosis 4A (MONDO:0011026), autosomal recessive congenital ichthyosis 4B (MONDO:0009443), lamellar ichthyosis (MONDO:0017778), breast ductal adenocarcinoma (MONDO:0005590), hereditary breast carcinoma (MONDO:0016419), ichthyosis (MONDO:0019269), congenital non-bullous ichthyosiform erythroderma (MONDO:0019306), autosomal recessive congenital ichthyosis (MONDO:0017265)

Orphanet (4): Lamellar ichthyosis (Orphanet:313), Harlequin ichthyosis (Orphanet:457), Hereditary breast cancer (Orphanet:227535), Ichthyosis (Orphanet:79354)

HPO phenotypes

54 total (30 of 54 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000083Renal insufficiency
HP:0000164Abnormality of the dentition
HP:0000232Everted lower lip vermilion
HP:0000364Hearing abnormality
HP:0000365Hearing impairment
HP:0000389Chronic otitis media
HP:0000457Depressed nasal ridge
HP:0000491Keratitis
HP:0000518Cataract
HP:0000520Proptosis
HP:0000656Ectropion
HP:0000958Dry skin
HP:0000962Hyperkeratosis
HP:0000966Hypohidrosis
HP:0000982Palmoplantar keratoderma
HP:0000989Pruritus
HP:0001019Erythroderma
HP:0001161Hand polydactyly
HP:0001217Clubbing
HP:0001258Spastic paraplegia
HP:0001270Motor delay
HP:0001376Limitation of joint mobility
HP:0001433Hepatosplenomegaly
HP:0001508Failure to thrive
HP:0001522Death in infancy
HP:0001596Alopecia
HP:0001597Abnormal nail morphology
HP:0001622Premature birth
HP:0001645Sudden cardiac death

GWAS associations

0 associations (top):

MeSH disease descriptors (4)

DescriptorNameTree numbers
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390
D007057IchthyosisC16.131.831.512; C16.614.492; C17.800.428.333; C17.800.804.512
C562840Breast Cancer, Familial (supp.)
C537264Lamellar ichthyosis, type 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

2 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2888327ABCA120.000
rs10182702ABCA120.000

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — ABCA subfamily

CTD chemical–gene interactions

49 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression5
Aflatoxin B1affects expression, decreases methylation, increases expression4
sodium arsenitedecreases methylation, increases expression3
Estradioldecreases expression, affects cotreatment3
Tetrachlorodibenzodioxindecreases expression, increases expression, affects cotreatment3
bisphenol Aincreases methylation, affects cotreatment, decreases methylation, decreases expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
Vincristinedecreases response to substance, increases expression2
Cadmium Chloridedecreases expression, increases expression2
aristolochic acid Idecreases expression1
sodium arsenatedecreases expression, increases abundance1
arseniteincreases expression1
butyraldehydedecreases expression1
S-(1,2-dichlorovinyl)cysteineincreases expression, affects cotreatment, affects response to substance1
avobenzonedecreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
nutlin 3affects cotreatment, increases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidineincreases expression, increases response to substance1
jinfukangaffects cotreatment, increases expression, decreases expression1
Docetaxelaffects expression, decreases response to substance1
Zoledronic Acidincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression1
Allergensincreases expression1
Amphotericin Bdecreases expression1
Arsenicdecreases expression, increases abundance1
Atrazineincreases expression1
Benzalkonium Compoundsincreases expression1

Clinical trials (associated diseases)

49 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04996485PHASE4UNKNOWNScientific Substantiation and Assessment of the Effectiveness of Pathogenetic Methods of Therapy for Congenital Ichthyosis in Children
NCT01222000PHASE3UNKNOWNTreatment of the Recessive Nonbullous Congenital Ichthyosis by the Epigallocatechine Cutaneous
NCT03414970PHASE3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00004690PHASE3COMPLETEDPhase III Study of Monolaurin Cream Therapy for Patients With Congenital Ichthyosis
NCT05295732PHASE3COMPLETEDThe ASCEND Study: Evaluating TMB-001 in the Treatment of RXLI or ARCI Ichthyosis
NCT03041038PHASE2COMPLETEDThe Efficacy and Safety of Secukinumab in Patients With Ichthyoses
NCT03738800PHASE2TERMINATEDA Safety, Efficacy and Systemic Exposure Study of CD5789 Cream in Adults and Adolescents With Lamellar Ichthyosis
NCT00461344PHASE2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999PHASE2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT02864082PHASE2COMPLETEDA Safety and Tolerability Study of Topical PAT-001 in Congenital Ichthyosis
NCT04154293PHASE2COMPLETEDA Vehicle Controlled Study to Evaluate Safety and Efficacy of Topical TMB-001 for Treatment of Congenital Ichthyosis
NCT04697056PHASE2TERMINATEDA Study to Evaluate the Efficacy and Safety of Imsidolimab (ANB019) in the Treatment of Participants With Ichthyosis
NCT06136403PHASE2RECRUITINGA 44-week Monocentric Open Study Assessing the Efficacy and Safety of Deucravacitinib in Adults With Inflammatory Genodermatoses
NCT06362447PHASE2NOT_YET_RECRUITINGEfficacy of Injectable Gentamicin in Hereditary Ichthyosis
NCT00001292Not specifiedCOMPLETEDStudy of Scaling Disorders and Other Inherited Skin Diseases
NCT05312073Not specifiedCOMPLETEDStudy of in Vivo and in Vitro Transcriptomic and Proteomic Signatures in Unhereditary Ichtyosis
NCT00637364PHASE1/PHASE2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855PHASE1/PHASE2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908EARLY_PHASE1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041EARLY_PHASE1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974Not specifiedACTIVE_NOT_RECRUITINGNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery
NCT00040222Not specifiedCOMPLETEDClinical, Genetic, Behavioral, Laboratory and Epidemiologic Characterization of Individuals and Families at High Risk of Breast/Ovarian Cancer
NCT02557776Not specifiedCOMPLETEDWritten Genetic Counseling and Mutation Analysis of BRCA1 and BRCA2 to Patients With Breast Cancer
NCT03495544Not specifiedUNKNOWNStudy Estimating Association Between Germline Mutations and PD-L1 Expression in Breast Cancer
NCT03959267Not specifiedCOMPLETEDTesting a Culturally Adapted Telephone Genetic Counseling Intervention
NCT04058418Not specifiedCOMPLETEDSpecialist Recommendation on FBC (Familial Breast Cancer) Chemoprevention Prescribing
NCT04125914Not specifiedACTIVE_NOT_RECRUITINGWeight Management and Health Behavior Intervention in Lowering Cancer Risk for BRCA Positive and Lynch Syndrome Families
NCT04169542Not specifiedRECRUITINGImpact of COVID-19 Pandemic on Out-of-Pocket Costs, Lost Wages, and Unemployment in Patients With Breast Cancer Undergoing Breast Surgery
NCT04197856Not specifiedACTIVE_NOT_RECRUITINGDirect Information to At-risk Relatives
NCT07292246Not specifiedRECRUITINGA Prospective CohorT Study of HandX - Assisted ENdoscopic MAstectomy: Feasibility and Safety (ATHENA I Study)
NCT07307664Not specifiedRECRUITINGIncreasing Germline Genetic Testing for Patients With Cancer
NCT04549792EARLY_PHASE1COMPLETEDAn Open-Label and Long-Term Extension Study to Evaluate the Efficacy and Safety of Ustekinumab in the Treatment of Patients With Ichthyoses
NCT07050810EARLY_PHASE1ENROLLING_BY_INVITATIONThera-Clean® Microbubbles System in Patients With Skin Diseases
NCT00074685Not specifiedCOMPLETEDNational Registry for Ichthyosis and Related Disorders
NCT02655861Not specifiedTERMINATEDA Multi-center, Prospective Evaluation of Infants and Children With Congenital Ichthyosis
NCT03051347Not specifiedCOMPLETEDAsthma and Atopic Dermatitis Validation of PROMIS Pediatric Instruments
NCT03417856Not specifiedENROLLING_BY_INVITATIONDefining the Skin and Blood Biomarkers of Ichthyosis