ABCD3 ATP binding cassette subfamily D member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ABCD3provided by HGNC
Official Full Name: ATP binding cassette subfamily D member 3provided by HGNC
Primary source: HGNC:HGNC:67
See related: Ensembl:ENSG00000117528 MIM:170995; AllianceGenome:HGNC:67
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: ZWS2; ABC43; CBAS5; PMP70; PXMP1
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 protein is a member of the ALD subfamily, which is involved in peroxisomal import of fatty acids and/or fatty acyl-CoAs in the organelle. All known peroxisomal ABC transporters are half transporters which require a partner half transporter molecule to form a functional homodimeric or heterodimeric transporter. This peroxisomal membrane protein likely plays an important role in peroxisome biogenesis. Mutations have been associated with some forms of Zellweger syndrome, a heterogeneous group of peroxisome assembly disorders. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in liver (RPKM 28.7), kidney (RPKM 21.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p21.3

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (94385131..94518663)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (94233380..94366700)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (94883945..94984219)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Peroxisomal ABC Transporters: An Update.
Title: Peroxisomal ABC Transporters: An Update.
In HEK293 cells, the D-bifunctional protein (HSD17B4) and the peroxisomal ABC transporter ABCD3 are essential in peroxisomal oxidation of lauric and palmitic acid.
Title: Peroxisomes can oxidize medium- and long-chain fatty acids through a pathway involving ABCD3 and HSD17B4.
ABCD1 and ABCD2 are involved in the transport of long and very long chain fatty acids (VLCFA) or their CoA-derivatives into peroxisomes with different substrate specificities, while ABCD3 is involved in the transport of branched chain acyl-CoA into peroxisomes.ABCD4 is deduced to take part in the transport of vitamin B12 from lysosomes into the cytosol.
Title: ABC Transporter Subfamily D: Distinct Differences in Behavior between ABCD1-3 and ABCD4 in Subcellular Localization, Function, and Human Disease.
Data show that ACBD3 can recruit PI4KB to model membranes as well as redirect PI4KB to cellular membranes where it is not naturally found. Also, results show that ACBD3 regulates the enzymatic activity of PI4KB kinase through membrane recruitment rather than allostery.
Title: Structural insights and in vitro reconstitution of membrane targeting and activation of human PI4KB by the ACBD3 protein.
The N-terminal motif of PMP70 suppresses cotranslational targeting to the endoplasmic reticulum.
Title: The N-terminal motif of PMP70 suppresses cotranslational targeting to the endoplasmic reticulum.
Increased ABCD3 expression correlates with Gleason Score.
Title: Immunohistological analysis of ABCD3 expression in Caucasian and African American prostate tumors.
Deficiency of peroxisomal ABCD3 resulted in bile acid biosynthesis defect.
Title: A novel bile acid biosynthesis defect due to a deficiency of peroxisomal ABCD3.
We postulate a role for human ABCD3 in the oxidation of dicarboxylic acids and a role in buffering fatty acids that are overflowing from the mitochondrial beta-oxidation system
Title: A role for the human peroxisomal half-transporter ABCD3 in the oxidation of dicarboxylic acids.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
investigation of organelle-targeting properties of N-terminal portions of peroxisomal PMP70; amino acid sequence and domain structure of human form discussed
Title: Multiple organelle-targeting signals in the N-terminal portion of peroxisomal membrane protein PMP70.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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
Congenital bile acid synthesis defect 5 MedGen: C4225390 OMIM: 616278 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	HIV-1 Vpr is identified to have a physical interaction with ATP-binding cassette, sub-family D (ALD), member 3 (ABCD3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G29187 (e-PCR)
- UniSTS:63752

D1S3571 (e-PCR)
- UniSTS:49528

ABCD3 (e-PCR)
- UniSTS:384

SHGC-75171 (e-PCR)
- UniSTS:384

G60300 (e-PCR)
- UniSTS:137405

1400 (e-PCR)
- UniSTS:18372

ABCD3_1048 (e-PCR)
- UniSTS:276953

GDB:196676 (e-PCR)
- UniSTS:155880

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ABC-type transporter activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IBA Inferred from Biological aspect of Ancestor more info
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	IDA Inferred from Direct Assay more info	PubMed
enables ATPase-coupled transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATPase-coupled transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables fatty acyl-CoA hydrolase activity	IDA Inferred from Direct Assay more info	PubMed
enables long-chain fatty acid transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables long-chain fatty acid transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in bile acid and bile salt transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in bile acid biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in fatty acid beta-oxidation	IBA Inferred from Biological aspect of Ancestor more info
involved_in fatty acid beta-oxidation	IDA Inferred from Direct Assay more info	PubMed
involved_in fatty acid beta-oxidation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in fatty acid biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in long-chain fatty acid import into peroxisome	IBA Inferred from Biological aspect of Ancestor more info
involved_in long-chain fatty acid import into peroxisome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peroxisome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in peroxisome organization	IDA Inferred from Direct Assay more info	PubMed
involved_in peroxisome organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phytanic acid metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to organic cyclic compound	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in very long-chain fatty acid catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in very long-chain fatty acid catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in very long-chain fatty acid metabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in membrane	HDA more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in peroxisomal matrix	IDA Inferred from Direct Assay more info	PubMed
located_in peroxisomal membrane	HDA more info	PubMed
is_active_in peroxisomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in peroxisomal membrane	TAS Traceable Author Statement more info
located_in peroxisome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ATP-binding cassette sub-family D member 3

Names: 70 kDa peroxisomal membrane protein; ATP-binding cassette, sub-family D (ALD), member 3; Peroxisomal membrane protein-1 (70kD); dJ824O18.1 (ATP-binding cassette, sub-family D (ALD), member 3 (PMP70, PXMP1)); peroxisomal membrane protein 1 (70kD, Zellweger syndrome); peroxisomal membrane protein 70 kDa

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_008865.2 RefSeqGene

Range

38260..138534

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001122674.2 → NP_001116146.1 ATP-binding cassette sub-family D member 3 isoform b

See identical proteins and their annotated locations for NP_001116146.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has multiple differences in the 3' coding region and 3' UTR and contains an alternate exon in the central coding region, compared to variant 1, that results in a protein (isoform b) with a shorter, distinct C-terminus when compared to isoform a.

Source sequence(s)

AC118469, BC009712, DC317792

Consensus CDS

CCDS44175.1

UniProtKB/Swiss-Prot

P28288

Related

ENSP00000326880.5, ENST00000315713.5

Conserved Domains (1) summary

TIGR00954
Location:1 → 234

3a01203; Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein
NM_002858.4 → NP_002849.1 ATP-binding cassette sub-family D member 3 isoform a

See identical proteins and their annotated locations for NP_002849.1

Status: REVIEWED

Description

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

Source sequence(s)

BC068509, DC317792, M81182

Consensus CDS

CCDS749.1

UniProtKB/Swiss-Prot

D3DT46, P28288, Q15271, Q6NUN5, Q96DA3, Q9H529

UniProtKB/TrEMBL

A0A3B3ITW3

Related

ENSP00000359233.4, ENST00000370214.9

Conserved Domains (1) summary

TIGR00954
Location:1 → 647

3a01203; Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

94385131..94518663

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047426556.1 → XP_047282512.1 ATP-binding cassette sub-family D member 3 isoform X3
XM_006710802.3 → XP_006710865.2 ATP-binding cassette sub-family D member 3 isoform X1

UniProtKB/TrEMBL

B4DL07

Conserved Domains (1) summary

TIGR00954
Location:1 → 671

3a01203; Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein
XM_047426549.1 → XP_047282505.1 ATP-binding cassette sub-family D member 3 isoform X3
XM_047426546.1 → XP_047282502.1 ATP-binding cassette sub-family D member 3 isoform X2
XM_047426554.1 → XP_047282510.1 ATP-binding cassette sub-family D member 3 isoform X3
XM_011541877.2 → XP_011540179.1 ATP-binding cassette sub-family D member 3 isoform X4

Conserved Domains (3) summary

PRK10247
Location:124 → 332

PRK10247; putative ABC transporter ATP-binding protein YbbL; Provisional

cd03223
Location:128 → 333

ABCD_peroxisomal_ALDP; ATP-binding cassette domain of peroxisomal transporter, subfamily D

cl00549
Location:1 → 26

ABC_membrane; ABC transporter transmembrane region
XM_047426559.1 → XP_047282515.1 ATP-binding cassette sub-family D member 3 isoform X4

Related

ENST00000484213.1

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

94233380..94366700

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054337991.1 → XP_054193966.1 ATP-binding cassette sub-family D member 3 isoform X3
XM_054337988.1 → XP_054193963.1 ATP-binding cassette sub-family D member 3 isoform X1
XM_054337989.1 → XP_054193964.1 ATP-binding cassette sub-family D member 3 isoform X3
XM_054337990.1 → XP_054193965.1 ATP-binding cassette sub-family D member 3 isoform X3
XM_054337993.1 → XP_054193968.1 ATP-binding cassette sub-family D member 3 isoform X4
XM_054337992.1 → XP_054193967.1 ATP-binding cassette sub-family D member 3 isoform X4