ABCD2

protein-coding

ATP binding cassette subfamily D member 2, the group of ATP binding cassette subfamily D

Gene 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. The function of this peroxisomal membrane protein is unknown; however this protein is speculated to function as a dimerization partner of ABCD1 and/or other peroxisomal ABC transporters. Mutations in this gene have been observed in patients with adrenoleukodystrophy, a severe demyelinating disease. This gene has been identified as a candidate for a modifier gene, accounting for the extreme variation among adrenoleukodystrophy phenotypes. This gene is also a candidate for a complement group of Zellweger syndrome, a genetically heterogeneous disorder of peroxisomal biogenesis. [provided by RefSeq, Jul 2008]

Previous symbols:
  • ALDL1

MANE transcript

NM_005164.4

Inheritance

—

ClinVar variants

U:71B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr12:39,550,033-39,619,803

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~69.8 kb
Loading mutation effect viewer...

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 ABCD2 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 69
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005164.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
69
clinvar
2
clinvar
71
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total00712073
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005164.4RefSeqNP_005155.110MANE Select
ENST00000308666.4EnsemblENSP00000310688.310MANE Select
NM_001412788.1RefSeqNP_001399717.110Standard
NM_001412789.1RefSeqNP_001399718.19Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Peroxisome - Homo sapiens (human)
  • ABC transporters - Homo sapiens (human)
  • Beta Oxidation of Very Long Chain Fatty Acids
  • Oxidation of Branched Chain Fatty Acids
  • Refsum Disease

Biological Process

  • very long-chain fatty acid metabolic process
  • fatty acid beta-oxidation
  • long-chain fatty acid transport
  • positive regulation of fatty acid beta-oxidation
  • very long-chain fatty acid catabolic process

Molecular Function

  • long-chain fatty acid transporter activity
  • protein binding
  • ATP binding
  • ATPase activity, coupled to transmembrane movement of substances
  • protein homodimerization activity

Cellular Component

  • peroxisome
  • peroxisomal membrane
  • cytosol
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000308666
Coding exons
10
Length
69719
Individuals with no LoFs
125715
Homozygous LoFs
0
Heterozygous LoFs
33
Defined
125748
p
0.000131
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.352673990.6690.00002004830
Missense (PolyPhen)65124.620.521571449
Synonymous0.4471331400.9520.000006861448
Loss of Function2.771430.50.4590.00000142410

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American0.000130.00012rare
Ashkenazi Jewish0.0000990.000099rare
East Asian00.0absent
Finnish0.000140.00014rare
European (Non-Finnish)0.000130.00013rare
South Asian0.000130.00013rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Probable transporter.;

Recessive Scores

pRec
0.199

Intolerance Scores

LoFtool
0.233
RVIS EVS
-0.09
RVIS percentile EVS
46.92

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.929

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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