ABCD2

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

Basic information

Region (hg38): 12:39550033-39619803

Previous symbols: [ "ALDL1" ]

Links

ENSG00000173208 ∙ NCBI:225 ∙ OMIM:601081 ∙ HGNC:66 ∙ Uniprot:Q9UBJ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCD2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in ABCD2

This is a list of pathogenic ClinVar variants found in the ABCD2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-39553926-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-39553995-G-T		not specified	Uncertain significance (Oct 20, 2023)
12-39553996-C-A		not specified	Uncertain significance (Aug 12, 2022)
12-39554084-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-39573755-C-G		not specified	Uncertain significance (Nov 22, 2023)
12-39573792-C-T		not specified	Uncertain significance (Dec 19, 2022)
12-39573859-C-G			Benign (-)
12-39586185-C-T		not specified	Uncertain significance (Feb 10, 2023)
12-39586196-A-G		not specified	Uncertain significance (Dec 05, 2022)
12-39586200-G-A		not specified	Likely benign (Feb 11, 2022)
12-39586203-C-T		not specified	Uncertain significance (Aug 26, 2022)
12-39586224-C-T		not specified	Uncertain significance (May 26, 2024)
12-39586276-A-C		not specified	Uncertain significance (Apr 28, 2023)
12-39603924-C-A		not specified	Uncertain significance (Aug 28, 2023)
12-39603937-A-G		not specified	Uncertain significance (Nov 23, 2022)
12-39603991-A-G		not specified	Uncertain significance (Jun 13, 2023)
12-39603996-A-C		not specified	Uncertain significance (Sep 14, 2021)
12-39604797-A-G		not specified	Uncertain significance (May 10, 2024)
12-39604840-C-T		not specified	Uncertain significance (Aug 21, 2023)
12-39607655-T-G		not specified	Uncertain significance (Nov 03, 2023)
12-39607681-C-T		not specified	Uncertain significance (Jun 21, 2023)
12-39617049-G-T		not specified	Uncertain significance (Jul 19, 2023)
12-39617093-A-G		not specified	Uncertain significance (May 26, 2023)
12-39617099-G-A		not specified	Uncertain significance (Jun 17, 2022)
12-39618736-A-G		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCD2	protein_coding	protein_coding	ENST00000308666	10	69719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000471	0.998	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.35	267	399	0.669	0.0000200	4830
Missense in Polyphen		65	124.62	0.52157		1449
Synonymous	0.447	133	140	0.952	0.00000686	1448
Loss of Function	2.77	14	30.5	0.459	0.00000142	410

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000439	0.000438
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transporter.
• Pathway: 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;Phytanic Acid Peroxisomal Oxidation;Adrenoleukodystrophy, X-linked;Carnitine-acylcarnitine translocase deficiency;Nuclear Receptors in Lipid Metabolism and Toxicity;ABC transporters in lipid homeostasis;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

• pRec: 0.199

Intolerance Scores

• loftool: 0.233
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.0848
• hipred: N
• hipred_score: 0.317
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcd2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• 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;myelin maintenance;transmembrane transport;negative regulation of cytokine production involved in inflammatory response;negative regulation of reactive oxygen species biosynthetic process;neuron projection maintenance;positive regulation of unsaturated fatty acid biosynthetic process
• Cellular component: peroxisome;peroxisomal membrane;cytosol;integral component of membrane
• Molecular function: long-chain fatty acid transporter activity;protein binding;ATP binding;ATPase activity, coupled to transmembrane movement of substances;protein homodimerization activity