Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Other IDs Associated diseases
Entrez ID	5826
Gene name	ATP binding cassette subfamily D member 4
Gene symbol	ABCD4
Synonyms (NCBI Gene)	ABC41EST352188MAHCJP70RP79RPMP69PXMP1L
Chromosome	14
Chromosome location	14q24.3
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, M

Show/Hide all (6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs45568335	G>A	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, intron variant, coding sequence variant, missense variant
rs141868117	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, intron variant, coding sequence variant, non coding transcript variant
rs201777056	T>C,G	Not-provided, pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs387907315	->GA	Pathogenic	Coding sequence variant, genic downstream transcript variant, frameshift variant, non coding transcript variant, 3 prime UTR variant
rs767795583	G>A	Pathogenic	Genic downstream transcript variant, stop gained, non coding transcript variant, synonymous variant, coding sequence variant
rs769364566	C>A,T	Pathogenic	Splice donor variant

Show/Hide all (89)

miRTarBase ID	miRNA	Experiments	Reference
MIRT030267	hsa-miR-26b-5p	Microarray	19088304
MIRT042098	hsa-miR-484	CLASH	23622248
MIRT758815	hsa-miR-3065-3p	CLIP-seq
MIRT758816	hsa-miR-3180-5p	CLIP-seq
MIRT758817	hsa-miR-342-3p	CLIP-seq
MIRT758818	hsa-miR-3674	CLIP-seq
MIRT758819	hsa-miR-409-3p	CLIP-seq
MIRT758820	hsa-miR-4476	CLIP-seq
MIRT758821	hsa-miR-4753-3p	CLIP-seq
MIRT758822	hsa-miR-4766-3p	CLIP-seq
MIRT758823	hsa-miR-4766-5p	CLIP-seq
MIRT758824	hsa-miR-4768-5p	CLIP-seq
MIRT758825	hsa-miR-493	CLIP-seq
MIRT758826	hsa-miR-498	CLIP-seq
MIRT758827	hsa-miR-520a-5p	CLIP-seq
MIRT758828	hsa-miR-525-5p	CLIP-seq
MIRT758829	hsa-miR-548ag	CLIP-seq
MIRT758830	hsa-miR-548ai	CLIP-seq
MIRT758831	hsa-miR-548p	CLIP-seq
MIRT758832	hsa-miR-579	CLIP-seq
MIRT1923725	hsa-miR-299-3p	CLIP-seq
MIRT758818	hsa-miR-3674	CLIP-seq
MIRT1923726	hsa-miR-576-3p	CLIP-seq
MIRT1923727	hsa-miR-760	CLIP-seq
MIRT2165255	hsa-miR-4302	CLIP-seq
MIRT1923727	hsa-miR-760	CLIP-seq
MIRT2165256	hsa-miR-922	CLIP-seq
MIRT2467240	hsa-miR-1343	CLIP-seq
MIRT2467241	hsa-miR-141	CLIP-seq
MIRT2467242	hsa-miR-149	CLIP-seq
MIRT2467243	hsa-miR-1827	CLIP-seq
MIRT2467244	hsa-miR-200a	CLIP-seq
MIRT2467245	hsa-miR-2467-5p	CLIP-seq
MIRT2467246	hsa-miR-3064-5p	CLIP-seq
MIRT758815	hsa-miR-3065-3p	CLIP-seq
MIRT758816	hsa-miR-3180-5p	CLIP-seq
MIRT2467247	hsa-miR-3192	CLIP-seq
MIRT2467248	hsa-miR-3612	CLIP-seq
MIRT758818	hsa-miR-3674	CLIP-seq
MIRT2467249	hsa-miR-4276	CLIP-seq
MIRT2165255	hsa-miR-4302	CLIP-seq
MIRT2467250	hsa-miR-4443	CLIP-seq
MIRT2467251	hsa-miR-4499	CLIP-seq
MIRT2467252	hsa-miR-4649-3p	CLIP-seq
MIRT2467253	hsa-miR-4724-5p	CLIP-seq
MIRT758821	hsa-miR-4753-3p	CLIP-seq
MIRT758822	hsa-miR-4766-3p	CLIP-seq
MIRT758823	hsa-miR-4766-5p	CLIP-seq
MIRT758824	hsa-miR-4768-5p	CLIP-seq
MIRT2467254	hsa-miR-4794	CLIP-seq
MIRT2467255	hsa-miR-4802-5p	CLIP-seq
MIRT758826	hsa-miR-498	CLIP-seq
MIRT758827	hsa-miR-520a-5p	CLIP-seq
MIRT758828	hsa-miR-525-5p	CLIP-seq
MIRT758831	hsa-miR-548p	CLIP-seq
MIRT758832	hsa-miR-579	CLIP-seq
MIRT2467256	hsa-miR-650	CLIP-seq
MIRT1923727	hsa-miR-760	CLIP-seq
MIRT2165256	hsa-miR-922	CLIP-seq
MIRT2467240	hsa-miR-1343	CLIP-seq
MIRT2467241	hsa-miR-141	CLIP-seq
MIRT2467242	hsa-miR-149	CLIP-seq
MIRT2467243	hsa-miR-1827	CLIP-seq
MIRT2467244	hsa-miR-200a	CLIP-seq
MIRT2467245	hsa-miR-2467-5p	CLIP-seq
MIRT2467246	hsa-miR-3064-5p	CLIP-seq
MIRT758815	hsa-miR-3065-3p	CLIP-seq
MIRT758816	hsa-miR-3180-5p	CLIP-seq
MIRT2467247	hsa-miR-3192	CLIP-seq
MIRT2467248	hsa-miR-3612	CLIP-seq
MIRT758818	hsa-miR-3674	CLIP-seq
MIRT2467250	hsa-miR-4443	CLIP-seq
MIRT2467251	hsa-miR-4499	CLIP-seq
MIRT2467252	hsa-miR-4649-3p	CLIP-seq
MIRT2467253	hsa-miR-4724-5p	CLIP-seq
MIRT758821	hsa-miR-4753-3p	CLIP-seq
MIRT758822	hsa-miR-4766-3p	CLIP-seq
MIRT758823	hsa-miR-4766-5p	CLIP-seq
MIRT758824	hsa-miR-4768-5p	CLIP-seq
MIRT2467254	hsa-miR-4794	CLIP-seq
MIRT2467255	hsa-miR-4802-5p	CLIP-seq
MIRT758826	hsa-miR-498	CLIP-seq
MIRT758827	hsa-miR-520a-5p	CLIP-seq
MIRT758828	hsa-miR-525-5p	CLIP-seq
MIRT758831	hsa-miR-548p	CLIP-seq
MIRT758832	hsa-miR-579	CLIP-seq
MIRT2467256	hsa-miR-650	CLIP-seq
MIRT1923727	hsa-miR-760	CLIP-seq
MIRT2165256	hsa-miR-922	CLIP-seq

Show/Hide all (39)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005324	Function	Long-chain fatty acid transmembrane transporter activity	IBA
GO:0005515	Function	Protein binding	IPI	25535791, 27456980, 28514442, 28572511, 33845046, 33961781
GO:0005524	Function	ATP binding	IBA
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	NAS	9266848
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IDA	33845046
GO:0005765	Component	Lysosomal membrane	IDA	27456980, 33845046
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005765	Component	Lysosomal membrane	TAS
GO:0005777	Component	Peroxisome	IDA	19010322, 27456980
GO:0005777	Component	Peroxisome	IDA	9302272, 14533738
GO:0005778	Component	Peroxisomal membrane	IBA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	27456980
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0006635	Process	Fatty acid beta-oxidation	IBA
GO:0007031	Process	Peroxisome organization	IBA
GO:0009235	Process	Cobalamin metabolic process	IDA	33845046
GO:0009235	Process	Cobalamin metabolic process	IMP	22922874
GO:0015420	Function	ABC-type vitamin B12 transporter activity	EXP	33845046
GO:0015420	Function	ABC-type vitamin B12 transporter activity	IDA	33845046
GO:0015420	Function	ABC-type vitamin B12 transporter activity	IMP	33845046
GO:0015889	Process	Cobalamin transport	IMP	33845046
GO:0015889	Process	Cobalamin transport	TAS
GO:0015910	Process	Long-chain fatty acid import into peroxisome	IBA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	9266848
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0042626	Function	ATPase-coupled transmembrane transporter activity	IBA
GO:0042626	Function	ATPase-coupled transmembrane transporter activity	NAS	9266848
GO:0042760	Process	Very long-chain fatty acid catabolic process	IBA
GO:0042802	Function	Identical protein binding	IPI	27456980
GO:0043190	Component	ATP-binding cassette (ABC) transporter complex	NAS	9266848
GO:0055085	Process	Transmembrane transport	IEA
GO:0055085	Process	Transmembrane transport	NAS	9266848
GO:0140359	Function	ABC-type transporter activity	IEA
GO:1990830	Process	Cellular response to leukemia inhibitory factor	IEA

MIM	HGNC	e!Ensembl
603214	68	ENSG00000119688

O14678

Protein name

Lysosomal cobalamin transporter ABCD4 (EC 7.6.2.8) (ATP-binding cassette sub-family D member 4) (PMP70-related protein) (P70R) (Peroxisomal membrane protein 1-like) (PXMP1-L) (Peroxisomal membrane protein 69) (PMP69)

Protein function

Lysosomal membrane protein that transports cobalamin (Vitamin B12) from the lysosomal lumen to the cytosol in an ATP-dependent manner (PubMed:22922874, PubMed:28572511, PubMed:31467407, PubMed:33845046). Targeted by LMBRD1 lysosomal chaperone fr

PDB

6JBJ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF06472	ABC_membrane_2	27 → 294	ABC transporter transmembrane region 2	Family
PF00005	ABC_tran	404 → 552	ABC transporter	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous.

Sequence

MAVAGPAPGAGARPRLDLQFLQRFLQILKVLFPSWSSQNALMFLTLLCLTLLEQFVIYQV
GLIPSQYYGVLGNKDLEGFKTLTFLAVMLIVLNSTLKSFDQFTCNLLYVSWRKDLTEHLH
RLYFRGRAYYTLNVLRDDIDNPDQRISQDVERFCRQLSSMASKLIISPFTLVYYTYQCFQ
STGWLGPVSIFGYFILGTVVNKTLMGPIVMKLVHQEKLEGDFRFKHMQIRVNAEPAAFYR
AGHVEHMRTDRRLQRLLQTQRELMSKELWLYIGINTFDYLGSILSYVVIAIPIFSGVYGD
LSPAELSTLVSKNAFVCIYLISCFTQLIDLSTTLSDVAGYTHRIGQLRETLLDMSLKSQD
CEILGESEWGLDTPPGWPAAEPADTAFLLERVSISAPSSDKPLIKDLSLKISEGQSLLIT
GNTGTGKTSLLRVLGGLWTSTRGSVQMLTDFGPHGVLFLPQKPFFTDGTLREQVIYPLKE
VYPDSGSADDERILRFLELAGLSNLVARTEGLDQQVDWNWYDVLSPGEMQRLSFARLFYL
QPKYAVLDEATSALTEEVESELYRIGQQLGMTFISVGHRQSLEKFHSLVLKLCGGGRWEL
MRIKVE

Sequence length

606

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cobalamin C disease	Likely pathogenic; Pathogenic	rs776529140, rs745414252, rs142443294, rs1390206641, rs780512428, rs767795583	RCV001844616 RCV002271817 RCV002510420 RCV003226759 RCV003486527 RCV002265867 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Familial cancer of breast	Likely pathogenic	rs142443294	RCV005931998	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Methylmalonic acidemia with homocystinuria, type cblJ	Pathogenic; Likely pathogenic	rs1435760575, rs1440898011, rs776529140, rs745414252, rs1159673131, rs2505333886, rs769364566, rs2505794258, rs769298254, rs1408519111, rs2505338898, rs2505983851, rs2505238680, rs1282760239, rs387907315 View all (3 more)	RCV001380867 RCV002542490 RCV005095315 RCV005008502 RCV003073986 View all (13 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ABCD4-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, CBLJ TYPE	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR SARCOIDOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VITAMIN B 12 DEFICIENCY	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (22)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adrenoleukodystrophy	Adrenoleukodystrophy	BEFREE	15800013, 20661612		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adrenoleukodystrophy	Adrenoleukodystrophy	LHGDN	15800013		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adrenoleukodystrophy	Adrenoleukodystrophy	Pubtator	20661612, 9599016	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Adrenomyeloneuropathy	Adrenomyeloneuropathy	BEFREE	15800013		★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	CTD_human_DG	22294766		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	CTD_human_DG	22294766		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fatigue Syndrome Chronic	Fatigue syndrome	Pubtator	16049284	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Homocystinuria	Homocystinuria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	CTD_human_DG	22922874		★★★★★ ★☆☆☆☆ Found in Text Mining only
Methylmalonic acidemia	Methylmalonic acidemia	Pubtator	28572511	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Methylmalonic acidemia with homocystinuria	Methylmalonic acidemia	Pubtator	34655177	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Methylmalonic acidemia with homocystinuria, type cblJ	Methylmalonic Acidemia With Homocystinuria	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Methylmalonic Aciduria and Homocystinuria CblF Type	Methylmalonic acidemia	Pubtator	33845046	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblJ TYPE	Methylmalonic acidemia with homocystinuria	UNIPROT_DG	22922874		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblJ TYPE	Methylmalonic acidemia with homocystinuria	GENOMICS_ENGLAND_DG	22922874, 23141461, 25234635		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblJ TYPE	Methylmalonic acidemia with homocystinuria	ORPHANET_DG	22922874		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblJ TYPE	Methylmalonic acidemia with homocystinuria	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblJ TYPE	Methylmalonic acidemia with homocystinuria	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neutropenia	Neutropenia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Vitamin B 12 Deficiency	Cobalamin deficiency	CTD_human_DG	22922874		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vitamin B 12 Deficiency	Vitamin b deficiency	Pubtator	22922874	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

ABCD4 (ATP binding cassette subfamily D member 4)