Gene Gene information from NCBI Gene database. Download as csv Download as pdf
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

6 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

89 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

39 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

KEGG Pathway	Reactome Pathway
ABC transporters	Cobalamin (Cbl, vitamin B12) transport and metabolism
Peroxisome	Defective ABCD4 causes methylmalonic aciduria and homocystinuria, cblj type (MAHCJ)
Vitamin digestion and absorption
Cobalamin transport and metabolism

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)

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)

Phenotype Name	Clinical Significance	Source	Reference	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. Show/Hide Unknown Diseases (16)
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	22294766	★★★★★ ★★☆☆☆ 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	32141793	★★★★★ ★★☆☆☆ 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	22922874	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining Show/Hide Text Mining Associations (22)
Adrenoleukodystrophy	Adrenoleukodystrophy	LHGDN	15800013		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adrenoleukodystrophy	Adrenoleukodystrophy	BEFREE	15800013, 20661612		★★★★★ ★☆☆☆☆ 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	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	UNIPROT_DG	22922874		★★★★★ ★★☆☆☆ 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
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblJ TYPE	Methylmalonic acidemia with homocystinuria	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neutropenia	Neutropenia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Vitamin B 12 Deficiency	Vitamin b deficiency	Pubtator	22922874	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vitamin B 12 Deficiency	Cobalamin deficiency	CTD_human_DG	22922874		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
LMBRD1	3	["Cobalamin c disease","Intracellular cobalamin metabolism disorder","Methylmalonic acidemia"]	3	["Vitamin digestion and absorption","Cobalamin transport and metabolism","Cobalamin (Cbl, vitamin B12) transport and metabolism"]	9	["Disgenet (Cobalamin c disease)","ClinVar (Intracellular cobalamin metabolism disorder)","CTD (Methylmalonic acidemia)","Disgenet (Methylmalonic acidemia)","ClinGen (Methylmalonic acidemia)","ClinVar (Methylmalonic acidemia)","GWAS catalog (Methylmalonic acidemia)","Orphanet (Methylmalonic acidemia)","HPO (Methylmalonic acidemia)"]
MMADHC	3	["Cobalamin c disease","Intracellular cobalamin metabolism disorder","Methylmalonic acidemia"]	2	["Cobalamin transport and metabolism","Cobalamin (Cbl, vitamin B12) transport and metabolism"]	7	["Disgenet (Cobalamin c disease)","ClinVar (Intracellular cobalamin metabolism disorder)","CTD (Methylmalonic acidemia)","Disgenet (Methylmalonic acidemia)","ClinVar (Methylmalonic acidemia)","Orphanet (Methylmalonic acidemia)","HPO (Methylmalonic acidemia)"]
MMACHC	3	["Cobalamin c disease","Intracellular cobalamin metabolism disorder","Methylmalonic acidemia"]	3	["Vitamin digestion and absorption","Cobalamin transport and metabolism","Cobalamin (Cbl, vitamin B12) transport and metabolism"]	4	["Disgenet (Cobalamin c disease)","ClinVar (Intracellular cobalamin metabolism disorder)","CTD (Methylmalonic acidemia)","Disgenet (Methylmalonic acidemia)"]
CD320	2	["Methylmalonic acidemia","Vitamin b deficiency"]	2	["Cobalamin transport and metabolism","Cobalamin (Cbl, vitamin B12) transport and metabolism"]	7	["CTD (Methylmalonic acidemia)","Disgenet (Methylmalonic acidemia)","ClinGen (Methylmalonic acidemia)","ClinVar (Methylmalonic acidemia)","GWAS catalog (Methylmalonic acidemia)","Orphanet (Methylmalonic acidemia)","HPO (Methylmalonic acidemia)"]
MMAA	2	["Methylmalonic acidemia","Vitamin b deficiency"]	2	["Cobalamin transport and metabolism","Cobalamin (Cbl, vitamin B12) transport and metabolism"]	6	["CTD (Methylmalonic acidemia)","Disgenet (Methylmalonic acidemia)","ClinGen (Methylmalonic acidemia)","ClinVar (Methylmalonic acidemia)","Orphanet (Methylmalonic acidemia)","HPO (Methylmalonic acidemia)"]

ABCD4 (ATP binding cassette subfamily D member 4)

Save This Analysis