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

330

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
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
Familial cancer of breast	Likely pathogenic	rs142443294	RCV005931998
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 RCV002643150 RCV000030861 RCV003445415 RCV003531448 RCV003534209 RCV003531775 RCV003648160 RCV003648439 RCV003873123 RCV000030860 RCV000030862 RCV000707417 RCV001254054

Show/Hide Unknown Diseases (12)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
ABCD4-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	rs142443294, rs745487022, rs557254765, rs767735716, rs147795328, rs45568335, rs141868117, rs373949463, rs188108983, rs370270229, rs370581068, rs542032495, rs747273884	RCV003904375 RCV003941419 RCV003961441 RCV003971766 RCV003902599 RCV004758013 RCV003959901 RCV003902727 RCV003927971 RCV003928023 RCV003945506 RCV003938183 RCV003903140
Acute myeloid leukemia	Benign	rs74063831, rs144451801	RCV005921844 RCV005896418
Clear cell carcinoma of kidney	Likely benign; Benign	rs138862492, rs11845976	RCV005921326 RCV005896410
Gastric cancer	Benign; Likely benign	rs74063831, rs138862492, rs11845976, rs144451801	RCV005921845 RCV005921327 RCV005896411 RCV005896420
Lung cancer	Benign	rs144451801	RCV005896424
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	rs151116417	RCV005901704
Ovarian serous cystadenocarcinoma	Benign	rs11845976, rs144451801	RCV005896412 RCV005896421
Sarcoma	Benign	rs144451801	RCV005896419
Thymoma	Benign	rs144451801	RCV005896423
Thyroid cancer, nonmedullary, 1	Likely benign; Benign	rs138862492, rs11845976	RCV005921329 RCV005896413
Uterine carcinosarcoma	Likely benign; Benign	rs138862492, rs144451801	RCV005921328 RCV005896422
Uterine corpus endometrial carcinoma	Benign	rs144451801	RCV005896425

Show/Hide Text Mining Associations (7)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adrenoleukodystrophy	Associate	20661612, 9599016
Fatigue Syndrome Chronic	Associate	16049284
Methylmalonic acidemia	Associate	28572511
Methylmalonic acidemia with homocystinuria	Associate	34655177
Methylmalonic Aciduria and Homocystinuria CblF Type	Associate	33845046
Muscle Hypotonia	Associate	28572511
Vitamin B 12 Deficiency	Associate	22922874

ABCD4 (ATP binding cassette subfamily D member 4)