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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	8813
Gene name	Dolichyl-phosphate mannosyltransferase subunit 1, catalytic
Gene symbol	DPM1
Synonyms (NCBI Gene)	CDGIEMPDS
Chromosome	20
Chromosome location	20q13.13
Summary	Dolichol-phosphate mannose (Dol-P-Man) serves as a donor of mannosyl residues on the lumenal side of the endoplasmic reticulum (ER). Lack of Dol-P-Man results in defective surface expression of GPI-anchored proteins. Dol-P-Man is synthesized from GDP-mann

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121908583	G>A,C,T	Pathogenic	Coding sequence variant, synonymous variant, stop gained, non coding transcript variant, missense variant
rs587777115	A>T	Pathogenic	Intron variant
rs1272097668	ATGTAGTTTCCTG>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant

Show/Hide all (32)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029861	hsa-miR-26b-5p	Microarray	19088304
MIRT042406	hsa-miR-18b-5p	CLASH	23622248
MIRT1979536	hsa-miR-203	CLIP-seq
MIRT1979537	hsa-miR-300	CLIP-seq
MIRT1979538	hsa-miR-3646	CLIP-seq
MIRT1979539	hsa-miR-381	CLIP-seq
MIRT1979540	hsa-miR-4282	CLIP-seq
MIRT1979541	hsa-miR-4666-3p	CLIP-seq
MIRT1979542	hsa-miR-4717-5p	CLIP-seq
MIRT1979543	hsa-miR-4789-5p	CLIP-seq
MIRT1979544	hsa-miR-490-3p	CLIP-seq
MIRT1979545	hsa-miR-649	CLIP-seq
MIRT1979546	hsa-miR-891b	CLIP-seq
MIRT1979547	hsa-miR-944	CLIP-seq
MIRT2214629	hsa-miR-1178	CLIP-seq
MIRT2214630	hsa-miR-146a	CLIP-seq
MIRT2214631	hsa-miR-146b-5p	CLIP-seq
MIRT1979536	hsa-miR-203	CLIP-seq
MIRT2214632	hsa-miR-3120-3p	CLIP-seq
MIRT1979538	hsa-miR-3646	CLIP-seq
MIRT2214633	hsa-miR-3647-3p	CLIP-seq
MIRT2214634	hsa-miR-3662	CLIP-seq
MIRT2214635	hsa-miR-4461	CLIP-seq
MIRT2214636	hsa-miR-4698	CLIP-seq
MIRT1979544	hsa-miR-490-3p	CLIP-seq
MIRT2214637	hsa-miR-545	CLIP-seq
MIRT2214638	hsa-miR-548ad	CLIP-seq
MIRT2214639	hsa-miR-548p	CLIP-seq
MIRT2214640	hsa-miR-570	CLIP-seq
MIRT2214641	hsa-miR-580	CLIP-seq
MIRT2214642	hsa-miR-589	CLIP-seq
MIRT1979545	hsa-miR-649	CLIP-seq

Show/Hide all (38)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004582	Function	Dolichyl-phosphate beta-D-mannosyltransferase activity	EXP	10835346
GO:0004582	Function	Dolichyl-phosphate beta-D-mannosyltransferase activity	IBA
GO:0004582	Function	Dolichyl-phosphate beta-D-mannosyltransferase activity	IDA	9535917, 10835346
GO:0004582	Function	Dolichyl-phosphate beta-D-mannosyltransferase activity	IEA
GO:0004582	Function	Dolichyl-phosphate beta-D-mannosyltransferase activity	IGI	16280320
GO:0005515	Function	Protein binding	IPI	10835346, 10944123, 16280320, 23856421, 25416956, 25910212, 32296183
GO:0005537	Function	D-mannose binding	IEA
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005783	Component	Endoplasmic reticulum	IDA	9724629
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	9724629
GO:0005789	Component	Endoplasmic reticulum membrane	NAS	9724629
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006486	Process	Protein glycosylation	IEA
GO:0006488	Process	Dolichol-linked oligosaccharide biosynthetic process	IBA
GO:0006506	Process	GPI anchor biosynthetic process	IBA
GO:0006506	Process	GPI anchor biosynthetic process	IDA	9535917, 9724629
GO:0006506	Process	GPI anchor biosynthetic process	IDA	9535917
GO:0006506	Process	GPI anchor biosynthetic process	IEA
GO:0006506	Process	GPI anchor biosynthetic process	IEA
GO:0006506	Process	GPI anchor biosynthetic process	IGI	16280320
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IDA	9535917
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0018279	Process	Protein N-linked glycosylation via asparagine	TAS
GO:0019673	Process	GDP-mannose metabolic process	IEA
GO:0033185	Component	Dolichol-phosphate-mannose synthase complex	IDA	9724629, 10835346
GO:0033185	Component	Dolichol-phosphate-mannose synthase complex	IPI	10835346
GO:0035269	Process	Protein O-linked glycosylation via mannose	IBA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IDA	9535917
GO:0043178	Function	Alcohol binding	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0046872	Function	Metal ion binding	ISS
GO:0070482	Process	Response to oxygen levels	IEA
GO:0180047	Process	Dolichol phosphate mannose biosynthetic process	IDA	10835346
GO:0180047	Process	Dolichol phosphate mannose biosynthetic process	ISS

MIM	HGNC	e!Ensembl
603503	3005	ENSG00000000419

O60762

Protein name

Dolichol-phosphate mannosyltransferase subunit 1 (EC 2.4.1.83) (Dolichol-phosphate mannose synthase subunit 1) (DPM synthase subunit 1) (Dolichyl-phosphate beta-D-mannosyltransferase subunit 1) (Mannose-P-dolichol synthase subunit 1) (MPD synthase subunit

Protein function

Transfers mannose from GDP-mannose to dolichol monophosphate to form dolichol phosphate mannose (Dol-P-Man) which is the mannosyl donor in pathways leading to N-glycosylation, glycosyl phosphatidylinositol membrane anchoring, and O-mannosylation

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00535	Glycos_transf_2	28 → 199	Glycosyl transferase family 2	Family

Sequence

MASLEVSRSPRRSRRELEVRSPRQNKYSVLLPTYNERENLPLIVWLLVKSFSESGINYEI
IIIDDGSPDGTRDVAEQLEKIYGSDRILLRPREKKLGLGTAYIHGMKHATGNYIIIMDAD
LSHHPKFIPEFIRKQKEGNFDIVSGTRYKGNGGVYGWDLKRKIISRGANFLTQILLRPGA
SDLTGSFRLYRKEVLEKLIEKCVSKGYVFQMEMIVRARQLNYTIGEVPISFVDRVYGESK
LGGNEIVSFLKGLLTLFATT

Sequence length

260

Interactions

View interactions

	KEGG		Reactome
	N-Glycan biosynthesis Metabolic pathways		Synthesis of dolichyl-phosphate mannose Defective DPM1 causes DPM1-CDG (CDG-1e) Defective DPM3 causes DPM3-CDG (CDG-1o) Defective DPM2 causes DPM2-CDG (CDG-1u)

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
Congenital disorder of glycosylation type 1E	Likely pathogenic; Pathogenic	rs587777114, rs587777115, rs587777116, rs2123115725, rs759278634, rs1324743951, rs1350257432, rs2515710056, rs2515710157, rs121908583, rs1568757730, rs777816615, rs753780084, rs1272097668, rs139624629, rs781115721 View all (1 more)	RCV000087034 RCV000087035 RCV000087036 RCV001420139 RCV001970123 View all (11 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
DPM1-related disorder	Pathogenic	rs121908583	RCV004757948	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Malignant tumor of urinary bladder	Pathogenic	rs753780084	RCV005896766	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (20)

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.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation	Benign; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IE	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDERS OF GLYCOSYLATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (29)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alzheimer Disease	Alzheimer disease	Pubtator	36405716	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Antithrombin III Deficiency	Antithrombin Deficiency	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Central visual impairment	Central Visual Impairment	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Camptodactyly	Congenital Camptodactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital disorder of glycosylation type 1q	Congenital Disorder Of Glycosylation	GENOMICS_ENGLAND_DG	10642597		★★★★★ ★☆☆☆☆ Found in Text Mining only
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ie	Congenital disorder of glycosylation	UNIPROT_DG	10642597, 10642602, 15669674, 23856421		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ie	Congenital disorder of glycosylation	GENOMICS_ENGLAND_DG	10642602, 15669674, 23856421, 27604308		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ie	Congenital disorder of glycosylation	BEFREE	15669674, 16641202, 23856421		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ie	Congenital disorder of glycosylation	CLINVAR_DG	23856421, 26729507		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ie	Congenital disorder of glycosylation	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	10642597, 23856421, 28743912		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	Pubtator	10642597, 23856421, 24243557, 36579437	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	GENOMICS_ENGLAND_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital muscular dystrophy (disorder)	Congenital muscular dystrophy	BEFREE	23856421		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	30092360		★★★★★ ★☆☆☆☆ Found in Text Mining only
DPM1-CDG	Congenital Disorder Of Glycosylation	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemangioma	Hemangioma	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
NAIL DISORDER, NONSYNDROMIC CONGENITAL, 9	Nail Diseases	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nail dysplasia	Nail dysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	19931263	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Protein C Deficiency	Protein C Deficiency	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

DPM1 (dolichyl-phosphate mannosyltransferase subunit 1, catalytic)