DPM1 (dolichyl-phosphate mannosyltransferase subunit 1, catalytic)

Gene

• Entrez ID: 8813
• Gene name: Dolichyl-phosphate mannosyltransferase subunit 1, catalytic
• Gene symbol: DPM1
• Synonyms (NCBI Gene): CDGIE, MPDS
• 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

SNPs

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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 603503
• HGNC: 3005
• e!Ensembl: ENSG00000000419

Protein

• UniProt ID: 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

Pathways

KEGG:

N-Glycan biosynthesis
Metabolic pathways

Reactome:

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)

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
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	RCV000087034 RCV000087035 RCV000087036 RCV001420139 RCV001970123 RCV001982510 RCV001939620 RCV002797005 RCV002858120 RCV000006676 RCV000006678 RCV003508225 RCV000541426 RCV000691834 RCV000821507 RCV001063137
DPM1-related disorder	Pathogenic	rs121908583	RCV004757948
Malignant tumor of urinary bladder	Pathogenic	rs753780084	RCV005896766

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Benign	rs60224379	RCV005886433
Cervical cancer	Benign	rs60224379	RCV005886435
Cholangiocarcinoma	Benign	rs60224379	RCV005886440
Clear cell carcinoma of kidney	Uncertain significance	rs559946698	RCV005901605
Congenital disorder of glycosylation	Benign; Likely benign; Uncertain significance	rs11480415, rs146262101	RCV000375652 RCV000388420 RCV000349084
Familial cancer of breast	Benign	rs60224379	RCV005886432
Gastric cancer	Benign	rs60224379	RCV005886438
Intellectual disability	Likely benign	rs1985883778	RCV001251751
Lung cancer	Benign	rs60224379	RCV005886441
Malignant lymphoma, large B-cell, diffuse	Benign	rs60224379	RCV005886436
Malignant tumor of esophagus	Benign	rs60224379	RCV005886434
Melanoma	Uncertain significance	rs559946698	RCV005901606
Ovarian serous cystadenocarcinoma	Benign	rs60224379	RCV005886439
Sarcoma	Benign	rs60224379	RCV005886437
Uterine corpus endometrial carcinoma	Benign	rs60224379	RCV005886442

Associations from Text Mining
Disease Name	Relationship Type	References
Altitude Sickness	Associate	32299499
Alzheimer Disease	Associate	36405716
Congenital Disorders of Glycosylation	Associate	10642597, 23856421, 24243557, 36579437
Gerstmann Straussler Scheinker Disease	Associate	36579437
Myasthenic Syndrome Congenital Ie	Associate	10642597
Pancreatic Neoplasms	Associate	19931263
Walker Warburg Syndrome	Associate	23856421, 35932216