DPM3 (dolichyl-phosphate mannosyltransferase subunit 3, regulatory)

Gene

• Entrez ID: 54344
• Gene name: Dolichyl-phosphate mannosyltransferase subunit 3, regulatory
• Gene symbol: DPM3
• Synonyms (NCBI Gene): CDG1O, MDDGB15, MDDGC15
• Chromosome: 1
• Chromosome location: 1q22
• 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
rs121908155	A>G,T	Pathogenic	Stop gained, missense variant, coding sequence variant
rs745692004	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs1057518905	A>T	Likely-pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT040333	hsa-miR-615-3p	CLASH	23622248
MIRT944130	hsa-miR-149	CLIP-seq
MIRT944131	hsa-miR-3153	CLIP-seq
MIRT944132	hsa-miR-3170	CLIP-seq
MIRT944133	hsa-miR-3202	CLIP-seq
MIRT944134	hsa-miR-3689a-3p	CLIP-seq
MIRT944135	hsa-miR-3689c	CLIP-seq
MIRT944136	hsa-miR-3929	CLIP-seq
MIRT944137	hsa-miR-4419b	CLIP-seq
MIRT944138	hsa-miR-4446-3p	CLIP-seq
MIRT944139	hsa-miR-4476	CLIP-seq
MIRT944140	hsa-miR-4478	CLIP-seq
MIRT944141	hsa-miR-4506	CLIP-seq
MIRT944142	hsa-miR-4668-5p	CLIP-seq
MIRT944143	hsa-miR-4675	CLIP-seq
MIRT944144	hsa-miR-4728-5p	CLIP-seq
MIRT944145	hsa-miR-4741	CLIP-seq
MIRT944146	hsa-miR-760	CLIP-seq
MIRT944147	hsa-miR-892b	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	10835346, 10944123, 23856421, 32296183
GO:0005783	Component	Endoplasmic reticulum	IDA	10835346
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	10835346
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	NAS	9724629
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006486	Process	Protein glycosylation	IEA
GO:0008047	Function	Enzyme activator activity	IDA	10835346
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0033185	Component	Dolichol-phosphate-mannose synthase complex	IBA
GO:0033185	Component	Dolichol-phosphate-mannose synthase complex	IDA	10835346
GO:0033185	Component	Dolichol-phosphate-mannose synthase complex	IPI	10835346
GO:0035269	Process	Protein O-linked glycosylation via mannose	ISS
GO:0160214	Function	Endoplasmic reticulum-plasma membrane adaptor activity	ISS
GO:0180047	Process	Dolichol phosphate mannose biosynthetic process	IDA	10835346

Other IDs

• MIM: 605951
• HGNC: 3007
• e!Ensembl: ENSG00000179085

Protein

• UniProt ID: Q9P2X0
• Protein name: Dolichol-phosphate mannosyltransferase subunit 3 (Dolichol-phosphate mannose synthase subunit 3) (DPM synthase subunit 3) (Dolichyl-phosphate beta-D-mannosyltransferase subunit 3) (Mannose-P-dolichol synthase subunit 3) (MPD synthase subunit 3) (Prostin-1
• Protein function: Stabilizer subunit of the dolichol-phosphate mannose (DPM) synthase complex; tethers catalytic subunit DPM1 to the endoplasmic reticulum.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08285	DPM3	1 → 91	Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)	Family

• Sequence:

  MTKLAQWLWGLAILGSTWVALTTGALGLELPLSCQEVLWPLPAYLLVSAGCYALGTVGYR
  VATFHDCEDAARELQSQIQEARADLARRGLRF

• Sequence length: 92

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
Cardiomyopathy	Likely pathogenic	rs1057518905	RCV000415253
DPM3-congenital disorder of glycosylation	Pathogenic; Likely pathogenic	rs1557794919, rs2102491600, rs749000879, rs121908155, rs2526669183, rs2526669346, rs2526668106, rs778481307, rs1444066075, rs745692004	RCV001370472 RCV001387278 RCV001985353 RCV000004967 RCV002786684 RCV002908626 RCV003503280 RCV000709623 RCV000815313 RCV000855549 RCV000855545
EMG: myopathic abnormalities	Likely pathogenic	rs1057518905	RCV000415253
Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 15	Likely pathogenic; Pathogenic	rs745692004, rs121908155	RCV001254824 RCV001254823
Myopathy	Likely pathogenic	rs1057518905	RCV000415253

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
DPM3-related disorder	Conflicting classifications of pathogenicity	rs193215070	RCV003949970

Associations from Text Mining
Disease Name	Relationship Type	References
Cardiomyopathies	Associate	35932216
Congenital Disorder Of Glycosylation Type Im	Associate	19576565
Congenital Disorders of Glycosylation	Associate	19576565
Intellectual Disability	Associate	35932216
Leukoencephalopathies	Associate	35932216
Muscle Neoplasms	Associate	35932216
Muscular Diseases	Associate	35932216
Muscular Dystrophies	Associate	19576565
Seizures	Associate	35932216
Walker Warburg Syndrome	Associate	19576565, 30060766, 35932216