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	54344
Gene name	Dolichyl-phosphate mannosyltransferase subunit 3, regulatory
Gene symbol	DPM3
Synonyms (NCBI Gene)	CDG1OMDDGB15MDDGC15
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

Show/Hide all (3)

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

Show/Hide all (19)

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

Show/Hide all (18)

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

MIM	HGNC	e!Ensembl
605951	3007	ENSG00000179085

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

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 (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cardiomyopathy	Likely pathogenic	rs1057518905	RCV000415253	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
DPM3-congenital disorder of glycosylation	Pathogenic; Likely pathogenic	rs1557794919, rs2102491600, rs749000879, rs121908155, rs2526669183, rs2526669346, rs2526668106, rs778481307, rs1444066075, rs745692004	RCV001370472 RCV001387278 RCV001985353 RCV000004967 RCV002786684 View all (6 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
EMG: myopathic abnormalities	Likely pathogenic	rs1057518905	RCV000415253	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 15	Likely pathogenic; Pathogenic	rs745692004, rs121908155	RCV001254824 RCV001254823	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Myopathy	Likely pathogenic	rs1057518905	RCV000415253	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (6)

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.
CARDIOMYOPATHIES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IO	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DPM3-related disorder	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★★★★ ★★☆☆☆ 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

Show/Hide Text Mining Associations (22)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
alpha-Dystroglycanopathies	alpha-Dystroglycanopathy	BEFREE	31266720		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carbohydrate deficient glycoprotein syndrome type 1o	Congenital disorder of glycosylation	GENOMICS_ENGLAND_DG	28357185		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	BEFREE	28803818		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cardiomyopathies	Cardiomyopathy	Pubtator	35932216	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cardiomyopathies	Cardiomyopathy	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cardiomyopathy, Dilated	Cardiomyopathy	BEFREE	31266720		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Dilated	Cardiomyopathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Disorder Of Glycosylation Type Im	Congenital disorder of glycosylation	Pubtator	19576565	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Disorder of Glycosylation, Type Io	Congenital disorder of glycosylation	GENOMICS_ENGLAND_DG	10835346, 19576565, 28803818		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorder of Glycosylation, Type Io	Congenital disorder of glycosylation	UNIPROT_DG	19576565		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorder of Glycosylation, Type Io	Congenital disorder of glycosylation	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorder of Glycosylation, Type Io	Congenital disorder of glycosylation	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	19576565, 30931530, 31266720		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	Pubtator	19576565	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
DPM3-CDG	Congenital Disorder Of Glycosylation	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	35932216	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	GENOMICS_ENGLAND_DG	19576565		★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	BEFREE	28803818, 31266720		★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Myopathy	Myopathy	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Prostatic Neoplasms	Prostatic Neoplasms	BEFREE	11420690		★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	35932216	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

DPM3 (dolichyl-phosphate mannosyltransferase subunit 3, regulatory)