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	2819
Gene name	Glycerol-3-phosphate dehydrogenase 1
Gene symbol	GPD1
Synonyms (NCBI Gene)	GPD-CGPDH-CHTGTI
Chromosome	12
Chromosome location	12q13.12
Summary	This gene encodes a member of the NAD-dependent glycerol-3-phosphate dehydrogenase family. The encoded protein plays a critical role in carbohydrate and lipid metabolism by catalyzing the reversible conversion of dihydroxyacetone phosphate (DHAP) and redu

Show/Hide all (5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs199673455	G>A,C	Pathogenic	Missense variant, coding sequence variant
rs200327418	G>C	Pathogenic	Splice acceptor variant
rs746781699	AA>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555188332	->A	Pathogenic	Frameshift variant, coding sequence variant
rs1592303371	G>A	Likely-pathogenic	Splice donor variant

Show/Hide all (98)

miRTarBase ID	miRNA	Experiments	Reference
MIRT001842	hsa-miR-103a-3p	Luciferase reporter assay	15131085
MIRT530781	hsa-miR-6793-3p	PAR-CLIP	22012620
MIRT530780	hsa-miR-361-3p	PAR-CLIP	22012620
MIRT530779	hsa-miR-3162-3p	PAR-CLIP	22012620
MIRT530778	hsa-miR-6752-3p	PAR-CLIP	22012620
MIRT530777	hsa-miR-5088-3p	PAR-CLIP	22012620
MIRT530776	hsa-miR-18a-3p	PAR-CLIP	22012620
MIRT530775	hsa-miR-18b-3p	PAR-CLIP	22012620
MIRT530774	hsa-miR-4757-5p	PAR-CLIP	22012620
MIRT530773	hsa-miR-6744-3p	PAR-CLIP	22012620
MIRT530772	hsa-miR-515-5p	PAR-CLIP	22012620
MIRT530771	hsa-miR-519e-5p	PAR-CLIP	22012620
MIRT530770	hsa-miR-3157-3p	PAR-CLIP	22012620
MIRT530781	hsa-miR-6793-3p	PAR-CLIP	22012620
MIRT530780	hsa-miR-361-3p	PAR-CLIP	22012620
MIRT530779	hsa-miR-3162-3p	PAR-CLIP	22012620
MIRT530778	hsa-miR-6752-3p	PAR-CLIP	22012620
MIRT530777	hsa-miR-5088-3p	PAR-CLIP	22012620
MIRT530776	hsa-miR-18a-3p	PAR-CLIP	22012620
MIRT530775	hsa-miR-18b-3p	PAR-CLIP	22012620
MIRT530774	hsa-miR-4757-5p	PAR-CLIP	22012620
MIRT530773	hsa-miR-6744-3p	PAR-CLIP	22012620
MIRT530772	hsa-miR-515-5p	PAR-CLIP	22012620
MIRT530771	hsa-miR-519e-5p	PAR-CLIP	22012620
MIRT530770	hsa-miR-3157-3p	PAR-CLIP	22012620
MIRT1028810	hsa-miR-1197	CLIP-seq
MIRT1028811	hsa-miR-1224-5p	CLIP-seq
MIRT1028812	hsa-miR-1270	CLIP-seq
MIRT1028813	hsa-miR-1289	CLIP-seq
MIRT1028814	hsa-miR-217	CLIP-seq
MIRT1028815	hsa-miR-3128	CLIP-seq
MIRT1028816	hsa-miR-3192	CLIP-seq
MIRT1028817	hsa-miR-3198	CLIP-seq
MIRT1028818	hsa-miR-3690	CLIP-seq
MIRT1028819	hsa-miR-3936	CLIP-seq
MIRT1028820	hsa-miR-4254	CLIP-seq
MIRT1028821	hsa-miR-4257	CLIP-seq
MIRT1028822	hsa-miR-4270	CLIP-seq
MIRT1028823	hsa-miR-4292	CLIP-seq
MIRT1028824	hsa-miR-4294	CLIP-seq
MIRT1028825	hsa-miR-4303	CLIP-seq
MIRT1028826	hsa-miR-4308	CLIP-seq
MIRT1028827	hsa-miR-4309	CLIP-seq
MIRT1028828	hsa-miR-4441	CLIP-seq
MIRT1028829	hsa-miR-4470	CLIP-seq
MIRT1028830	hsa-miR-4649-3p	CLIP-seq
MIRT1028831	hsa-miR-4651	CLIP-seq
MIRT1028832	hsa-miR-4683	CLIP-seq
MIRT1028833	hsa-miR-4720-5p	CLIP-seq
MIRT1028834	hsa-miR-4751	CLIP-seq
MIRT1028835	hsa-miR-4762-3p	CLIP-seq
MIRT1028836	hsa-miR-4799-3p	CLIP-seq
MIRT1028837	hsa-miR-608	CLIP-seq
MIRT1028838	hsa-miR-620	CLIP-seq
MIRT1028839	hsa-miR-767-3p	CLIP-seq
MIRT2005218	hsa-miR-2114	CLIP-seq
MIRT2005219	hsa-miR-2116	CLIP-seq
MIRT2005220	hsa-miR-2467-3p	CLIP-seq
MIRT2005221	hsa-miR-3150a-3p	CLIP-seq
MIRT2005222	hsa-miR-3175	CLIP-seq
MIRT2005223	hsa-miR-3909	CLIP-seq
MIRT1028819	hsa-miR-3936	CLIP-seq
MIRT1028823	hsa-miR-4292	CLIP-seq
MIRT1028826	hsa-miR-4308	CLIP-seq
MIRT2005224	hsa-miR-4667-3p	CLIP-seq
MIRT2005225	hsa-miR-4667-5p	CLIP-seq
MIRT2005226	hsa-miR-4677-5p	CLIP-seq
MIRT2005227	hsa-miR-4700-5p	CLIP-seq
MIRT2005228	hsa-miR-483-3p	CLIP-seq
MIRT2005229	hsa-miR-939	CLIP-seq
MIRT1028813	hsa-miR-1289	CLIP-seq
MIRT2005218	hsa-miR-2114	CLIP-seq
MIRT2237903	hsa-miR-2964a-5p	CLIP-seq
MIRT2005221	hsa-miR-3150a-3p	CLIP-seq
MIRT2005222	hsa-miR-3175	CLIP-seq
MIRT1028817	hsa-miR-3198	CLIP-seq
MIRT1028819	hsa-miR-3936	CLIP-seq
MIRT1028822	hsa-miR-4270	CLIP-seq
MIRT1028823	hsa-miR-4292	CLIP-seq
MIRT1028824	hsa-miR-4294	CLIP-seq
MIRT1028826	hsa-miR-4308	CLIP-seq
MIRT1028827	hsa-miR-4309	CLIP-seq
MIRT1028828	hsa-miR-4441	CLIP-seq
MIRT1028831	hsa-miR-4651	CLIP-seq
MIRT2005225	hsa-miR-4667-5p	CLIP-seq
MIRT2005227	hsa-miR-4700-5p	CLIP-seq
MIRT2237904	hsa-miR-4708-3p	CLIP-seq
MIRT2237905	hsa-miR-4723-5p	CLIP-seq
MIRT2237906	hsa-miR-519a	CLIP-seq
MIRT2237907	hsa-miR-519b-3p	CLIP-seq
MIRT2237908	hsa-miR-519c-3p	CLIP-seq
MIRT1028837	hsa-miR-608	CLIP-seq
MIRT2005229	hsa-miR-939	CLIP-seq
MIRT2005221	hsa-miR-3150a-3p	CLIP-seq
MIRT2005222	hsa-miR-3175	CLIP-seq
MIRT2005225	hsa-miR-4667-5p	CLIP-seq
MIRT2005227	hsa-miR-4700-5p	CLIP-seq
MIRT2005229	hsa-miR-939	CLIP-seq

Show/Hide all (23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005975	Process	Carbohydrate metabolic process	IEA
GO:0006072	Process	Glycerol-3-phosphate metabolic process	IBA
GO:0006072	Process	Glycerol-3-phosphate metabolic process	IEA
GO:0006072	Process	Glycerol-3-phosphate metabolic process	IEA
GO:0006094	Process	Gluconeogenesis	IEA
GO:0006127	Process	Glycerol-3-phosphate shuttle	IEA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0016616	Function	Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	IEA
GO:0042803	Function	Protein homodimerization activity	IEA
GO:0045821	Process	Positive regulation of glycolytic process	IEA
GO:0046168	Process	Glycerol-3-phosphate catabolic process	IEA
GO:0047952	Function	Glycerol-3-phosphate dehydrogenase [NAD(P)+] activity	IBA
GO:0051287	Function	NAD binding	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0071320	Process	Cellular response to cAMP	IEA
GO:0071356	Process	Cellular response to tumor necrosis factor	IEA
GO:0141152	Function	Glycerol-3-phosphate dehydrogenase (NAD+) activity	IEA
GO:0141152	Function	Glycerol-3-phosphate dehydrogenase (NAD+) activity	TAS	7772607

MIM	HGNC	e!Ensembl
138420	4455	ENSG00000167588

P21695

Protein name

Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic (GPD-C) (GPDH-C) (EC 1.1.1.8)

Protein function

Has glycerol-3-phosphate dehydrogenase activity.

PDB

1WPQ , 1X0V , 1X0X , 6E8Y , 6E8Z , 6E90 , 6PYP

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01210	NAD_Gly3P_dh_N	5 → 174	NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus	Family
PF07479	NAD_Gly3P_dh_C	193 → 340	NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in liver (at protein level). {ECO:0000269|PubMed:7772607}.

Sequence

MASKKVCIVGSGNWGSAIAKIVGGNAAQLAQFDPRVTMWVFEEDIGGKKLTEIINTQHEN
VKYLPGHKLPPNVVAVPDVVQAAEDADILIFVVPHQFIGKICDQLKGHLKANATGISLIK
GVDEGPNGLKLISEVIGERLGIPMSVLMGANIASEVADEKFCETTIGCKDPAQGQLLKEL
MQTPNFRITVVQEVDTVEICGALKNVVAVGAGFCDGLGFGDNTKAAVIRLGLMEMIAFAK
LFCSGPVSSATFLESCGVADLITTCYGGRNRKVAEAFARTGKSIEQLEKELLNGQKLQGP
ETARELYSILQHKGLVDKFPLFMAVYKVCYEGQPVGEFIHCLQNHPEHM

Sequence length

349

Interactions

View interactions

	KEGG		Reactome
	Glycerophospholipid metabolism		Synthesis of PA

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Transient infantile hypertriglyceridemia and hepatosteatosis	Likely pathogenic; Pathogenic	rs2137920303, rs199673455, rs2137920321, rs369575243, rs1950990228, rs2539528280, rs200327418, rs1592303371	RCV001542683 RCV000144887 RCV002251093 RCV004573501 RCV004573502 RCV004573504 RCV000022593 RCV000991446

Show/Hide Unknown Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs35256655	RCV005918651
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	rs2539529835	RCV004560297
Gastric cancer	Conflicting classifications of pathogenicity	rs35256655	RCV005918652
GPD1-related disorder	Conflicting classifications of pathogenicity; Benign; Likely benign	rs146239968, rs2232207, rs761342764, rs148598781, rs750177685, rs2232202, rs34013306, rs35428353, rs34783513, rs201027631, rs200453933, rs143492152, rs376214632	RCV004756212 RCV004756271 RCV003416615 RCV003926670 RCV003929440 RCV003908266 RCV003908202 RCV003413697 RCV003920406 RCV003948178 RCV003955692 RCV003932930 RCV003977999
Lung cancer	Conflicting classifications of pathogenicity	rs35256655	RCV005918655
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	rs35256655	RCV005918649
Melanoma	Conflicting classifications of pathogenicity	rs35256655	RCV005918654
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity	rs35256655	RCV005918650
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs35256655	RCV005918653

Show/Hide Text Mining Associations (23)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Brain Infarction	Associate	36529041
Breast Neoplasms	Associate	22552268, 34657876, 39684297
Carcinogenesis	Associate	39684297
Carcinoma Hepatocellular	Associate	22226083, 40500772
Carcinoma Ovarian Epithelial	Associate	35563509
Carcinoma Pancreatic Ductal	Associate	38366633
Fatty Liver	Associate	22226083, 24549054, 33907148
Fatty Liver Alcoholic	Associate	35450873
Glyceraldehyde 3 phosphate dehydrogenase deficiency	Associate	35450873
Hepatic Adenomas Familial	Associate	35365473
Hepatomegaly	Associate	24549054, 33907148
Hypertriglyceridemia	Associate	22226083, 24549054, 29910226, 33907148, 39849455
Jaundice	Associate	33907148
Liver Cirrhosis	Associate	22226083, 33907148
Neoplasms	Inhibit	22552268, 35836291
Neoplasms	Associate	35563509, 39684297
Obesity	Associate	39849455
Pancreatitis	Associate	39849455
Refsum Disease Infantile	Associate	8730284
Sleep Apnea Obstructive	Associate	20404019
Sleep Deprivation	Stimulate	20404019
Triple Negative Breast Neoplasms	Associate	34657876
Urinary Bladder Neoplasms	Inhibit	35836291

GPD1 (glycerol-3-phosphate dehydrogenase 1)