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

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 (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
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 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (10)

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.
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GPD1-related disorder	Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTRIGLYCERIDEMIA, TRANSIENT INFANTILE	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (50)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Brain Infarction	Brain infarction	Pubtator	36529041	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	29254166, 31467232, 9010319		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	22552268, 34657876, 39684297	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	39684297	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	22226083, 40500772	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Ovarian Epithelial	Epithelial ovarian carcinoma	Pubtator	35563509	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	38366633	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	LHGDN	11822825		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	8621016, 8792098, 9070847		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	28944580		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	22226083, 24549054, 28944580		★★★★★ ★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty liver	Pubtator	22226083, 24549054, 33907148	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty Liver	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Fatty Liver Alcoholic	Fatty liver, alcoholic	Pubtator	35450873	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Fibrosis, Liver	Liver Fibrosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	31303549		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	31303549		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	31303549		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hepatic Adenomas Familial	Hepatic adenoma	Pubtator	35365473	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hepatomegaly	Hepatomegaly	Pubtator	24549054, 33907148	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypercholesterolemia	Hypercholesterolemia	BEFREE	8190122		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypercholesterolemia	Hypercholesterolemia	GENOMICS_ENGLAND_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypertriglyceridemia	Hypertriglyceridemia	Pubtator	22226083, 24549054, 29910226, 33907148, 39849455	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
HYPERTRIGLYCERIDEMIA, TRANSIENT INFANTILE	HYPERTRIGLYCERIDEMIA	GENOMICS_ENGLAND_DG	22226083, 24549054		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTRIGLYCERIDEMIA, TRANSIENT INFANTILE	HYPERTRIGLYCERIDEMIA	UNIPROT_DG	22226083, 24549054		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTRIGLYCERIDEMIA, TRANSIENT INFANTILE	HYPERTRIGLYCERIDEMIA	ORPHANET_DG	22226083		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTRIGLYCERIDEMIA, TRANSIENT INFANTILE	HYPERTRIGLYCERIDEMIA	BEFREE	28944580, 29940878		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTRIGLYCERIDEMIA, TRANSIENT INFANTILE	HYPERTRIGLYCERIDEMIA	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTRIGLYCERIDEMIA, TRANSIENT INFANTILE	HYPERTRIGLYCERIDEMIA	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	BEFREE	27368975		★★★★★ ★☆☆☆☆ Found in Text Mining only
Infantile Refsum Disease (disorder)	Infantile Refsum Disease	BEFREE	8730284		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	22226083		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver Cirrhosis	Liver cirrhosis	Pubtator	22226083, 33907148	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	29254166, 31467232, 9010319		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	29254166		★★★★★ ★☆☆☆☆ Found in Text Mining only
Maturity onset diabetes mellitus in young	Mason type diabetes	BEFREE	8621016		★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple congenital anomalies	Multiple Congenital Anomalies	CLINVAR_DG	22226083, 24549054, 28944580		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29254166, 31303549		★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	20404019, 28944580		★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	39849455	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatitis	Pancreatitis	Pubtator	39849455	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Apnea Obstructive	Sleep apnea	Pubtator	20404019	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Apnea, Obstructive	Sleep Apnea	BEFREE	20404019		★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Deprivation	Sleep deprivation	Pubtator	20404019	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Steatohepatitis	Fatty Liver	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Transient infantile hypertriglyceridemia and hepatosteatosis	Transient Hypertriglyceridemia And Hepatosteatosis	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	34657876	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	35836291	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Zellweger Syndrome	Zellweger Syndrome	BEFREE	8730284		★★★★★ ★☆☆☆☆ Found in Text Mining only

GPD1 (glycerol-3-phosphate dehydrogenase 1)