FDPS (farnesyl diphosphate synthase)

Gene

• Entrez ID: 2224
• Gene name: Farnesyl diphosphate synthase
• Gene symbol: FDPS
• Synonyms (NCBI Gene): FPPS, FPS, POROK9
• Chromosome: 1
• Chromosome location: 1q22
• Summary: This gene encodes an enzyme that catalyzes the production of geranyl pyrophosphate and farnesyl pyrophosphate from isopentenyl pyrophosphate and dimethylallyl pyrophosphate. The resulting product, farnesyl pyrophosphate, is a key intermediate in cholester

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs2297480	T>A,G	Drug-response	Intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT051567	hsa-let-7e-5p	CLASH	23622248
MIRT038702	hsa-miR-30c-2-3p	CLASH	23622248

Transcription factors

Transcription factor	Regulation	Reference
NFYC	Unknown	20450493
SREBF1	Unknown	8798690
SREBF2	Unknown	20450493
YY1	Unknown	10318878

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003723	Function	RNA binding	HDA	22658674
GO:0004161	Function	Dimethylallyltranstransferase activity	IBA
GO:0004161	Function	Dimethylallyltranstransferase activity	IEA
GO:0004337	Function	(2E,6E)-farnesyl diphosphate synthase activity	IBA
GO:0004337	Function	(2E,6E)-farnesyl diphosphate synthase activity	IEA
GO:0004659	Function	Prenyltransferase activity	IEA
GO:0005515	Function	Protein binding	IPI	16713569, 32296183, 32814053
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005759	Component	Mitochondrial matrix	IDA	17198737
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005777	Component	Peroxisome	IDA	17198737
GO:0005777	Component	Peroxisome	IEA
GO:0005829	Component	Cytosol	IDA	17198737
GO:0005829	Component	Cytosol	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006694	Process	Steroid biosynthetic process	IEA
GO:0006695	Process	Cholesterol biosynthetic process	IC	2690933
GO:0006695	Process	Cholesterol biosynthetic process	IEA
GO:0006695	Process	Cholesterol biosynthetic process	TAS	2690933
GO:0008202	Process	Steroid metabolic process	IEA
GO:0008203	Process	Cholesterol metabolic process	IEA
GO:0008299	Process	Isoprenoid biosynthetic process	IEA
GO:0016126	Process	Sterol biosynthetic process	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016765	Function	Transferase activity, transferring alkyl or aryl (other than methyl) groups	IEA
GO:0033384	Process	Geranyl diphosphate biosynthetic process	IEA
GO:0045337	Process	Farnesyl diphosphate biosynthetic process	IBA
GO:0045337	Process	Farnesyl diphosphate biosynthetic process	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 134629
• HGNC: 3631
• e!Ensembl: ENSG00000160752

Protein

• UniProt ID: P14324
• Protein name: Farnesyl pyrophosphate synthase (FPP synthase) (FPS) (EC 2.5.1.10) ((2E,6E)-farnesyl diphosphate synthase) (Dimethylallyltranstransferase) (EC 2.5.1.1) (Farnesyl diphosphate synthase) (Geranyltranstransferase)
• Protein function: Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate
• PDB: 1YQ7, 1YV5, 1ZW5, 2F7M, 2F89, 2F8C, 2F8Z, 2F92, 2F94, 2F9K, 2OPM, 2OPN, 2QIS, 2RAH, 2VF6, 3B7L, 3CP6, 3N1V, 3N1W, 3N3L, 3N45, 3N46, 3N49, 3N5H, 3N5J, 3N6K, 3RYE, 3S4J, 4DEM, 4GA3, 4H5C, 4H5D, 4H5E, 4JVJ, 4KFA, 4KPD, 4KPJ, 4KQ5, 4KQS, 4KQU, 4L2X, 4LFV, 4LPG, 4LPH, 4N1Z, 4N9U, 4NFI, 4NFJ, 4NFK, 4NG6, 4NKE
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00348	polyprenyl_synt	108 → 374	Polyprenyl synthetase	Domain

• Sequence:

  MPLSRWLRSVGVFLLPAPYWAPRERWLGSLRRPSLVHGYPVLAWHSARCWCQAWTEEPRA
  LCSSLRMNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAI
  GGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRG
  QICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLD
  LLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLE
  MGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKE
  AEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK

• Sequence length: 419

Pathways

KEGG:

Terpenoid backbone biosynthesis
Metabolic pathways
Influenza A
Human T-cell leukemia virus 1 infection

Reactome:

Cholesterol biosynthesis
Activation of gene expression by SREBF (SREBP)

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Porokeratosis 9, multiple types	Pathogenic	rs863225241, rs769193201	RCV000201791 RCV000201790	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARPAL TUNNEL SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DISSEMINATED SUPERFICIAL ACTINIC POROKERATOSIS	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FDPS-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPOROSIS, POSTMENOPAUSAL	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POROKERATOSIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POROKERATOSIS 9, MULTIPLE TYPE S	—	CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POROKERATOSIS, DISSEMINATED SUPERFICIAL ACTINIC	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	17387528	Associate	★☆☆☆☆ Found in Text Mining only
Anaplastic thyroid carcinoma	Anaplastic thyroid cancer	BEFREE	15613457		★☆☆☆☆ Found in Text Mining only
Anemia, Sickle Cell	Anemia	BEFREE	30044349		★☆☆☆☆ Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA	Syndromic microphthalmia	BEFREE	28867179		★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	BEFREE	28190665		★☆☆☆☆ Found in Text Mining only
Anxiety Disorders	Anxiety Disorder	BEFREE	28190665		★☆☆☆☆ Found in Text Mining only
Arteriosclerosis	Arteriosclerosis	BEFREE	28339090		★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	BEFREE	28339090		★☆☆☆☆ Found in Text Mining only
Bone Diseases	Bone disease	Pubtator	16698791	Associate	★☆☆☆☆ Found in Text Mining only
Bone Diseases	Bone Disease	BEFREE	29080272		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	BEFREE	28419419		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain neoplasms	Pubtator	28419419	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	36634566, 37190091	Associate	★☆☆☆☆ Found in Text Mining only
Calcinosis	Calcinosis	Pubtator	39289624	Inhibit	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	12824919	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	34513998	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	Pubtator	34783037	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy Dilated	Dilated cardiomyopathy	Pubtator	34783037	Associate	★☆☆☆☆ Found in Text Mining only
Chronic Obstructive Airway Disease	Chronic Obstructive Pulmonary Disease	BEFREE	28148566		★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognitive disorder	BEFREE	29248482		★☆☆☆☆ Found in Text Mining only
Colitis	Colitis	BEFREE	30542111		★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic Neoplasms	LHGDN	15713990		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	16101154	Associate	★☆☆☆☆ Found in Text Mining only
Congestive heart failure	Congestive Heart Failure	BEFREE	23180723		★☆☆☆☆ Found in Text Mining only
Coronary Arteriosclerosis	Coronary Arteriosclerosis	BEFREE	28544034, 29864496		★☆☆☆☆ Found in Text Mining only
Depressive disorder	Mental Depression	BEFREE	29455896		★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	29948786, 30393200		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	29948786, 30393200		★☆☆☆☆ Found in Text Mining only
Disseminated superficial actinic porokeratosis	Disseminated Superficial Actinic Porokeratosis	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Enteritis	Enteritis	BEFREE	30542111		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	20298756, 29075041, 30333528		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	26469958, 29075041, 30333528	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	20298756, 29075041, 30333528		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	28419419	Associate	★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease 0 Muscle	Glycogen storage disease	Pubtator	34783037	Inhibit	★☆☆☆☆ Found in Text Mining only
Heart failure	Heart Failure	BEFREE	23180723		★☆☆☆☆ Found in Text Mining only
Heart valve disease	Cardiac valvular disease	BEFREE	23180723		★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	29248482		★☆☆☆☆ Found in Text Mining only
Leprosy	Leprosy	Pubtator	34449765	Associate	★☆☆☆☆ Found in Text Mining only
Lymphoid leukemia	Lymphoid leukemia	BEFREE	28300835		★☆☆☆☆ Found in Text Mining only
Malignant Fibrous Histiocytoma	Malignant Histiocytoma	BEFREE	17094458		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of brain	Brain Neoplasms	BEFREE	28419419		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	25025965, 31725297		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	21196316, 24713434, 30914801		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24713434, 29075041, 30333528, 30914801, 31785819		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	29030460		★☆☆☆☆ Found in Text Mining only
Mental Depression	Mental Depression	BEFREE	29455896		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	21196316		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy Duchenne	Duchenne muscular dystrophy	Pubtator	17368768	Associate	★☆☆☆☆ Found in Text Mining only
Myocardial Ischemia	Myocardial Ischemia	BEFREE	28544034, 29864496		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	17094458, 2555699, 27669433, 29075041, 30914801, 31725297		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	24911527		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	29455896		★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	Pubtator	16698791, 31437227, 31774873	Associate	★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	BEFREE	24534219, 30014569, 30096489, 30333528, 31279300, 31774873		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	LHGDN	18494934		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	18494934	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	25025965, 31725297		★☆☆☆☆ Found in Text Mining only
Porokeratosis	Porokeratosis	Pubtator	26202976	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Porokeratosis	Porokeratosis	BEFREE	28765912		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Porokeratosis	Porokeratosis	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POROKERATOSIS 9, MULTIPLE TYPES	Porokeratosis	UNIPROT_DG	26202976		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
POROKERATOSIS 9, MULTIPLE TYPES	Porokeratosis	GENOMICS_ENGLAND_DG	26202976, 27422687		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
POROKERATOSIS 9, MULTIPLE TYPES	Porokeratosis	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
POROKERATOSIS 9, MULTIPLE TYPES	Porokeratosis	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Porokeratosis of Mibelli	Porokeratosis	BEFREE	28765912		★☆☆☆☆ Found in Text Mining only
Porokeratosis, Disseminated Superficial Actinic	Porokeratosis	ORPHANET_DG	26202976		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Progeria	Progeria	BEFREE	26890144		★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	21196316, 24713434, 30914801		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	24713434	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary Emphysema	Pulmonary Emphysema	BEFREE	28148566		★☆☆☆☆ Found in Text Mining only
Renal fibrosis	Renal fibrosis	BEFREE	30393200		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Subarachnoid Hemorrhage	Subarachnoid hemorrhage	BEFREE	28606778		★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	37190091	Stimulate	★☆☆☆☆ Found in Text Mining only