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Aliases for FDFT1 Gene

Aliases for FDFT1 Gene

  • Farnesyl-Diphosphate Farnesyltransferase 1 2 3 5
  • FPP:FPP Farnesyltransferase 3 4
  • Squalene Synthase 2 3
  • EC 4 56
  • SQS 3 4
  • SS 3 4
  • Farnesyl-Diphosphate Farnesyltransferase 4
  • Presqualene-Di-Diphosphate Synthase 3
  • Squalene Synthetase 3
  • DGPT 3
  • ERG9 3

External Ids for FDFT1 Gene

Previous GeneCards Identifiers for FDFT1 Gene

  • GC08P011723
  • GC08P011524
  • GC08P011697
  • GC08P010591
  • GC08P011653

Summaries for FDFT1 Gene

Entrez Gene Summary for FDFT1 Gene

  • This gene encodes a membrane-associated enzyme located at a branch point in the mevalonate pathway. The encoded protein is the first specific enzyme in cholesterol biosynthesis, catalyzing the dimerization of two molecules of farnesyl diphosphate in a two-step reaction to form squalene. [provided by RefSeq, Jul 2008]

GeneCards Summary for FDFT1 Gene

FDFT1 (Farnesyl-Diphosphate Farnesyltransferase 1) is a Protein Coding gene. Diseases associated with FDFT1 include Smith-Lemli-Opitz Syndrome and Phencyclidine Abuse. Among its related pathways are Regulation of cholesterol biosynthesis by SREBP (SREBF) and cholesterol biosynthesis I. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity and farnesyl-diphosphate farnesyltransferase activity.

Additional gene information for FDFT1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FDFT1 Gene

Genomics for FDFT1 Gene

GeneHancer (GH) Regulatory Elements for FDFT1 Gene

Promoters and enhancers for FDFT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08I011799 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 571.7 +9.2 9249 11.2 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 GLIS1 FDFT1 PINX1 LOC101929290 NEIL2 CTSB FAM86B2 LOC105379241 BLK RPS3AP34 ENSG00000255122
GH08I011795 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 561.1 +1.1 1077 2.6 HDAC1 PKNOX1 ZNF335 ATF7 SMARCA5 NFYC ZNF148 ZFP69B ZSCAN16 BCL6B FDFT1 NEIL2 CTSB C8orf49 LOC105379243
GH08I011874 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 20.7 +81.8 81785 6 PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B YY1 ZNF766 E2F8 FOS FDFT1 CTSB LOC105379243 DEFB136 DEFB135 NEIL2 PIR55200
GH08I011851 Enhancer 1.4 Ensembl ENCODE dbSUPER 19.8 +58.2 58165 3.9 PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 FOS PAF1 SP5 FDFT1 CTSB LOC105379243 NEIL2 GC08M011864 PIR38437
GH08I011768 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 12.6 -25.7 -25677 2.7 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 POLR2B NEIL2 PIR40911 FDFT1 LOC105379243 C8orf49 CTSB LOC105379241 BLK ENSG00000269918
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around FDFT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FDFT1 gene promoter:

Genomic Locations for FDFT1 Gene

Genomic Locations for FDFT1 Gene
43,737 bases
Plus strand

Genomic View for FDFT1 Gene

Genes around FDFT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FDFT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FDFT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FDFT1 Gene

Proteins for FDFT1 Gene

  • Protein details for FDFT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Squalene synthase
    Protein Accession:
    Secondary Accessions:
    • B3KQ95
    • B4DJE5
    • B4DT56
    • B7Z1J3
    • Q96GT0

    Protein attributes for FDFT1 Gene

    417 amino acids
    Molecular mass:
    48115 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for FDFT1 Gene

    Alternative splice isoforms for FDFT1 Gene


neXtProt entry for FDFT1 Gene

Selected DME Specific Peptides for FDFT1 Gene


Post-translational modifications for FDFT1 Gene

  • Ubiquitination at Lys30, posLast=4141, posLast=4545, Lys93, Lys117, posLast=138138, posLast=170170, Lys213, posLast=318318, and posLast=358358
  • Modification sites at PhosphoSitePlus

Domains & Families for FDFT1 Gene

Gene Families for FDFT1 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the phytoene/squalene synthase family.
  • Belongs to the phytoene/squalene synthase family.
genes like me logo Genes that share domains with FDFT1: view

Function for FDFT1 Gene

Molecular function for FDFT1 Gene

GENATLAS Biochemistry:
farnesyl diphosphate,farnesyltransferase
UniProtKB/Swiss-Prot CatalyticActivity:
2 farnesyl diphosphate + NAD(P)H = squalene + 2 diphosphate + NAD(P)(+).

Enzyme Numbers (IUBMB) for FDFT1 Gene

Phenotypes From GWAS Catalog for FDFT1 Gene

Gene Ontology (GO) - Molecular Function for FDFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004310 farnesyl-diphosphate farnesyltransferase activity TAS --
GO:0005515 protein binding IPI 25910212
GO:0016491 oxidoreductase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups IEA --
genes like me logo Genes that share ontologies with FDFT1: view
genes like me logo Genes that share phenotypes with FDFT1: view

Animal Models for FDFT1 Gene

MGI Knock Outs for FDFT1:

Animal Model Products

Clone Products

  • Addgene plasmids for FDFT1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for FDFT1 Gene

Localization for FDFT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FDFT1 Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FDFT1 gene
Compartment Confidence
endoplasmic reticulum 5
cytosol 3
plasma membrane 2
extracellular 2
nucleus 2
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FDFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA,IDA --
GO:0005789 endoplasmic reticulum membrane TAS,IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,TAS --
GO:0043231 intracellular membrane-bounded organelle IEA --
genes like me logo Genes that share ontologies with FDFT1: view

Pathways & Interactions for FDFT1 Gene

genes like me logo Genes that share pathways with FDFT1: view

UniProtKB/Swiss-Prot P37268-FDFT_HUMAN

  • Pathway: Terpene metabolism; lanosterol biosynthesis; lanosterol from farnesyl diphosphate: step 1/3.

Gene Ontology (GO) - Biological Process for FDFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006694 steroid biosynthetic process TAS 8474436
GO:0006695 cholesterol biosynthetic process IBA,TAS --
GO:0006696 ergosterol biosynthetic process IEA --
GO:0008152 metabolic process IEA --
genes like me logo Genes that share ontologies with FDFT1: view

No data available for SIGNOR curated interactions for FDFT1 Gene

Drugs & Compounds for FDFT1 Gene

(43) Drugs for FDFT1 Gene - From: DrugBank, ApexBio, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Magnesium Approved Nutra 0
TAK-475 Investigational Pharma Target 0
zaragozic acid A Pharma Inhibition, Inhibitor 0
(1-methyl-1-{[3-(3-phenoxyphenyl)propyl]carbamoyl}ethyl)phosphonate Pharma Inhibition, Inhibitor 0

(24) Additional Compounds for FDFT1 Gene - From: HMDB, Novoseek, and IUPHAR

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 2'-(Dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) Adenosine 5'-ester with 1,4-dihydro-1-b-D-ribofuranosylnicotinamide
  • 2'-(Dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) Adenosine 5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosylnicotinamide
  • Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) P'-5'-ester with 1,4-dihydro-1-beta-D-ribofuranosyl-3-pyridinecarboxamide
  • Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) P'-5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosyl-3-pyridinecarboxamide
  • b-NADPH
Presqualene diphosphate
  • (1alpha,2beta(E),3beta(1E,5E))-Diphosphoric acid mono((2-(4,8-dimethyl-3,7-nonadienyl)-2-methyl-3-(2,6,10-trimethyl-1,5,9-undecatrienyl)cyclopropyl)methyl) ester
  • Presqualene diphosphate
  • Presqualene pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
Inhibition, Inhibitor
Inhibition, Inhibitor

(1) ApexBio Compounds for FDFT1 Gene

Compound Action Cas Number
Costundide 553-21-9
genes like me logo Genes that share compounds with FDFT1: view

Drug Products

Transcripts for FDFT1 Gene

Unigene Clusters for FDFT1 Gene

Farnesyl-diphosphate farnesyltransferase 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for FDFT1

Alternative Splicing Database (ASD) splice patterns (SP) for FDFT1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11
SP1: - - - - - -
SP3: -
SP4: - - -
SP5: - - - - - - - - - - - -
SP6: - -

Relevant External Links for FDFT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FDFT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FDFT1 Gene

Protein differential expression in normal tissues from HIPED for FDFT1 Gene

This gene is overexpressed in Fetal testis (32.0) and Bone (26.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for FDFT1 Gene

Protein tissue co-expression partners for FDFT1 Gene

NURSA nuclear receptor signaling pathways regulating expression of FDFT1 Gene:


SOURCE GeneReport for Unigene cluster for FDFT1 Gene:


Evidence on tissue expression from TISSUES for FDFT1 Gene

  • Nervous system(5)
  • Lung(4.8)
  • Liver(4.7)
  • Muscle(4.5)
  • Skin(4.2)
  • Blood(4.1)
  • Intestine(4)
  • Eye(2.9)
  • Pancreas(2.6)
  • Heart(2.2)
genes like me logo Genes that share expression patterns with FDFT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for FDFT1 Gene

Orthologs for FDFT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for FDFT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FDFT1 33 34
  • 99.44 (n)
(Canis familiaris)
Mammalia FDFT1 33 34
  • 89.77 (n)
(Bos Taurus)
Mammalia FDFT1 33 34
  • 87.77 (n)
(Mus musculus)
Mammalia Fdft1 33 16 34
  • 85.31 (n)
(Rattus norvegicus)
Mammalia Fdft1 33
  • 84.42 (n)
(Monodelphis domestica)
Mammalia FDFT1 34
  • 76 (a)
(Gallus gallus)
Aves FDFT1 33 34
  • 75.63 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 73 (a)
-- 34
  • 68 (a)
-- 34
  • 66 (a)
-- 34
  • 65 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia fdft1 33
  • 72.03 (n)
Str.13257 33
(Danio rerio)
Actinopterygii si:ch73-107c13.2 33
  • 67.25 (n)
FDFT1 34
  • 67 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR444C 33
  • 52.88 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D08866g 33
  • 50.92 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ERG9 33 34 36
  • 50.7 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons SQS1 33
  • 50.73 (n)
(Glycine max)
eudicotyledons Gma.8028 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3819 33
(Oryza sativa)
Liliopsida Os07g0200700 33
  • 52.41 (n)
(Hordeum vulgare)
Liliopsida Hv.10521 33
(Zea mays)
Liliopsida Zm.13795 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes erg9 33
  • 53.76 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06054 33
  • 51.77 (n)
Species where no ortholog for FDFT1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for FDFT1 Gene

Gene Tree for FDFT1 (if available)
Gene Tree for FDFT1 (if available)

Paralogs for FDFT1 Gene

No data available for Paralogs for FDFT1 Gene

Variants for FDFT1 Gene

Sequence variations from dbSNP and Humsavar for FDFT1 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000053648 -- 11,816,529(+) C/T intron_variant
rs1000054229 -- 11,826,495(+) C/G intron_variant
rs1000069977 -- 11,821,535(+) G/T intron_variant
rs1000073785 -- 11,812,216(+) C/G intron_variant
rs1000082458 -- 11,809,095(+) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for FDFT1 Gene

Variant ID Type Subtype PubMed ID
esv3572514 CNV loss 25503493
nsv1018042 CNV gain 25217958
nsv1032739 CNV loss 25217958
nsv1034132 CNV gain 25217958
nsv1076058 CNV deletion 25765185
nsv525089 CNV loss 19592680

Variation tolerance for FDFT1 Gene

Residual Variation Intolerance Score: 34.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.67; 57.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FDFT1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FDFT1 Gene

Disorders for FDFT1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for FDFT1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search FDFT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for FDFT1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with FDFT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FDFT1 Gene

Publications for FDFT1 Gene

  1. K45R variant of squalene synthase increases total cholesterol levels in two study samples from a French Canadian population. (PMID: 18350552) Do R … Engert JC (Human mutation 2008) 3 4 22 44 58
  2. Studies of CTNNBL1 and FDFT1 variants and measures of obesity: analyses of quantitative traits and case-control studies in 18,014 Danes. (PMID: 19245693) Andreasen CH … Hansen T (BMC medical genetics 2009) 3 22 44 58
  3. Identification of a chromosome 8p locus for early-onset coronary heart disease in a French Canadian population. (PMID: 17805225) Engert JC … Gaudet D (European journal of human genetics : EJHG 2008) 3 22 44 58
  4. Crystal structure of human squalene synthase. A key enzyme in cholesterol biosynthesis. (PMID: 10896663) Pandit J … Harwood HJ (The Journal of biological chemistry 2000) 3 4 22 58
  5. Expression, purification, and characterization of the human squalene synthase: use of yeast and baculoviral systems. (PMID: 7864626) Soltis DA … Cornell-Kennon SA (Archives of biochemistry and biophysics 1995) 3 4 22 58

Products for FDFT1 Gene

  • Addgene plasmids for FDFT1

Sources for FDFT1 Gene

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