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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 58
  • 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 Keratolytic Winter Erythema. Among its related pathways are Statin Pathway and Terpenoid backbone biosynthesis. 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

Regulatory Elements for FDFT1 Gene

Enhancers for FDFT1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08H011874 2 FANTOM5 Ensembl ENCODE dbSUPER 20.7 +81.8 81786 6 PKNOX1 FOXA2 MLX ARNT ARID4B YY1 ZNF766 FOS SP5 ZNF592 FDFT1 CTSB LOC105379243 DEFB136 DEFB135 NEIL2 PIR55200
GH08H011851 1.6 Ensembl ENCODE dbSUPER 19.8 +58.2 58166 3.9 PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 FOS PAF1 SP5 FDFT1 CTSB LOC105379243 NEIL2 PIR38437 GC08M011864
GH08H011799 1.4 ENCODE dbSUPER 21.6 +9.2 9249 11.2 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 RPS3AP35 PINX1 FDFT1 DEFB135 LINC00208 ZNF705D ZNF705CP LINC00529 ENSG00000249316 OR7E10P
GH08H011819 0.9 ENCODE dbSUPER 22.6 +25.3 25294 2.5 HDAC1 PKNOX1 KLF1 SOX6 ARID4B MNT FOXA1 OSR2 ZFP69B CTBP1 FDFT1 CTSB PIR48315 LOC105379243
GH08H011823 0.8 Ensembl ENCODE dbSUPER 21.7 +28.6 28614 1.3 FDFT1 LOC105379243 CTSB FAM66A PIR48315
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around FDFT1 on UCSC Golden Path with GeneCards custom track

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 isoforms=530, posLast=4141, posLast=4545, isoforms=2, 3, 593, isoforms=2, 3, 4117, posLast=138138, posLast=170170, isoforms=2, 3, 4, 5213, posLast=318318, and isoforms=2, 3, 4, 5358
  • 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 17353931
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

miRNA for FDFT1 Gene

Clone Products

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 IDA,IEA --
GO:0005789 endoplasmic reticulum membrane IBA,TAS --
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 TAS,IBA --
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
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
(1-phosphonato-4-{4-[4-(trifluoromethyl)phenyl]phenyl}butyl)phosphonate Pharma Inhibition, Inhibitor 0

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

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 Sequence Context AA Info Type
rs1000053648 -- 11,816,529(+) TATGG(C/T)CTCTT intron-variant
rs1000054229 -- 11,826,495(+) GTGCA(C/G)TAGCT intron-variant
rs1000069977 -- 11,821,535(+) GCAGT(G/T)AGCTG intron-variant
rs1000073785 -- 11,812,216(+) TGTAC(C/G)ACGTT intron-variant
rs1000082458 -- 11,809,095(+) CCAGC(C/T)TTTCA intron-variant, upstream-variant-2KB

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

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

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)

Relevant External Links for FDFT1 Gene

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

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

Disorders for FDFT1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
smith-lemli-opitz syndrome
  • rutledge lethal multiple congenital anomaly syndrome
keratolytic winter erythema
  • erythrokeratolysis hiemalis ichthyosis
phencyclidine abuse
  • pcp abuse
  • phytosterolemia
smoldering myeloma
- elite association - COSMIC cancer census association via MalaCards
Search FDFT1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for FDFT1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 45 60
  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 45 60
  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 45 60
  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 60
  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 60

Products for FDFT1 Gene

Sources for FDFT1 Gene

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