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    FDFT1 farnesyl-diphosphate farnesyltransferase 1 [ Homo sapiens (human) ]

    Gene ID: 2222, updated on 7-Sep-2023

    Summary

    Official Symbol
    FDFT1provided by HGNC
    Official Full Name
    farnesyl-diphosphate farnesyltransferase 1provided by HGNC
    Primary source
    HGNC:HGNC:3629
    See related
    Ensembl:ENSG00000079459 MIM:184420; AllianceGenome:HGNC:3629
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SS; SQS; DGPT; ERG9; SQSD
    Summary
    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]
    Expression
    Ubiquitous expression in testis (RPKM 32.6), colon (RPKM 26.2) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See FDFT1 in Genome Data Viewer
    Location:
    8p23.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (11795582..11839309)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (7900999..7944714, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (11653091..11696818)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901888 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:11627369-11627869 Neighboring gene nei like DNA glycosylase 2 Neighboring gene uncharacterized LOC105379243 Neighboring gene Sharpr-MPRA regulatory region 11637 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11657524-11658167 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11658297-11659039 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11659040-11659781 Neighboring gene SUB1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11705639-11706333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11706334-11707027 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11710619-11711226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11714811-11715344 Neighboring gene cathepsin B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11734657-11735174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11735175-11735690 Neighboring gene CRISPRi-validated cis-regulatory element chr8.429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11759741-11760242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11768552-11769052 Neighboring gene olfactory receptor family 7 subfamily E member 158 pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Squalene synthase deficiency
    MedGen: C4748427 OMIM: 618156 GeneReviews: Squalene Synthase Deficiency
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.
    EBI GWAS Catalog
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables farnesyl-diphosphate farnesyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables squalene synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cholesterol biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in farnesyl diphosphate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in steroid biosynthetic process TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
     
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    squalene synthase
    Names
    FPP:FPP farnesyltransferase
    presqualene-di-diphosphate synthase
    squalene synthetase
    NP_001274671.1
    NP_001274672.1
    NP_001274673.1
    NP_001274674.1
    NP_001274676.1
    NP_001274677.1
    NP_001274678.1
    NP_001274679.1
    NP_001274680.1
    NP_001274685.1
    NP_004453.3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001287742.2NP_001274671.1  squalene synthase isoform 1

      See identical proteins and their annotated locations for NP_001274671.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript (1) and encodes the longest isoform (1). Variants 1-3 encode the same isoform.
      Source sequence(s)
      AC069185
      Consensus CDS
      CCDS5985.1
      UniProtKB/Swiss-Prot
      B3KQ95, B4DJE5, B4DT56, B7Z1J3, P37268, Q96GT0
      UniProtKB/TrEMBL
      E9PNM1, Q6IAX1
      Conserved Domains (1) summary
      TIGR01559
      Location:38370
      squal_synth; farnesyl-diphosphate farnesyltransferase
    2. NM_001287743.2NP_001274672.1  squalene synthase isoform 1

      See identical proteins and their annotated locations for NP_001274672.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks a 5' non-coding exon compared to variant 1. Variants 1-3 encode the same isoform (1).
      Source sequence(s)
      AC069185
      Consensus CDS
      CCDS5985.1
      UniProtKB/Swiss-Prot
      B3KQ95, B4DJE5, B4DT56, B7Z1J3, P37268, Q96GT0
      UniProtKB/TrEMBL
      E9PNM1, Q6IAX1
      Related
      ENSP00000481481.1, ENST00000615631.4
      Conserved Domains (1) summary
      TIGR01559
      Location:38370
      squal_synth; farnesyl-diphosphate farnesyltransferase
    3. NM_001287744.2NP_001274673.1  squalene synthase isoform 2

      See identical proteins and their annotated locations for NP_001274673.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks 2 exons in the 5' region and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
      Source sequence(s)
      AC069185
      Consensus CDS
      CCDS75696.1
      UniProtKB/Swiss-Prot
      P37268
      UniProtKB/TrEMBL
      B7Z9R8
      Conserved Domains (1) summary
      cl00210
      Location:1306
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    4. NM_001287745.2NP_001274674.1  squalene synthase isoform 2

      See identical proteins and their annotated locations for NP_001274674.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs at the 5' end and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
      Source sequence(s)
      AC069185
      Consensus CDS
      CCDS75696.1
      UniProtKB/Swiss-Prot
      P37268
      UniProtKB/TrEMBL
      B7Z9R8
      Conserved Domains (1) summary
      cl00210
      Location:1306
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    5. NM_001287747.1NP_001274676.1  squalene synthase isoform 2

      See identical proteins and their annotated locations for NP_001274676.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs at the 5' end and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
      Source sequence(s)
      AA679352, AK057726, AK316033, BE384903, X69141
      Consensus CDS
      CCDS75696.1
      UniProtKB/Swiss-Prot
      P37268
      UniProtKB/TrEMBL
      B7Z9R8
      Related
      ENSP00000431749.1, ENST00000528812.5
      Conserved Domains (1) summary
      cl00210
      Location:1306
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    6. NM_001287748.1NP_001274677.1  squalene synthase isoform 2

      See identical proteins and their annotated locations for NP_001274677.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs at the 5' end and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
      Source sequence(s)
      AA679352, AK057726, AK316351, DC387479, X69141
      Consensus CDS
      CCDS75696.1
      UniProtKB/Swiss-Prot
      P37268
      UniProtKB/TrEMBL
      B7Z9R8
      Related
      ENSP00000484122.1, ENST00000622850.3
      Conserved Domains (1) summary
      cl00210
      Location:1306
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    7. NM_001287749.2NP_001274678.1  squalene synthase isoform 2

      See identical proteins and their annotated locations for NP_001274678.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) differs at the 5' end and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
      Source sequence(s)
      AC069185
      Consensus CDS
      CCDS75696.1
      UniProtKB/Swiss-Prot
      P37268
      UniProtKB/TrEMBL
      B7Z9R8
      Related
      ENSP00000432331.1, ENST00000530664.5
      Conserved Domains (1) summary
      cl00210
      Location:1306
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    8. NM_001287750.2NP_001274679.1  squalene synthase isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) lacks several exons from the 5' end, contains an alternate 5' terminal exon, and initiates translation from an alternate in-frame start codon compared to variant 1. The resulting longer isoform (3) has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC069185
      Consensus CDS
      CCDS87579.1
      UniProtKB/Swiss-Prot
      P37268
      UniProtKB/TrEMBL
      A0A1W2PQ47, B4DND3
      Related
      ENSP00000491537.1, ENST00000525954.5
      Conserved Domains (1) summary
      TIGR01559
      Location:97429
      squal_synth; farnesyl-diphosphate farnesyltransferase
    9. NM_001287751.2NP_001274680.1  squalene synthase isoform 4

      See identical proteins and their annotated locations for NP_001274680.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) lacks several exons from the 5' end, contains an alternate 5' terminal exon, and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (4) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC069185
      Consensus CDS
      CCDS75697.1
      UniProtKB/Swiss-Prot
      P37268
      UniProtKB/TrEMBL
      B7Z9R8
      Related
      ENSP00000431649.1, ENST00000528643.5
      Conserved Domains (1) summary
      cl00210
      Location:1285
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    10. NM_001287756.2NP_001274685.1  squalene synthase isoform 5

      See identical proteins and their annotated locations for NP_001274685.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11) differs at the 5' end, lacks several internal exons, uses alternate donor and acceptor splice sites, and initiates translation from an alternate start codon compared to variant 1. The resulting shorter isoform (5) has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC069185
      UniProtKB/Swiss-Prot
      P37268
      UniProtKB/TrEMBL
      B4DWP0
      Related
      ENST00000446331.6
      Conserved Domains (1) summary
      cl00210
      Location:22203
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    11. NM_004462.5NP_004453.3  squalene synthase isoform 1

      See identical proteins and their annotated locations for NP_004453.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same isoform (1).
      Source sequence(s)
      AC069185
      Consensus CDS
      CCDS5985.1
      UniProtKB/Swiss-Prot
      B3KQ95, B4DJE5, B4DT56, B7Z1J3, P37268, Q96GT0
      UniProtKB/TrEMBL
      E9PNM1, Q6IAX1
      Related
      ENSP00000220584.4, ENST00000220584.9
      Conserved Domains (1) summary
      TIGR01559
      Location:38370
      squal_synth; farnesyl-diphosphate farnesyltransferase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      11795582..11839309
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_018654717.1 Reference GRCh38.p14 PATCHES

      Range
      1508763..1552517 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      7900999..7944714 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)