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

Gene ID: 2222, updated on 3-Nov-2024

Summary

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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
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Genomic context

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See FDFT1 in Genome Data Viewer
Location:
8p23.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (11795582..11839298)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (7901010..7944714, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (11653091..11696807)

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 ATAC-STARR-seq lymphoblastoid active region 27032 Neighboring gene SUB1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27033 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11705639-11706333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11706334-11707027 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:11707258-11707440 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11710619-11711226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11714811-11715344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27036 Neighboring gene cathepsin B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18945 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 ReSE screen-validated silencer GRCh37_chr8:11748634-11748817 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Spectroscopic diagnosis and metabolite characterization of cisplatin resistance regulated by FDFT1 in bladder cancer tissue.
    Title: Spectroscopic diagnosis and metabolite characterization of cisplatin resistance regulated by FDFT1 in bladder cancer tissue.
  2. Intramembrane protease SPP defines a cholesterol-regulated abundance control of the mevalonate pathway enzyme squalene synthase.
    Title: Intramembrane protease SPP defines a cholesterol-regulated abundance control of the mevalonate pathway enzyme squalene synthase.
  3. Squalene synthase predicts poor prognosis in stage I-III colon adenocarcinoma and synergizes squalene epoxidase to promote tumor progression.
    Title: Squalene synthase predicts poor prognosis in stage I-III colon adenocarcinoma and synergizes squalene epoxidase to promote tumor progression.
  4. Ubiquitin specific peptidase 32 acts as an oncogene in epithelial ovarian cancer by deubiquitylating farnesyl-diphosphate farnesyltransferase 1.
    Title: Ubiquitin specific peptidase 32 acts as an oncogene in epithelial ovarian cancer by deubiquitylating farnesyl-diphosphate farnesyltransferase 1.
  5. FDFT1 is a key downstream target of the fasting response and may be involved in CRC cell glucose metabolism.
    Title: Fasting inhibits aerobic glycolysis and proliferation in colorectal cancer via the Fdft1-mediated AKT/mTOR/HIF1α pathway suppression.
  6. We have demonstrated the differential relative expression levels of FDFT1 mRNA and protein in various types of cancer based on TMAs and IHC for protein expression, and qPCR analysis for the illustration of mRNA expression.
    Title: Characterization of farnesyl diphosphate farnesyl transferase 1 (FDFT1) expression in cancer.
  7. The results indicate that the ennea-peptide CLSPHSMFC, tetra-peptides SMFC, CKTE, and WHQW can effectively inhibit Squalene Synthase activities (IC50 values equal to 64, 76, 87, and 90 muM, respectively)
    Title: Discovering Peptide Inhibitors of Human Squalene Synthase Through Screening the Phage-Displayed Cyclic Peptide c7c Library.
  8. The minor allele in FDFT1 was associated with advanced fibrosis in the non-steatotic but not in the steatotic subgroup in patients with chronic hepatitis C.
    Title: Role of FDFT1 polymorphism for fibrosis progression in patients with chronic hepatitis C.
  9. Up-regulation of SQS promotes metastasis of lung cancer by enhancing tumor necrosis factor-alpha receptor 1 and nuclear factor-kappaB activation and matrix metallopeptidase 1 expression.
    Title: Squalene synthase induces tumor necrosis factor receptor 1 enrichment in lipid rafts to promote lung cancer metastasis.
  10. Several critical residues that are involved in binding of NADPH have been identified in the active site of squalene synthase.
    Title: Structural insights into the catalytic mechanism of human squalene synthase.
Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 [NAD(P)H] activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cholesterol biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in farnesyl diphosphate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
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

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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)

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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_001287742.2 → NP_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:38 → 370
    squal_synth; farnesyl-diphosphate farnesyltransferase

  2. NM_001287743.2 → NP_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, ENST00000615631.5
    Conserved Domains (1) summary
    TIGR01559
    Location:38 → 370
    squal_synth; farnesyl-diphosphate farnesyltransferase

  3. NM_001287744.2 → NP_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/TrEMBL
    B7Z9R8
    Conserved Domains (1) summary
    cl00210
    Location:1 → 306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

  4. NM_001287745.2 → NP_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/TrEMBL
    B7Z9R8
    Conserved Domains (1) summary
    cl00210
    Location:1 → 306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

  5. NM_001287747.2 → NP_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)
    AC069185
    Consensus CDS
    CCDS75696.1
    UniProtKB/TrEMBL
    B7Z9R8
    Related
    ENSP00000431749.1, ENST00000528812.5
    Conserved Domains (1) summary
    cl00210
    Location:1 → 306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

  6. NM_001287748.2 → NP_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)
    AC069185
    Consensus CDS
    CCDS75696.1
    UniProtKB/TrEMBL
    B7Z9R8
    Related
    ENSP00000484122.1, ENST00000622850.3
    Conserved Domains (1) summary
    cl00210
    Location:1 → 306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

  7. NM_001287749.2 → NP_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/TrEMBL
    B7Z9R8
    Related
    ENSP00000432331.1, ENST00000530664.5
    Conserved Domains (1) summary
    cl00210
    Location:1 → 306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

  8. NM_001287750.2 → NP_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/TrEMBL
    A0A1W2PQ47, B4DND3
    Related
    ENSP00000491537.1, ENST00000525954.5
    Conserved Domains (1) summary
    TIGR01559
    Location:97 → 429
    squal_synth; farnesyl-diphosphate farnesyltransferase

  9. NM_001287751.2 → NP_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/TrEMBL
    B7Z9R8
    Related
    ENSP00000431649.1, ENST00000528643.5
    Conserved Domains (1) summary
    cl00210
    Location:1 → 285
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

  10. NM_001287756.2 → NP_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/TrEMBL
    B4DWP0
    Related
    ENST00000446331.6
    Conserved Domains (1) summary
    cl00210
    Location:22 → 203
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

  11. NM_004462.5 → NP_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:38 → 370
    squal_synth; farnesyl-diphosphate farnesyltransferase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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..11839298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    1508774..1552517 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    7901010..7944714 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P37268.1 GenPept UniProtKB/Swiss-Prot:P37268

Gene LinkOut

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