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    RFT1 RFT1 homolog [ Homo sapiens (human) ]

    Gene ID: 91869, updated on 9-Dec-2024

    Summary

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    Official Symbol
    RFT1provided by HGNC
    Official Full Name
    RFT1 homologprovided by HGNC
    Primary source
    HGNC:HGNC:30220
    See related
    Ensembl:ENSG00000163933 MIM:611908; AllianceGenome:HGNC:30220
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDG1N
    Summary
    This gene encodes an enzyme which catalyzes the translocation of the Man(5)GlcNAc (2)-PP-Dol intermediate from the cytoplasmic to the luminal side of the endoplasmic reticulum membrane in the pathway for the N-glycosylation of proteins. Mutations in this gene are associated with congenital disorder of glycosylation type In.[provided by RefSeq, Dec 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 1.9), testis (RPKM 1.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RFT1 in Genome Data Viewer
    Location:
    3p21.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (53066853..53130435, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (53099771..53163318, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (53122499..53164451, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70661 Neighboring gene Scm like with four mbt domains 1 Neighboring gene Sharpr-MPRA regulatory region 7399 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:53032540-53033040 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:53033923-53034166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19949 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:53064883-53065417 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53080405-53080906 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53080907-53081406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53106949-53107566 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 3047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19952 Neighboring gene NANOG hESC enhancer GRCh37_chr3:53136831-53137332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19953 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53148350-53149549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53182771-53183578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53190496-53190996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53201730-53202410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53202411-53203091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19961 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53208863-53209718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19967 Neighboring gene Sharpr-MPRA regulatory region 8375 Neighboring gene protein kinase C delta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53236717-53237216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14463 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53261945-53263144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53270389-53271197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53274891-53275886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14464 Neighboring gene transketolase

    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
    • 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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    Related articles in PubMed

    1. Human RFT1 deficiency leads to a disorder of N-linked glycosylation. Haeuptle MA, et al. Am J Hum Genet, 2008 Mar. PMID 18313027, Free PMC Article
    2. RFT1-CDG: deafness as a novel feature of congenital disorders of glycosylation. Jaeken J, et al. J Inherit Metab Dis, 2009 Dec. PMID 19856127
    3. RFT1-CDG in adult siblings with novel mutations. Ondruskova N, et al. Mol Genet Metab, 2012 Dec. PMID 23111317
    4. RFT1-congenital disorder of glycosylation (CDG) syndrome: a cause of early-onset severe epilepsy. Aeby A, et al. Epileptic Disord, 2016 Mar. PMID 26892341
    5. A family with floppy neonates with severe respiratory insufficiency: A lethal phenotype of RFT1-CDG due to a novel mutation. Abiramalatha T, et al. Eur J Med Genet, 2019 Apr. PMID 30071302

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Molecular characterization of Rft1, an ER membrane protein associated with congenital disorder of glycosylation RFT1-CDG.
      Title: Molecular characterization of Rft1, an ER membrane protein associated with congenital disorder of glycosylation RFT1-CDG.
    2. A novel RFT1 missense mutation was identified in a family with history of neonatal deaths due to severe respiratory insufficiency.
      Title: A family with floppy neonates with severe respiratory insufficiency: A lethal phenotype of RFT1-CDG due to a novel mutation.
    3. showed that this patient was compound heterozygous for two mutations in the RFT1 gene: c.1325G>A (p.R442Q) and c.110G>T (p.R37L)
      Title: RFT1-congenital disorder of glycosylation (CDG) syndrome: a cause of early-onset severe epilepsy.
    4. Six patients with RFT1-CDG show sensorineural deafness as part of a severe neurological syndrome
      Title: RFT1-CDG: deafness as a novel feature of congenital disorders of glycosylation.
    5. Identification of novel missense mutations in exon 12 of the RFT1 gene in adult siblings with congenital disorder of glycosylation (CDG) syndrome caused by RFT1 deficiency.
      Title: RFT1-CDG in adult siblings with novel mutations.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. RFT1 deficiency in both yeast and human cells leads to the accumulation of incomplete DolPP-GlcNAc(2)Man(5) and to a profound glycosylation disorder in humans.
      Title: Human RFT1 deficiency leads to a disorder of N-linked glycosylation.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    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)

    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

    Clone Names

    • FLJ25945, DKFZp667J092

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables glycolipid floppase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in dolichol-linked oligosaccharide biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glycolipid translocation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in glycolipid translocation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in protein N-linked glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endoplasmic reticulum membrane IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1
    Names
    RFT1, requiring fifty three 1 homolog
    congenital disorder of glycosylation 1N
    protein RFT1 homolog
    putative endoplasmic reticulum multispan transmembrane protein

    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.

    Genomic

    1. NG_009203.1 RefSeqGene

      Range
      5020..46972
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_052859.4 → NP_443091.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1

      See identical proteins and their annotated locations for NP_443091.1

      Status: REVIEWED

      Source sequence(s)
      AC096887, AL713685, BC043595
      Consensus CDS
      CCDS2869.1
      UniProtKB/Swiss-Prot
      Q96AA3, Q96J03
      UniProtKB/TrEMBL
      A0A291FGD9
      Related
      ENSP00000296292.3, ENST00000296292.8
      Conserved Domains (1) summary
      pfam04506
      Location:14 → 524
      Rft-1; Rft protein

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      53066853..53130435 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534215.4 → XP_011532517.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X2

      Related
      ENSP00000520849.1, ENST00000850556.1
      Conserved Domains (1) summary
      cl09326
      Location:11 → 403
      MATE_like; Multidrug and toxic compound extrusion family and similar proteins

    2. XM_011534214.3 → XP_011532516.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X1

      Conserved Domains (1) summary
      cl09326
      Location:11 → 403
      MATE_like; Multidrug and toxic compound extrusion family and similar proteins

    3. XM_006713384.4 → XP_006713447.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X3

      Conserved Domains (1) summary
      cl09326
      Location:11 → 403
      MATE_like; Multidrug and toxic compound extrusion family and similar proteins

    4. XM_011534216.4 → XP_011532518.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X5

      Conserved Domains (1) summary
      cl09326
      Location:22 → 305
      MATE_like; Multidrug and toxic compound extrusion family and similar proteins

    5. XM_005265537.5 → XP_005265594.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X4

      Conserved Domains (1) summary
      cl09326
      Location:11 → 368
      MATE_like; Multidrug and toxic compound extrusion family and similar proteins

    RNA

    1. XR_007095765.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      53099771..53163318 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348362.1 → XP_054204337.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X2

    2. XM_054348361.1 → XP_054204336.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X1

    3. XM_054348363.1 → XP_054204338.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X3

    4. XM_054348365.1 → XP_054204340.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X5

    5. XM_054348364.1 → XP_054204339.1  man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1 isoform X4

    RNA

    1. XR_008486849.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96AA3.1 GenPept UniProtKB/Swiss-Prot:Q96AA3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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