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RFT1 RFT1 homolog [ Homo sapiens (human) ]

Gene ID: 91869, updated on 11-Apr-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
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Genomic context

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Location:
3p21.1
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (53066853..53130435, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (53099771..53163318, complement)
105.20220307 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. 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
  2. RFT1-congenital disorder of glycosylation (CDG) syndrome: a cause of early-onset severe epilepsy. Aeby A, et al. Epileptic Disord, 2016 Mar. PMID 26892341
  3. RFT1-CDG in adult siblings with novel mutations. Ondruskova N, et al. Mol Genet Metab, 2012 Dec. PMID 23111317
  4. RFT1-CDG: deafness as a novel feature of congenital disorders of glycosylation. Jaeken J, et al. J Inherit Metab Dis, 2009 Dec. PMID 19856127
  5. 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

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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)

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

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 IEA
Inferred from Electronic Annotation
more info
  
involved_in glycolipid translocation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
protein RFT1 homolog
Names
RFT1, requiring fifty three 1 homolog
congenital disorder of glycosylation 1N
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  protein RFT1 homolog

    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_2023_10

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  protein RFT1 homolog isoform X2

    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  protein RFT1 homolog 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  protein RFT1 homolog 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  protein RFT1 homolog 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  protein RFT1 homolog 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  protein RFT1 homolog isoform X2

  2. XM_054348361.1 → XP_054204336.1  protein RFT1 homolog isoform X1

  3. XM_054348363.1 → XP_054204338.1  protein RFT1 homolog isoform X3

  4. XM_054348365.1 → XP_054204340.1  protein RFT1 homolog isoform X5

  5. XM_054348364.1 → XP_054204339.1  protein RFT1 homolog 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

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