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Aliases for RFT1 Gene

Aliases for RFT1 Gene

  • RFT1 Homolog 2 3 5
  • Congenital Disorder Of Glycosylation 1N 2 3
  • Putative Endoplasmic Reticulum Multispan Transmembrane Protein 3
  • RFT1, Requiring Fifty Three 1 Homolog (S. Cerevisiae) 2
  • RFT1, Requiring Fifty Three 1 Homolog 3
  • RFT1 Homolog (S. Cerevisiae) 2
  • Protein RFT1 Homolog 3
  • CDG1N 3

External Ids for RFT1 Gene

Previous GeneCards Identifiers for RFT1 Gene

  • GC03U990226
  • GC03M052377
  • GC03M052980
  • GC03M053082
  • GC03M053100

Summaries for RFT1 Gene

Entrez Gene Summary for RFT1 Gene

  • 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]

GeneCards Summary for RFT1 Gene

RFT1 (RFT1 Homolog) is a Protein Coding gene. Diseases associated with RFT1 include Congenital Disorder Of Glycosylation, Type In. Among its related pathways are Transport to the Golgi and subsequent modification and Synthesis of substrates in N-glycan biosythesis. GO annotations related to this gene include lipid transporter activity. An important paralog of this gene is ENSG00000272305.

UniProtKB/Swiss-Prot for RFT1 Gene

  • May be involved in N-linked oligosaccharide assembly. May participate in the translocation of oligosaccharide from the cytoplasmic side to the lumenal side of the endoplasmic reticulum membrane.

Gene Wiki entry for RFT1 Gene

Additional gene information for RFT1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFT1 Gene

Genomics for RFT1 Gene

Regulatory Elements for RFT1 Gene

Enhancers for RFT1 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
GH03H053071 1.5 FANTOM5 Ensembl ENCODE 44.6 +57.5 57462 2.3 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ETS1 ZNF143 ZNF207 SP5 RFT1 ITIH4 TMEM110 ITIH1 TMEM110-MUSTN1 MUSTN1 ENSG00000243696 SFMBT1 DCP1A GC03M053066
GH03H053090 0.9 ENCODE 55.3 +37.7 37658 5.6 FOXA2 ARID4B RAD21 RARA YY1 MIXL1 THAP11 HMG20B CEBPB PPARG RFT1 ITIH4 TMEM110 TMEM110-MUSTN1 MUSTN1 ENSG00000243696 ENSG00000272305 GC03M053066
GH03H053195 1.5 Ensembl ENCODE dbSUPER 24.7 -66.1 -66101 1.8 HDGF PKNOX1 ARNT ARID4B YBX1 ZNF2 ZBTB7B BRCA1 GLIS2 ZNF143 RFT1 PRKCD PBRM1 SNORD38C TKT DCP1A ITIH4
GH03H053140 1.6 FANTOM5 Ensembl ENCODE dbSUPER 22.2 -10.6 -10640 1.4 HDGF ZSCAN26 ZSCAN4 ZNF133 MAX EBF1 PAX8 SALL2 ZFHX2 FOXK2 GLT8D1 RFT1 NISCH PBRM1 PRKCD ACTR8 NEK4 TMEM110 ITIH4 DCP1A
GH03H053043 1 ENCODE 26.3 +85.2 85173 3.9 FOXA2 ARNT SIN3A ZNF766 GLIS2 ELK1 ZNF143 ZNF207 ATF7 SMARCA4 ITIH4 RFT1 PBRM1 SFMBT1 TMEM110 SNORD19B PRKCD ITIH3 GC03P053048 LOC105377135
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RFT1 on UCSC Golden Path with GeneCards custom track

Promoters for RFT1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000152635 162 1401 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207

Genomic Locations for RFT1 Gene

Genomic Locations for RFT1 Gene
chr3:53,071,152-53,130,462
(GRCh38/hg38)
Size:
59,311 bases
Orientation:
Minus strand
chr3:53,122,499-53,164,478
(GRCh37/hg19)

Genomic View for RFT1 Gene

Genes around RFT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RFT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RFT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RFT1 Gene

Proteins for RFT1 Gene

  • Protein details for RFT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96AA3-RFT1_HUMAN
    Recommended name:
    Protein RFT1 homolog
    Protein Accession:
    Q96AA3
    Secondary Accessions:
    • Q96J03

    Protein attributes for RFT1 Gene

    Size:
    541 amino acids
    Molecular mass:
    60335 Da
    Quaternary structure:
    No Data Available

neXtProt entry for RFT1 Gene

Post-translational modifications for RFT1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RFT1 Gene

Domains & Families for RFT1 Gene

Gene Families for RFT1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for RFT1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RFT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96AA3

UniProtKB/Swiss-Prot:

RFT1_HUMAN :
  • Belongs to the RFT1 family.
Family:
  • Belongs to the RFT1 family.
genes like me logo Genes that share domains with RFT1: view

Function for RFT1 Gene

Molecular function for RFT1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in N-linked oligosaccharide assembly. May participate in the translocation of oligosaccharide from the cytoplasmic side to the lumenal side of the endoplasmic reticulum membrane.

Phenotypes From GWAS Catalog for RFT1 Gene

Gene Ontology (GO) - Molecular Function for RFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005319 lipid transporter activity IEA --
genes like me logo Genes that share ontologies with RFT1: view
genes like me logo Genes that share phenotypes with RFT1: view

Human Phenotype Ontology for RFT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for RFT1 Gene

miRTarBase miRNAs that target RFT1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for RFT1 Gene

Localization for RFT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFT1 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
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 RFT1 gene
Compartment Confidence
endoplasmic reticulum 4
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005789 endoplasmic reticulum membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with RFT1: view

Pathways & Interactions for RFT1 Gene

genes like me logo Genes that share pathways with RFT1: view

Gene Ontology (GO) - Biological Process for RFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006869 lipid transport IEA --
GO:0008643 carbohydrate transport IEA --
GO:0034203 glycolipid translocation IBA --
genes like me logo Genes that share ontologies with RFT1: view

No data available for SIGNOR curated interactions for RFT1 Gene

Drugs & Compounds for RFT1 Gene

No Compound Related Data Available

Transcripts for RFT1 Gene

Unigene Clusters for RFT1 Gene

RFT1 homolog (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RFT1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13
SP1: -
SP2: -
SP3: - -
SP4:
SP5: - -

Relevant External Links for RFT1 Gene

GeneLoc Exon Structure for
RFT1
ECgene alternative splicing isoforms for
RFT1

Expression for RFT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RFT1 Gene

Protein differential expression in normal tissues from HIPED for RFT1 Gene

This gene is overexpressed in Monocytes (12.1), Heart (11.3), and Lymph node (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RFT1 Gene



NURSA nuclear receptor signaling pathways regulating expression of RFT1 Gene:

RFT1

SOURCE GeneReport for Unigene cluster for RFT1 Gene:

Hs.631910

Evidence on tissue expression from TISSUES for RFT1 Gene

  • Nervous system(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RFT1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • chin
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • outer ear
  • pituitary gland
  • skull
Thorax:
  • breast
  • heart
  • lung
Abdomen:
  • liver
Pelvis:
  • ovary
  • testicle
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • blood
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
genes like me logo Genes that share expression patterns with RFT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for RFT1 Gene

Orthologs for RFT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RFT1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RFT1 33 34
  • 99.38 (n)
dog
(Canis familiaris)
Mammalia RFT1 33 34
  • 89.77 (n)
cow
(Bos Taurus)
Mammalia RFT1 34 33
  • 89.4 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rft1 33 16 34
  • 85.34 (n)
rat
(Rattus norvegicus)
Mammalia Rft1 33
  • 85.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 79 (a)
OneToMany
-- 34
  • 76 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia RFT1 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves RFT1 34 33
  • 71.08 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFT1 34
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rft1 33
  • 65.47 (n)
zebrafish
(Danio rerio)
Actinopterygii rft1 34 33
  • 65.24 (n)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG3149 33 34
  • 48.6 (n)
BcDNA:GH08388 35
  • 37 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004419 33
  • 47.12 (n)
worm
(Caenorhabditis elegans)
Secernentea ZK180.3 35 33 34
  • 43.69 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR015W 33
  • 42.75 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RFT1 33 34 36
  • 42.28 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E10451g 33
  • 41.12 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G07630 33
  • 44.92 (n)
rice
(Oryza sativa)
Liliopsida Os07g0486100 33
  • 47.96 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 49 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU05783 33
  • 41.31 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rft1 33
  • 41.06 (n)
Species where no ortholog for RFT1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RFT1 Gene

ENSEMBL:
Gene Tree for RFT1 (if available)
TreeFam:
Gene Tree for RFT1 (if available)

Paralogs for RFT1 Gene

Paralogs for RFT1 Gene

genes like me logo Genes that share paralogs with RFT1: view

Variants for RFT1 Gene

Sequence variations from dbSNP and Humsavar for RFT1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs118203913 Pathogenic, Congenital disorder of glycosylation 1N (CDG1N) [MIM:612015] 53,123,791(-) CCTTC(C/T)GCAGA nc-transcript-variant, reference, missense, utr-variant-5-prime
rs763862849 Pathogenic, Congenital disorder of glycosylation 1N (CDG1N) [MIM:612015] 53,122,376(+) GACCT(C/G/T)GAGCT nc-transcript-variant, reference, missense, utr-variant-5-prime
rs796053521 Pathogenic, Congenital disorder of glycosylation 1N (CDG1N) [MIM:612015] 53,105,738(-) TAGAG(A/G)AAAGT nc-transcript-variant, reference, missense
rs749968109 Pathogenic 53,092,502(+) TGATC(C/T)GAATG intron-variant, nc-transcript-variant, reference, missense
rs772820136 Pathogenic 53,105,743(+) CCTCT(A/C/G/T)TTGGC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for RFT1 Gene

Variant ID Type Subtype PubMed ID
nsv834699 CNV loss 17160897
nsv822095 CNV gain 20364138
nsv590357 CNV loss 21841781
nsv590356 CNV loss 21841781
nsv473275 CNV novel sequence insertion 20440878
nsv460553 CNV loss 19166990
nsv1136725 CNV deletion 24896259
esv3596167 CNV loss 21293372

Variation tolerance for RFT1 Gene

Residual Variation Intolerance Score: 65.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.98; 68.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RFT1 Gene

Human Gene Mutation Database (HGMD)
RFT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFT1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFT1 Gene

Disorders for RFT1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RFT1 Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
congenital disorder of glycosylation, type in
  • congenital disorder of glycosylation
- elite association - COSMIC cancer census association via MalaCards
Search RFT1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RFT1_HUMAN
  • Congenital disorder of glycosylation 1N (CDG1N) [MIM:612015]: A form of congenital disorder of glycosylation, a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269 PubMed:18313027, ECO:0000269 PubMed:19701946}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RFT1

Genetic Association Database (GAD)
RFT1
Human Genome Epidemiology (HuGE) Navigator
RFT1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RFT1
genes like me logo Genes that share disorders with RFT1: view

No data available for Genatlas for RFT1 Gene

Publications for RFT1 Gene

  1. Human RFT1 deficiency leads to a disorder of N-linked glycosylation. (PMID: 18313027) Haeuptle MA … Hennet T (American journal of human genetics 2008) 2 3 4 60
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  5. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 60

Products for RFT1 Gene

Sources for RFT1 Gene

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