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] See more...

Aliases for RFT1 Gene

Aliases for RFT1 Gene

  • RFT1 Homolog 2 3 5
  • Congenital Disorder Of Glycosylation 1N 2 3
  • Protein RFT1 Homolog 3 4
  • 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
  • CDG1N 3

External Ids for RFT1 Gene

Previous GeneCards Identifiers for RFT1 Gene

  • GC03U990226
  • GC03M052377
  • GC03M052980
  • GC03M053082
  • GC03M053100
  • GC03M053122

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 Metabolism of proteins and Transport to the Golgi and subsequent modification. Gene Ontology (GO) annotations related to this gene include lipid transporter activity. An important paralog of this gene is ENSG00000272305.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for RFT1 Gene

Genomics for RFT1 Gene

GeneHancer (GH) Regulatory Elements for RFT1 Gene

Promoters and enhancers for RFT1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J053129 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 516.1 -0.2 -241 3 ZNF217 EP300 CTCF SIN3A MYC POLR2G NCOR1 GTF2E2 PHF8 TEAD4 RFT1 SFMBT1 piR-36495
GH03J053128 Enhancer 0.2 dbSUPER 516.6 +1.8 1770 0.7 RFT1 piR-48759-205
GH03J053071 Enhancer 1.3 FANTOM5 ENCODE CraniofacialAtlas 44.6 +57.5 57458 2.3 ZBTB40 CTCF SIN3A POLR2G ZFX ZBTB11 ZNF423 GABPA REST MYC RFT1 ITIH4 STIMATE ITIH1 STIMATE-MUSTN1 ENSG00000243696 MUSTN1 SFMBT1 DCP1A lnc-RFT1-3
GH03J052683 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 24 +444.2 444237 5.2 FOXK2 ZBTB40 ZNF217 EP300 SIN3A TCF12 NRF1 MYC POLR2G USF1 PBRM1 GNL3 HSALNG0026174 RRP9 RFT1 ABHD14B GLT8D1 SNORD19B NISCH RPL29
GH03J053090 Enhancer 1 Ensembl ENCODE 55.3 +37.8 37768 5.8 EP300 NCOR1 ZIC2 TCF7 ZBTB7A SKI ZBTB26 FOXA2 CEBPB SAP130 RFT1 ITIH4 STIMATE STIMATE-MUSTN1 ENSG00000243696 MUSTN1 lnc-RFT1-1-002 ENSG00000272305
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RFT1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RFT1

Top Transcription factor binding sites by QIAGEN in the RFT1 gene promoter:
  • AP-1
  • CREB
  • deltaCREB
  • p53
  • STAT3

Genomic Locations for RFT1 Gene

Genomic Locations for RFT1 Gene
chr3:53,071,152-53,130,459
(GRCh38/hg38)
Size:
59,308 bases
Orientation:
Minus strand
chr3:53,122,499-53,164,478
(GRCh37/hg19)
Size:
41,980 bases
Orientation:
Minus strand

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:
  • Protein RFT1 homolog (RFT1_HUMAN)

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

Animal Models for RFT1 Gene

MGI Knock Outs for RFT1:
  • Rft1 Rft1<tm1b(KOMP)Wtsi>

Animal Model Products

CRISPR Products

miRNA for RFT1 Gene

miRTarBase miRNAs that target RFT1

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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 3
plasma membrane 2

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 21873635
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:0006869 lipid transport IEA --
GO:0008643 carbohydrate transport IEA --
GO:0034203 glycolipid translocation IBA 21873635
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

mRNA/cDNA for RFT1 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

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

Expression for RFT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for RFT1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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
Regions:
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 31 30
  • 99.38 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RFT1 31 30
  • 89.77 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RFT1 31 30
  • 89.4 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rft1 17 31 30
  • 85.34 (n)
rat
(Rattus norvegicus)
Mammalia Rft1 30
  • 85.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 79 (a)
OneToMany
-- 31
  • 76 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia RFT1 31
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves RFT1 31 30
  • 71.08 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFT1 31
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rft1 30
  • 65.47 (n)
zebrafish
(Danio rerio)
Actinopterygii rft1 31 30
  • 65.24 (n)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG3149 31 30
  • 48.6 (n)
OneToMany
BcDNA:GH08388 32
  • 37 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004419 30
  • 47.12 (n)
worm
(Caenorhabditis elegans)
Secernentea ZK180.3 31 32 30
  • 43.69 (n)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR015W 30
  • 42.75 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RFT1 33 31 30
  • 42.28 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E10451g 30
  • 41.12 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G07630 30
  • 44.92 (n)
rice
(Oryza sativa)
Liliopsida Os07g0486100 30
  • 47.96 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 49 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU05783 30
  • 41.31 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rft1 30
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RFT1: view image

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RFT1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
638394 Uncertain Significance: Congenital disorder of glycosylation type 1N 53,106,867(-) C/T MISSENSE_VARIANT
651416 Uncertain Significance: Congenital disorder of glycosylation type 1N 53,130,345(-) A/G MISSENSE_VARIANT
697945 Likely Benign: not provided 53,130,396(-) C/T MISSENSE_VARIANT
703886 Likely Benign: not provided 53,092,427(-) A/C MISSENSE_VARIANT
705706 Likely Benign: not provided 53,103,981(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for RFT1 Gene

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

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

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)

Additional Variant Information for RFT1 Gene

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

SNP Genotyping and Copy Number Assay Products

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: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
congenital disorder of glycosylation, type in
  • cdg1n
- 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.

Additional Disease Information for RFT1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 54
  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 41 54
  3. A family with floppy neonates with severe respiratory insufficiency: A lethal phenotype of RFT1-CDG due to a novel mutation. (PMID: 30071302) Abiramalatha T … Thomas N (European journal of medical genetics 2019) 3 54
  4. Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability. (PMID: 30194290) Adhikari H … Counter CM (Nature communications 2018) 3 54
  5. Single-center experience of N-linked Congenital Disorders of Glycosylation with a Summary of Molecularly Characterized Cases in Arabs. (PMID: 28940310) Bastaki F … Hamzeh AR (Annals of human genetics 2018) 3 54

Products for RFT1 Gene

Sources for RFT1 Gene