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    EDEM3 ER degradation enhancing alpha-mannosidase like protein 3 [ Homo sapiens (human) ]

    Gene ID: 80267, updated on 27-Nov-2024

    Summary

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    Official Symbol
    EDEM3provided by HGNC
    Official Full Name
    ER degradation enhancing alpha-mannosidase like protein 3provided by HGNC
    Primary source
    HGNC:HGNC:16787
    See related
    Ensembl:ENSG00000116406 MIM:610214; AllianceGenome:HGNC:16787
    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
    CDG2V; C1orf22
    Summary
    Quality control in the endoplasmic reticulum (ER) ensures that only properly folded proteins are retained in the cell through recognition and degradation of misfolded or unassembled proteins. EDEM3 belongs to a group of proteins that accelerate degradation of misfolded glycoproteins in the ER (Hirao et al., 2006 [PubMed 16431915]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in stomach (RPKM 15.9), colon (RPKM 13.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EDEM3 in Genome Data Viewer
    Location:
    1q25.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (184690237..184754858, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (184053426..184118046, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (184659371..184723992, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2235 Neighboring gene uncharacterized LOC105371648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2238 Neighboring gene uncharacterized LOC105371649 Neighboring gene uncharacterized LOC107985238 Neighboring gene niban apoptosis regulator 1 Neighboring gene RNA, U7 small nuclear 13 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
    • 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. Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer. Scott E, et al. Int J Mol Sci, 2022 Jul 25. PMID 35897761, Free PMC Article
    2. Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation. Polla DL, et al. Am J Hum Genet, 2021 Jul 1. PMID 34143952, Free PMC Article
    3. Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD. George G, et al. Elife, 2021 Oct 26. PMID 34698634, Free PMC Article
    4. IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality. Kofanova O, et al. J Immunol Methods, 2019 Feb. PMID 30496732
    5. Glycoprotein folding and the role of EDEM1, EDEM2 and EDEM3 in degradation of folding-defective glycoproteins. Olivari S, et al. FEBS Lett, 2007 Jul 31. PMID 17499246

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer.
      Title: Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer.
    2. Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD.
      Title: Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD.
    3. Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation.
      Title: Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation.
    4. EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning.
      Title: EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning.
    5. IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality.
      Title: IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality.
    6. the mannose-trimming activity of EDEM3 toward the model misfolded substrate, the glycoprotein T-cell receptor alpha locus (TCRalpha), was reconstituted only when ERp46 had established a covalent interaction with EDEM3
      Title: ER-resident protein 46 (ERp46) triggers the mannose-trimming activity of ER degradation-enhancing α-mannosidase-like protein 3 (EDEM3).
    7. The data corroborated herein suggest that besides ER residents, EDEM3 interacts also with proteins involved in the ERAD cargo recognition and targeting to degradation translocation into the cytosol, including UBA1 and UBA2 ubiquitinating enzymes. In addition, the results indicate that this network of EDEM3 interactors is highly sensitive to interfering with early ER N-glycan processing.
      Title: Inhibition of N-glycan processing modulates the network of EDEM3 interactors.
    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

    Associated conditions

    Description Tests
    Congenital disorder of glycosylation, type 2v
    MedGen: C5561971 OMIM: 619493 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with ER degradation enhancer, mannosidase alpha-like 3 (EDEM3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with EDEM3; predicted interaction to be within the endoplasmic reticulum and function as chaperone for endoplasmic reticulum-associated degradation PubMed

    Go to the HIV-1, Human Interaction Database

    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 calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endoplasmic reticulum mannose trimming IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endoplasmic reticulum unfolded protein response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mannoprotein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mannoprotein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein glycosylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent glycoprotein ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum lumen IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum quality control compartment TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ER degradation-enhancing alpha-mannosidase-like protein 3
    Names
    ER degradation enhancer, mannosidase alpha-like 3
    ER degradation-enhancing -mannosidase-like protein 3
    ER degradation-enhancing alpha-mannosidase-like 3
    alpha-1,2-mannosidase EDEM3
    NP_001306889.1
    NP_079467.3
    XP_005245556.1
    XP_011508314.1
    XP_054194843.1
    XP_054194844.1

    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_001319960.2 → NP_001306889.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AI521228, AL096819, BC016464, BC144149, DA724785
      Consensus CDS
      CCDS91128.1
      UniProtKB/TrEMBL
      A0A8I5KTR7, A0A8J8YX80
      Related
      ENSP00000356482.4, ENST00000367512.8
      Conserved Domains (2) summary
      cd02126
      Location:664 → 789
      PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...
      pfam01532
      Location:59 → 498
      Glyco_hydro_47; Glycosyl hydrolase family 47

    2. NM_025191.4 → NP_079467.3  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_079467.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AF288393, AI521228, AL096819, BC016464, DA724785
      Consensus CDS
      CCDS1363.2
      UniProtKB/Swiss-Prot
      B2RCH6, B7ZLZ2, Q0VGM5, Q5TEZ0, Q7L2Y5, Q9BZQ6, Q9HCW1, Q9UFV7
      UniProtKB/TrEMBL
      A0A8I5KTR7
      Related
      ENSP00000318147.7, ENST00000318130.13
      Conserved Domains (2) summary
      cd02126
      Location:664 → 789
      PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...
      pfam01532
      Location:59 → 498
      Glyco_hydro_47; Glycosyl hydrolase family 47

    RNA

    1. NR_135118.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI521228, AL096819, BC016464, BC144150, DA724785

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      184690237..184754858 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510012.2 → XP_011508314.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8I5KWI4
      Related
      ENSP00000509571.1, ENST00000687113.1
      Conserved Domains (2) summary
      cd02126
      Location:588 → 713
      PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...
      pfam01532
      Location:1 → 421
      Glyco_hydro_47; Glycosyl hydrolase family 47

    2. XM_005245499.3 → XP_005245556.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I5KTR7
      Conserved Domains (2) summary
      cd02126
      Location:665 → 790
      PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...
      pfam01532
      Location:59 → 498
      Glyco_hydro_47; Glycosyl hydrolase family 47

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      184053426..184118046 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338869.1 → XP_054194844.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

    2. XM_054338868.1 → XP_054194843.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZQ6.2 GenPept UniProtKB/Swiss-Prot:Q9BZQ6

    Gene LinkOut

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

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