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    EMC1 ER membrane protein complex subunit 1 [ Homo sapiens (human) ]

    Gene ID: 23065, updated on 10-Dec-2024

    Summary

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    Official Symbol
    EMC1provided by HGNC
    Official Full Name
    ER membrane protein complex subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:28957
    See related
    Ensembl:ENSG00000127463 MIM:616846; AllianceGenome:HGNC:28957
    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
    CAVIPMR; KIAA0090
    Summary
    This gene encodes a single-pass type I transmembrane protein, which is a subunit of the endoplasmic reticulum membrane protein complex (EMC). Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2012]
    Expression
    Ubiquitous expression in placenta (RPKM 10.5), brain (RPKM 9.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EMC1 in Genome Data Viewer
    Location:
    1p36.13
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (19215660..19251524, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (19039172..19075048, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (19542154..19578018, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376815 Neighboring gene MPRA-validated peak97 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19334779-19335422 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:19337151-19338350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19338425-19339336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19354797-19355297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19362307-19362878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19370112-19371086 Neighboring gene Sharpr-MPRA regulatory region 2200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19396435-19397360 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:19403898-19404066 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:19407589-19408788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 295 Neighboring gene ubiquitin protein ligase E3 component n-recognin 4 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:19446050-19447249 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:19448647-19449846 Neighboring gene NANOG hESC enhancer GRCh37_chr1:19453252-19454051 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:19465867-19466616 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:19482517-19483716 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:19487245-19488444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19528831-19529332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 297 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 351 Neighboring gene EMC1 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:19562203-19562373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19577931-19578436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19580253-19580754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19580755-19581254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19595541-19596389 Neighboring gene MRT4 homolog, ribosome maturation factor Neighboring gene aldo-keto reductase family 7 like (gene/pseudogene)

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. EMC1-dependent stabilization drives membrane penetration of a partially destabilized non-enveloped virus. Bagchi P, et al. Elife, 2016 Dec 24. PMID 28012275, Free PMC Article
    2. Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay, Hypotonia, Scoliosis, and Cerebellar Atrophy. Harel T, et al. Am J Hum Genet, 2016 Mar 3. PMID 26942288, Free PMC Article
    3. Novel truncating and missense variants extending the spectrum of EMC1-related phenotypes, causing autism spectrum disorder, severe global development delay and visual impairment. Cabet S, et al. Eur J Med Genet, 2020 Jun. PMID 32092440
    4. Structural basis for membrane insertion by the human ER membrane protein complex. Pleiner T, et al. Science, 2020 Jul 24. PMID 32439656, Free PMC Article
    5. EMC Is Required to Initiate Accurate Membrane Protein Topogenesis. Chitwood PJ, et al. Cell, 2018 Nov 29. PMID 30415835, Free PMC Article

    See all (104) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel truncating and missense variants extending the spectrum of EMC1-related phenotypes, causing autism spectrum disorder, severe global development delay and visual impairment.
      Title: Novel truncating and missense variants extending the spectrum of EMC1-related phenotypes, causing autism spectrum disorder, severe global development delay and visual impairment.
    2. The authors find that a member of the endoplasmic reticulum membrane protein complex (EMC) called EMC1 promotes SV40 virus endoplasmic reticulum membrane transport and infection.
      Title: EMC1-dependent stabilization drives membrane penetration of a partially destabilized non-enveloped virus.
    3. EMC1 is a gene in which either biallelic or monoallelic variants might lead to a syndrome including intellectual disability and preferential degeneration of the cerebellum.
      Title: Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay, Hypotonia, Scoliosis, and Cerebellar Atrophy.
    4. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Novel breast cancer risk alleles and interaction with ionizing radiation among U.S. radiologic technologists.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Cerebellar atrophy, visual impairment, and psychomotor retardation;
    MedGen: C4225172 OMIM: 616875 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Voxelwise genome-wide association study (vGWAS).
    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 transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with KIAA0090 in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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

    Clone Names

    • KIAA0090

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to membrane insertase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein insertion into ER membrane by stop-transfer membrane-anchor sequence IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein insertion into ER membrane by stop-transfer membrane-anchor sequence IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tail-anchored membrane protein insertion into ER membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of EMC complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of EMC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of EMC complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of EMC complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ER membrane protein complex subunit 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.

    Genomic

    1. NG_032948.1 RefSeqGene

      Range
      5036..40900
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001271427.2 → NP_001258356.1  ER membrane protein complex subunit 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001258356.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal aa, compared to isoform 1.
      Source sequence(s)
      AL357564, BX648708, D42044, DB097686
      Consensus CDS
      CCDS59191.1
      UniProtKB/TrEMBL
      A0A8I5KW55
      Related
      ENSP00000364345.3, ENST00000375199.7
      Conserved Domains (2) summary
      pfam07774
      Location:786 → 991
      DUF1620; Protein of unknown function (DUF1620)
      pfam13360
      Location:59 → 218
      PQQ_2; PQQ-like domain

    2. NM_001271428.2 → NP_001258357.1  ER membrane protein complex subunit 1 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central region, compared to variant 1. The resulting isoform (2) lacks an internal aa, compared to isoform 1.
      Source sequence(s)
      AL357564, BC034589, BX648708, DB097686
      UniProtKB/TrEMBL
      A0A8I5KW55
      Related
      ENSP00000510231.1, ENST00000688219.1
      Conserved Domains (2) summary
      pfam07774
      Location:786 → 991
      DUF1620; Protein of unknown function (DUF1620)
      pfam13360
      Location:59 → 218
      PQQ_2; PQQ-like domain

    3. NM_001271429.2 → NP_001258358.1  ER membrane protein complex subunit 1 isoform 4 precursor

      See identical proteins and their annotated locations for NP_001258358.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (4) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AK075563, AL357564, BC034589, BX648708, DB097686
      Consensus CDS
      CCDS59190.1
      UniProtKB/TrEMBL
      A0A8I5KW55
      Related
      ENSP00000364354.3, ENST00000375208.7
      Conserved Domains (1) summary
      pfam07774
      Location:765 → 970
      DUF1620; Protein of unknown function (DUF1620)

    4. NM_001375820.1 → NP_001362749.1  ER membrane protein complex subunit 1 isoform 5 precursor

      Status: REVIEWED

      Source sequence(s)
      AL035413, AL357564
      Consensus CDS
      CCDS90871.1
      UniProtKB/TrEMBL
      A0A8I5KW55, H7C5A2
      Related
      ENSP00000419345.2, ENST00000486405.2
      Conserved Domains (2) summary
      pfam07774
      Location:790 → 995
      DUF1620; Protein of unknown function (DUF1620)
      pfam13360
      Location:60 → 218
      PQQ_2; PQQ-like domain

    5. NM_001375821.1 → NP_001362750.1  ER membrane protein complex subunit 1 isoform 6 precursor

      Status: REVIEWED

      Source sequence(s)
      AL035413, AL357564
      UniProtKB/TrEMBL
      A0A8I5KW55
      Conserved Domains (2) summary
      pfam07774
      Location:789 → 994
      DUF1620; Protein of unknown function (DUF1620)
      pfam13360
      Location:60 → 218
      PQQ_2; PQQ-like domain

    6. NM_015047.3 → NP_055862.1  ER membrane protein complex subunit 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_055862.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL357564, BC034589, BX648708
      Consensus CDS
      CCDS190.1
      UniProtKB/Swiss-Prot
      A8K6F3, Q14700, Q5TG62, Q63HL0, Q63HL3, Q8N766, Q8NBH8
      UniProtKB/TrEMBL
      A0A8I5KW55
      Related
      ENSP00000420608.1, ENST00000477853.6
      Conserved Domains (2) summary
      pfam07774
      Location:787 → 992
      DUF1620; Protein of unknown function (DUF1620)
      pfam13360
      Location:59 → 218
      PQQ_2; PQQ-like domain

    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
      19215660..19251524 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      19039172..19075048 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N766.1 GenPept UniProtKB/Swiss-Prot:Q8N766

    Gene LinkOut

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

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