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

Gene ID: 23065, updated on 7-Apr-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
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Genomic context

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Location:
1p36.13
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (19215660..19251524, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (19039172..19075048, complement)
105.20220307 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: 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. 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
  2. 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
  3. 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
  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 (91) 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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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
Cerebellar atrophy, visual impairment, and psychomotor retardation;
MedGen: C4225172 OMIM: 616875 GeneReviews: Not available
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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)

Genotypes

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_2023_10

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

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