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    CD46 CD46 molecule [ Homo sapiens (human) ]

    Gene ID: 4179, updated on 13-Jan-2020

    Summary

    Official Symbol
    CD46provided by HGNC
    Official Full Name
    CD46 moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:6953
    See related
    Ensembl:ENSG00000117335 MIM:120920
    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
    MCP; TLX; AHUS2; MIC10; TRA2.10
    Summary
    The protein encoded by this gene is a type I membrane protein and is a regulatory part of the complement system. The encoded protein has cofactor activity for inactivation of complement components C3b and C4b by serum factor I, which protects the host cell from damage by complement. In addition, the encoded protein can act as a receptor for the Edmonston strain of measles virus, human herpesvirus-6, and type IV pili of pathogenic Neisseria. Finally, the protein encoded by this gene may be involved in the fusion of the spermatozoa with the oocyte during fertilization. Mutations at this locus have been associated with susceptibility to hemolytic uremic syndrome. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2010]
    Expression
    Ubiquitous expression in adrenal (RPKM 99.0), placenta (RPKM 71.8) and 25 other tissues See more
    Orthologs

    Genomic context

    See CD46 in Genome Data Viewer
    Location:
    1q32.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (207752038..207795516)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (207925383..207968861)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr1.11362 Neighboring gene Sharpr-MPRA regulatory region 12474 Neighboring gene cell division cycle associated 4 pseudogene 4 Neighboring gene MIR29B2 and MIR29C host gene Neighboring gene microRNA 29b-2 Neighboring gene microRNA 29c

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Atypical hemolytic-uremic syndrome 2 Compare labs

    NHGRI GWAS Catalog

    Description
    A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits.
    NHGRI GWA Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    NHGRI GWA Catalog
    Common variants associated with general and MMR vaccine-related febrile seizures.
    NHGRI GWA Catalog
    Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.
    NHGRI GWA Catalog
    Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis.
    NHGRI GWA Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of CD46 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef HIV-1 Nef downregulates the cell surface expression of CD46 PubMed
    Pr55(Gag) gag HIV-1 Gag associates with CD46 weakly in HeLa cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC26544

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cadherin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    signaling receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    virus receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    T cell mediated immunity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    adaptive immune response IC
    Inferred by Curator
    more info
    PubMed 
    complement activation, classical pathway IEA
    Inferred from Electronic Annotation
    more info
     
    innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    interleukin-10 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of T cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of interleukin-10 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of memory T cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of regulatory T cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transforming growth factor beta production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of Notch signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of complement activation TAS
    Traceable Author Statement
    more info
     
    sequestering of extracellular ligand from receptor IDA
    Inferred from Direct Assay
    more info
    PubMed 
    single fertilization IEA
    Inferred from Electronic Annotation
    more info
     
    viral entry into host cell IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome HDA PubMed 
    focal adhesion HDA PubMed 
    inner acrosomal membrane IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    membrane cofactor protein
    Names
    CD46 antigen, complement regulatory protein
    CD46 molecule, complement regulatory protein
    antigen identified by monoclonal antibody TRA-2-10
    complement membrane cofactor protein
    measles virus receptor
    membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)
    trophoblast leucocyte common antigen
    trophoblast leukocyte common antigen
    trophoblast-lymphocyte cross-reactive antigen

    NCBI Reference Sequences (RefSeq)

    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_009296.1 RefSeqGene

      Range
      4982..48460
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_155

    mRNA and Protein(s)

    1. NM_002389.4NP_002380.3  membrane cofactor protein isoform 1 precursor

      See identical proteins and their annotated locations for NP_002380.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (a) represents the longest transcript and encodes isoform 1.
      Source sequence(s)
      AI589224, BC030594, DB078198, X59410
      Consensus CDS
      CCDS1485.1
      UniProtKB/Swiss-Prot
      P15529
      Related
      ENSP00000350893.2, ENST00000358170.6
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    2. NM_153826.4NP_722548.1  membrane cofactor protein isoform 4 precursor

      See identical proteins and their annotated locations for NP_722548.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (d) lacks an alternate in-frame exon and an exon containing the stop codon as compared to variant a. The resulting isoform (4) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC030594, DB078198
      Consensus CDS
      CCDS1480.1
      UniProtKB/Swiss-Prot
      P15529
      Related
      ENSP00000346912.1, ENST00000354848.5
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    3. NM_172350.3NP_758860.1  membrane cofactor protein isoform 14 precursor

      See identical proteins and their annotated locations for NP_758860.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (n) lacks three alternate in-frame exons as well as an alternate segment compared to variant a, which causes a frameshift. The resulting isoform (14) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC030594, D84105, DB078198
      Consensus CDS
      CCDS1479.1
      UniProtKB/Swiss-Prot
      P15529
      Related
      ENSP00000314664.5, ENST00000322918.9
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    4. NM_172351.3NP_758861.1  membrane cofactor protein isoform 3 precursor

      See identical proteins and their annotated locations for NP_758861.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (c) lacks an alternate in-frame exon compared to variant a, resulting in a shorter isoform (3) compared to isoform 1.
      Source sequence(s)
      DB078198, X59405
      Consensus CDS
      CCDS31008.1
      UniProtKB/Swiss-Prot
      P15529
      Related
      ENSP00000356009.1, ENST00000367042.5
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    5. NM_172352.3NP_758862.1  membrane cofactor protein isoform 5 precursor

      See identical proteins and their annotated locations for NP_758862.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (e) lacks an alternate in-frame segment compared to variant a, resulting in a shorter isoform (5) compared to isoform 1.
      Source sequence(s)
      BC030594, DB078198, X59406
      Consensus CDS
      CCDS31009.1
      UniProtKB/Swiss-Prot
      P15529
      Related
      ENSP00000356008.1, ENST00000367041.5
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    6. NM_172353.3NP_758863.1  membrane cofactor protein isoform 6 precursor

      See identical proteins and their annotated locations for NP_758863.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (f) lacks an alternate in-frame exon and an exon containing the stop codon compared to variant a. The resulting isoform (6) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC030594, DB078198, X59407
      Consensus CDS
      CCDS1481.1
      UniProtKB/Swiss-Prot
      P15529
      Related
      ENSP00000350346.1, ENST00000357714.5
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    7. NM_172355.3NP_758865.1  membrane cofactor protein isoform 9 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (i) lacks two alternate in-frame exons compared to variant a, resulting in a shorter isoform (9) compared to isoform 1.
      Source sequence(s)
      AL035209, AL365178
      Conserved Domains (1) summary
      cl27761
      Location:54285
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    8. NM_172356.3NP_758866.1  membrane cofactor protein isoform 10 precursor

      Status: REVIEWED

      Source sequence(s)
      AL035209, AL365178
      Consensus CDS
      CCDS86048.1
      Related
      ENSP00000418471.1, ENST00000480003.5
      Conserved Domains (1) summary
      cl27761
      Location:54285
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    9. NM_172357.3NP_758867.1  membrane cofactor protein isoform 11 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (k) lacks an alternate in-frame segment compared to variant a, resulting in a shorter isoform (11) compared to isoform 1.
      Source sequence(s)
      AL035209, AL365178
      Conserved Domains (1) summary
      cl27761
      Location:54285
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    10. NM_172358.3NP_758868.1  membrane cofactor protein isoform 13 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (m) lacks an alternate in-frame exon, an alternate exon containing the stop codon, and an alternate segment compared to variant a, which causes a frameshift. The resulting isoform (13) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL035209, AL365178
      Conserved Domains (1) summary
      cl27761
      Location:54285
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    11. NM_172359.3NP_758869.1  membrane cofactor protein isoform 2 precursor

      See identical proteins and their annotated locations for NP_758869.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (b) lacks an alternate exon containing the stop codon compared to variant a. The resulting isoform (2) is longer and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK222822, BC030594, DB078198, X59410
      Consensus CDS
      CCDS1482.1
      UniProtKB/Swiss-Prot
      P15529
      Related
      ENSP00000313875.4, ENST00000322875.8
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    12. NM_172361.3NP_758871.1  membrane cofactor protein isoform 12 precursor

      See identical proteins and their annotated locations for NP_758871.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (l) lacks an alternate in-frame segment and an exon containing the stop codon as compared to variant a. The resulting isoform (12) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC030594, DB078198, EF076057
      Consensus CDS
      CCDS1484.1
      UniProtKB/Swiss-Prot
      P15529
      Related
      ENSP00000353342.2, ENST00000360212.6
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      207752038..207795516
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001308.2XP_016856797.1  membrane cofactor protein isoform X2

      UniProtKB/Swiss-Prot
      P15529
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    2. XM_011509563.2XP_011507865.1  membrane cofactor protein isoform X1

      See identical proteins and their annotated locations for XP_011507865.1

      UniProtKB/Swiss-Prot
      P15529
      Conserved Domains (2) summary
      cd00033
      Location:99158
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00032
      Location:3588
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)

    RNA

    1. XR_002956622.1 RNA Sequence

    2. XR_002956621.1 RNA Sequence

    3. XR_001737177.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_172354.1: Suppressed sequence

      Description
      NM_172354.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    2. NM_172360.1: Suppressed sequence

      Description
      NM_172360.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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