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CD46 CD46 molecule [ Homo sapiens (human) ]

Gene ID: 4179, updated on 19-Sep-2024

Summary

Official Symbol
CD46provided by HGNC
Official Full Name
CD46 moleculeprovided by HGNC
Primary source
HGNC:HGNC:6953
See related
Ensembl:ENSG00000117335 MIM:120920; AllianceGenome:HGNC:6953
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
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Genomic context

See CD46 in Genome Data Viewer
Location:
1q32.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (207752038..207795516)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (206998784..207042279)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (207925383..207968861)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene complement C3b/C4b receptor 1 like Neighboring gene complement C3b/C4b receptor 1 (Knops blood group) pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207903492-207904170 Neighboring gene CRISPRi-validated cis-regulatory element chr1.11362 Neighboring gene Sharpr-MPRA regulatory region 12474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2449 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:207925929-207926286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207935554-207936354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207936355-207937153 Neighboring gene cell division cycle associated 4 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2452 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 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

EBI GWAS Catalog

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

Clone Names

  • MGC26544

Gene Ontology Provided by GOA

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

NEW Try the new Transcript table

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
    A0T1T0, A0T1T1, A0T1T2, P15529, Q15429, Q53GV9, Q5HY94, Q5VWS6, Q5VWS7, Q5VWS8, Q5VWS9, Q5VWT0, Q5VWT1, Q5VWT2, Q6N0A1, Q7Z3R5, Q9NNW2, Q9NNW3, Q9NNW4, Q9UCJ4
    UniProtKB/TrEMBL
    A0A8Q3WKR0
    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/TrEMBL
    A0A8Q3WKR0
    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/TrEMBL
    A0A8Q3WLU6
    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/TrEMBL
    A0A8Q3WKR0
    Related
    ENSP00000356009.1, ENST00000367042.6
    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)
  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/TrEMBL
    A0A8Q3WKR0
    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/TrEMBL
    A0A8Q3WKR0
    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
    UniProtKB/TrEMBL
    A0A8Q3WKR0
    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
    UniProtKB/TrEMBL
    A0A8Q3WKR0
    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
    UniProtKB/TrEMBL
    A0A8Q3WKR0
    Related
    ENST00000695779.1
    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
    UniProtKB/TrEMBL
    A0A8Q3WLA6, A0A8Q3WLU6
    Related
    ENSP00000512167.1, ENST00000695777.1
    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/TrEMBL
    A0A8Q3WKR0
    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/TrEMBL
    A0A8Q3WKR0
    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: 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
    207752038..207795516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509563.3XP_011507865.1  membrane cofactor protein isoform X2

    See identical proteins and their annotated locations for XP_011507865.1

    UniProtKB/TrEMBL
    A0A8Q3WKR0
    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_047420888.1XP_047276844.1  membrane cofactor protein isoform X1

    UniProtKB/Swiss-Prot
    A0T1T0, A0T1T1, A0T1T2, P15529, Q15429, Q53GV9, Q5HY94, Q5VWS6, Q5VWS7, Q5VWS8, Q5VWS9, Q5VWT0, Q5VWT1, Q5VWT2, Q6N0A1, Q7Z3R5, Q9NNW2, Q9NNW3, Q9NNW4, Q9UCJ4
    UniProtKB/TrEMBL
    A0A8Q3WKR0
  3. XM_047420894.1XP_047276850.1  membrane cofactor protein isoform X3

    UniProtKB/TrEMBL
    A0A8Q3WKR0
  4. XM_047420901.1XP_047276857.1  membrane cofactor protein isoform X4

    UniProtKB/TrEMBL
    A0A8Q3WKR0
  5. XM_047420909.1XP_047276865.1  membrane cofactor protein isoform X5

    UniProtKB/TrEMBL
    A0A8Q3WKR0

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    206998784..207042279
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336646.1XP_054192621.1  membrane cofactor protein isoform X2

    UniProtKB/TrEMBL
    A0A8Q3WKR0
  2. XM_054336645.1XP_054192620.1  membrane cofactor protein isoform X1

    UniProtKB/Swiss-Prot
    A0T1T0, A0T1T1, A0T1T2, P15529, Q15429, Q53GV9, Q5HY94, Q5VWS6, Q5VWS7, Q5VWS8, Q5VWS9, Q5VWT0, Q5VWT1, Q5VWT2, Q6N0A1, Q7Z3R5, Q9NNW2, Q9NNW3, Q9NNW4, Q9UCJ4
    UniProtKB/TrEMBL
    A0A8Q3WKR0
  3. XM_054336647.1XP_054192622.1  membrane cofactor protein isoform X3

    UniProtKB/TrEMBL
    A0A8Q3WKR0
  4. XM_054336648.1XP_054192623.1  membrane cofactor protein isoform X4

    UniProtKB/TrEMBL
    A0A8Q3WKR0
  5. XM_054336649.1XP_054192624.1  membrane cofactor protein isoform X5

    UniProtKB/TrEMBL
    A0A8Q3WKR0

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.