Human Gene CD46 (ENST00000367042.6_9) from GENCODE V47lift37
  Description: CD46 molecule, transcript variant i (from RefSeq NM_172355.3)
Gencode Transcript: ENST00000367042.6_9
Gencode Gene: ENSG00000117335.21_16
Transcript (Including UTRs)
   Position: hg19 chr1:207,925,399-207,968,849 Size: 43,451 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr1:207,925,558-207,963,649 Size: 38,092 Coding Exon Count: 12 

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Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:207,925,399-207,968,849)mRNA (may differ from genome)Protein (377 aa)
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-  Comments and Description Text from UniProtKB
  ID: MCP_HUMAN
DESCRIPTION: RecName: Full=Membrane cofactor protein; AltName: Full=TLX; AltName: Full=Trophoblast leukocyte common antigen; AltName: CD_antigen=CD46; Flags: Precursor;
FUNCTION: Acts as a cofactor for complement factor I, a serine protease which protects autologous cells against complement- mediated injury by cleaving C3b and C4b deposited on host tissue. May be involved in the fusion of the spermatozoa with the oocyte during fertilization. Also acts as a costimulatory factor for T- cells which induces the differentiation of CD4+ into T-regulatory 1 cells. T-regulatory 1 cells suppress immune responses by secreting interleukin-10, and therefore are thought to prevent autoimmunity. A number of viral and bacterial pathogens seem to exploit this property and directly induce an immunosuppressive phenotype in T-cells by binding to CD46.
SUBUNIT: Interacts with C3b and C4b. Binds to Measles virus H protein, to Human herpesvirus 6 GH protein and to human adenovirus B/D PIV/fiber protein, and acts as a receptor for these viruses. Binds to Streptococcus pyogenes M protein and to type IV pili from Neisseria, and may act as a receptor for these pathogenic bacteria.
SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle, acrosome inner membrane; Single-pass type I membrane protein. Note=Inner acrosomal membrane of spermatozoa. Internalized upon binding of Measles virus, Herpesvirus 6 or Neisseria gonorrhoeae, which results in an increased susceptibility of infected cells to complement-mediated injury. In cancer cells or cells infected by Neisseria, shedding leads to a soluble peptide.
TISSUE SPECIFICITY: Expressed by all cells except erythrocytes.
DOMAIN: Sushi domains 1 and 2 are required for interaction with human adenovirus B PIV/FIBER protein and with Measles virus H protein. Sushi domains 2 and 3 are required for Herpesvirus 6 binding. Sushi domain 3 is required for Neisseria binding. Sushi domains 3 and 4 are required for interaction with Streptococcus pyogenes M protein and are the most important for interaction with C3b and C4b.
PTM: N-glycosylated on Asn-83; Asn-114 and Asn-273 in most tissues, but probably less N-glycosylated in testis. N- glycosylation on Asn-114 and Asn-273 is required for cytoprotective function. N-glycosylation on Asn-114 is required for Measles virus binding. N-glycosylation on Asn-273 is required for Neisseria binding. N-glycosylation is not required for human adenovirus binding.
PTM: Extensively O-glycosylated in the Ser/Thr-rich domain. O- glycosylation is required for Neisseria binding but not for Measles virus or human adenovirus binding.
PTM: In epithelial cells, isoforms B/D/F/H/J/L/3 are phosphorylated by YES1 in response to infection by Neisseria gonorrhoeae; which promotes infectivity. In T-cells, these isoforms may be phosphorylated by Lck.
DISEASE: Defects in CD46 are a cause of susceptibility to hemolytic uremic syndrome atypical type 2 (AHUS2) [MIM:612922]. An atypical form of hemolytic uremic syndrome. It is a complex genetic disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, renal failure and absence of episodes of enterocolitis and diarrhea. In contrast to typical hemolytic uremic syndrome, atypical forms have a poorer prognosis, with higher death rates and frequent progression to end-stage renal disease. Note=Susceptibility to the development of atypical hemolytic uremic syndrome can be conferred by mutations in various components of or regulatory factors in the complement cascade system. Other genes may play a role in modifying the phenotype. Patients with CD46 mutations seem to have an overall better prognosis compared to patients carrying CFH mutations.
SIMILARITY: Contains 4 Sushi (CCP/SCR) domains.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CD46";
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/mcp/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CD46
Diseases sorted by gene-association score: hemolytic uremic syndrome, atypical 2* (1655), measles (110), cd46-related atypical hemolytic-uremic syndrome* (100), hemolytic-uremic syndrome (43), hellp syndrome* (26), panencephalitis, subacute sclerosing (26), necrotizing fasciitis (23), shipyard eye (21), exanthema subitum (16), c3 deficiency (12), arthus reaction (11), fasciitis (11), thrombotic thrombocytopenic purpura (11), mumps (9), complement factor h deficiency (9), variola minor (9), thrombotic thrombocytopenic purpura, acquired (8), otosclerosis (7), membranoproliferative glomerulonephritis (7), afibrinogenemia (5), methylmalonic aciduria and homocystinuria, cblc type (5), neisseria meningitidis infection (3), macular degeneration, age-related, 1 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 70.16 RPKM in Adrenal Gland
Total median expression: 1302.49 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -62.90159-0.396 Picture PostScript Text
3' UTR -497.402027-0.245 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016060 - Complement_control_module
IPR017341 - M_CF_CD46
IPR000436 - Sushi_SCR_CCP

Pfam Domains:
PF00084 - Sushi repeat (SCR repeat)

SCOP Domains:
57535 - Complement control module/SCR domain
57184 - Growth factor receptor domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1CKL - X-ray MuPIT 1HR4 - Model 2O39 - X-ray 3INB - X-ray MuPIT 3L89 - X-ray MuPIT 3O8E - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P15529
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001618 virus receptor activity
GO:0005515 protein binding
GO:0038023 signaling receptor activity
GO:0045296 cadherin binding

Biological Process:
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0002456 T cell mediated immunity
GO:0006958 complement activation, classical pathway
GO:0007165 signal transduction
GO:0007338 single fertilization
GO:0008593 regulation of Notch signaling pathway
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0016032 viral process
GO:0030449 regulation of complement activation
GO:0032613 interleukin-10 production
GO:0032733 positive regulation of interleukin-10 production
GO:0035581 sequestering of extracellular ligand from receptor
GO:0042102 positive regulation of T cell proliferation
GO:0043382 positive regulation of memory T cell differentiation
GO:0045087 innate immune response
GO:0045591 positive regulation of regulatory T cell differentiation
GO:0046718 viral entry into host cell
GO:0071636 positive regulation of transforming growth factor beta production

Cellular Component:
GO:0002079 inner acrosomal membrane
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005925 focal adhesion
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031410 cytoplasmic vesicle
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BX537451 - Homo sapiens mRNA; cDNA DKFZp686I12109 (from clone DKFZp686I12109).
BX649050 - Homo sapiens mRNA; cDNA DKFZp779J0825 (from clone DKFZp779J0825).
X59405 - H.sapiens, gene for Membrane cofactor protein.
X59408 - H.sapiens, gene for Membrane cofactor protein.
BX640613 - Homo sapiens mRNA; cDNA DKFZp686A02252 (from clone DKFZp686A02252).
AK291227 - Homo sapiens cDNA FLJ76828 complete cds, highly similar to Homo sapiens membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen) (MCP), transcript variant d, mRNA.
AK296819 - Homo sapiens cDNA FLJ58072 complete cds, highly similar to Membrane cofactor protein precursor.
BC026273 - Homo sapiens cDNA clone IMAGE:4250653, containing frame-shift errors.
BC030594 - Homo sapiens CD46 molecule, complement regulatory protein, mRNA (cDNA clone MGC:26544 IMAGE:4823040), complete cds.
JD482505 - Sequence 463529 from Patent EP1572962.
X59406 - H.sapiens, gene for Membrane cofactor protein.
X59407 - H.sapiens, gene for Membrane cofactor protein.
X59409 - H.sapiens, gene for Membrane cofactor protein.
X59410 - H.sapiens, gene for Membrane cofactor protein.
AK222822 - Homo sapiens mRNA for membrane cofactor protein isoform 2 precursor variant, clone: HEP05768.
JD538421 - Sequence 519445 from Patent EP1572962.
BC007046 - Homo sapiens cDNA clone IMAGE:3996343, containing frame-shift errors.
S51940 - membrane cofactor protein [human, testis, mRNA, 1248 nt].
JD259599 - Sequence 240623 from Patent EP1572962.
Y00651 - Human mRNA for membrane cofactor protein.
EF076055 - Homo sapiens isolate GS CD46 mRNA, complete cds.
EF076056 - Homo sapiens isolate GL CD46 mRNA, complete cds.
EF076057 - Homo sapiens isolate GL CD46 mRNA, complete cds.
EF076058 - Homo sapiens cell-line HT1080 CD46 mRNA, complete cds.
A18585 - complete nucleotide sequence of the pm5.1 clone of CD46.
M58050 - Human membrane cofactor protein (MCP) mRNA, complete cds.
D84105 - Homo sapiens CD46 mRNA, complete cds.
KJ897179 - Synthetic construct Homo sapiens clone ccsbBroadEn_06573 CD46 gene, encodes complete protein.
AB462973 - Synthetic construct DNA, clone: pF1KB4619, Homo sapiens CD46 gene for CD46 molecule, complement regulatory protein, without stop codon, in Flexi system.
DQ890901 - Synthetic construct clone IMAGE:100003531; FLH166932.01X; RZPDo839F0288D CD46 molecule, complement regulatory protein (CD46) gene, encodes complete protein.
DQ894054 - Synthetic construct Homo sapiens clone IMAGE:100008514; FLH166928.01L; RZPDo839F0287D CD46 molecule, complement regulatory protein (CD46) gene, encodes complete protein.
AF209712 - Homo sapiens membrane cofactor protein CD46 variant (MCP) mRNA, partial cds.
AF209713 - Homo sapiens membrane cofactor protein CD46 variant (MCP) mRNA, partial cds.
AF209714 - Homo sapiens membrane cofactor protein CD46 variant (MCP) mRNA, partial cds.
JD024089 - Sequence 5113 from Patent EP1572962.
JD029322 - Sequence 10346 from Patent EP1572962.
JD029189 - Sequence 10213 from Patent EP1572962.
Y07713 - H.sapiens mRNA for membrane cofactor protein CD46.
A18589 - Carboxyl-terminal partial CD46 gene.
AK129560 - Homo sapiens cDNA FLJ26049 fis, clone PRS02694.
JD470931 - Sequence 451955 from Patent EP1572962.
JD285744 - Sequence 266768 from Patent EP1572962.
JD239527 - Sequence 220551 from Patent EP1572962.
JD531133 - Sequence 512157 from Patent EP1572962.
A18587 - 3' untranslated region of the pm5.1 sequence in A18585.
JD308573 - Sequence 289597 from Patent EP1572962.
JD500797 - Sequence 481821 from Patent EP1572962.
JD171737 - Sequence 152761 from Patent EP1572962.
JD334970 - Sequence 315994 from Patent EP1572962.
JD513801 - Sequence 494825 from Patent EP1572962.
JD334206 - Sequence 315230 from Patent EP1572962.
JD037792 - Sequence 18816 from Patent EP1572962.
JD042704 - Sequence 23728 from Patent EP1572962.
JD297208 - Sequence 278232 from Patent EP1572962.
JD097917 - Sequence 78941 from Patent EP1572962.
JD350341 - Sequence 331365 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P15529 (Reactome details) participates in the following event(s):

R-HSA-1006143 CD46 binds C3b
R-HSA-8951486 CD46 binds C4b
R-HSA-977615 Factor I inactivates MCP/CR1-bound C4b/C3b
R-HSA-977602 Complement factor I binds to MCP, CR1:C4b, C3b
R-HSA-977606 Regulation of Complement cascade
R-HSA-166658 Complement cascade
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A0T1T0, A0T1T1, A0T1T2, ENST00000367042.1, ENST00000367042.2, ENST00000367042.3, ENST00000367042.4, ENST00000367042.5, MCP, MCP_HUMAN, MIC10, NM_172355, P15529, Q15429, Q53GV9, Q5HY94, Q5VWS6, Q5VWS7, Q5VWS8, Q5VWS9, Q5VWT0, Q5VWT1, Q5VWT2, Q6N0A1, Q7Z3R5, Q9NNW2, Q9NNW3, Q9NNW4, Q9UCJ4, uc318fou.1, uc318fou.2
UCSC ID: ENST00000367042.6_9
RefSeq Accession: NM_172351.3
Protein: P15529 (aka MCP_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CD46:
husa (Genetic Atypical Hemolytic-Uremic Syndrome)
mpgn (C3 Glomerulopathy)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.