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    CD164 CD164 molecule [ Homo sapiens (human) ]

    Gene ID: 8763, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CD164provided by HGNC
    Official Full Name
    CD164 moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:1632
    See related
    Ensembl:ENSG00000135535 MIM:603356; AllianceGenome:HGNC:1632
    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
    DFNA66; MGC-24; MUC-24; MGC-24v; endolyn
    Summary
    This gene encodes a transmembrane sialomucin and cell adhesion molecule that regulates the proliferation, adhesion and migration of hematopoietic progenitor cells. The encoded protein also interacts with the C-X-C chemokine receptor type 4 and may regulate muscle development. Elevated expression of this gene has been observed in human patients with Sezary syndrome, a type of blood cancer, and a mutation in this gene may be associated with impaired hearing. [provided by RefSeq, Oct 2016]
    Expression
    Ubiquitous expression in thyroid (RPKM 246.6), fat (RPKM 191.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CD164 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (109366514..109382467, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (110544551..110560504, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (109687717..109703670, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 162, pseudogene Neighboring gene RNY3 pseudogene 11 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:109649788-109650315 Neighboring gene ribosomal protein L7 pseudogene 28 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17458 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:109703563-109704072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24923 Neighboring gene Sharpr-MPRA regulatory region 15445 Neighboring gene peptidylprolyl isomerase like 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:109761883-109762088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109775979-109776487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24928 Neighboring gene microtubule associated monooxygenase, calponin and LIM domain containing 1 Neighboring gene sphingomyelin phosphodiesterase 2 Neighboring gene zinc finger and BTB domain containing 24

    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 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. Cis-regulatory functions of overlapping HIF-1alpha/E-box/AP-1-like sequences of CD164. Tang J, et al. BMC Mol Biol, 2011 Oct 14. PMID 21999799, Free PMC Article
    2. A novel core protein as well as polymorphic epithelial mucin carry peanut agglutinin binding sites in human gastric carcinoma cells: sequence analysis and examination of gene expression. Masuzawa Y, et al. J Biochem, 1992 Nov. PMID 1478919
    3. CD164, a novel sialomucin on CD34(+) and erythroid subsets, is located on human chromosome 6q21. Watt SM, et al. Blood, 1998 Aug 1. PMID 9680353
    4. The sialomucin CD164 (MGC-24v) is an adhesive glycoprotein expressed by human hematopoietic progenitors and bone marrow stromal cells that serves as a potent negative regulator of hematopoiesis. Zannettino AC, et al. Blood, 1998 Oct 15. PMID 9763543
    5. CD164 monoclonal antibodies that block hemopoietic progenitor cell adhesion and proliferation interact with the first mucin domain of the CD164 receptor. Doyonnas R, et al. J Immunol, 2000 Jul 15. PMID 10878358

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus.
      Title: Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus.
    2. Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
      Title: Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
    3. CD164 is a host factor for lymphocytic choriomeningitis virus entry.
      Title: CD164 is a host factor for lymphocytic choriomeningitis virus entry.
    4. RP11619L19.2 promotes colon cancer development by regulating the miR12715p/CD164 axis.
      Title: RP11‑619L19.2 promotes colon cancer development by regulating the miR‑1271‑5p/CD164 axis.
    5. miR-219a-5p enhances the radiosensitivity of non-small cell lung cancer cells through targeting CD164.
      Title: miR-219a-5p enhances the radiosensitivity of non-small cell lung cancer cells through targeting CD164.
    6. Long non-coding RNA LINC00152/miR-613/CD164 axis regulates cell proliferation, apoptosis, migration and invasion in glioma via PI3K/AKT pathway.
      Title: Long non-coding RNA LINC00152/miR-613/CD164 axis regulates cell proliferation, apoptosis, migration and invasion in glioma via PI3K/AKT pathway.
    7. CD164 was associated with the poor clinical outcomes of BC patients. Silencing of CD164 could inhibit the progression of tumors in vivo and in vitro, which may become an effective target in the treatment of bladder cancer.
      Title: CD164 promotes tumor progression and predicts the poor prognosis of bladder cancer.
    8. CD164 is expressed by cells that are multipotent until just beyond the first erythroid-megakaryocyte progenitors/lymphoid-myeloid progenitors branch point.
      Title: A comprehensive single cell transcriptional landscape of human hematopoietic progenitors.
    9. CD164 expression may have affected the proliferation and apoptosis of human glioma cells via the PTEN/phosphoinositide 3-kinase/AKT pathway.
      Title: CD164 regulates proliferation and apoptosis by targeting PTEN in human glioma.
    10. The expression of Sezary signature genes: FCRL3, Tox, and miR-214, was significantly higher in samples from Sezary syndrome patients with CD164 expressing CD4(+) T cells.
      Title: CD164 identifies CD4(+) T cells highly expressing genes associated with malignancy in Sézary syndrome: the Sézary signature genes, FCRL3, Tox, and miR-214.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    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
    Autosomal dominant nonsyndromic hearing loss 66
    MedGen: C4283893 OMIM: 616969 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.
    EBI GWAS Catalog
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
    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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    Replication interactions

    Interaction Pubs
    Infectious wild type HIV-1 production is restricted by 293T cells over-expressing CD164 PubMed
    Knockdown of CD164 molecule (sialomucin) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD164 PubMed
    Vpu vpu Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD164 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in hemopoiesis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in immune response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in muscle organ development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cell adhesion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sialomucin core protein 24
    Names
    CD164 antigen, sialomucin
    multi-glycosylated core protein 24

    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_051926.1 RefSeqGene

      Range
      5346..21299
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1419

    mRNA and Protein(s)

    1. NM_001142401.3 → NP_001135873.1  sialomucin core protein 24 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001135873.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
      Source sequence(s)
      AF299343, BM668503, DC402684
      Consensus CDS
      CCDS47464.1
      UniProtKB/Swiss-Prot
      Q04900
      Related
      ENSP00000275080.7, ENST00000275080.11
      Conserved Domains (1) summary
      pfam05283
      Location:60 → 184
      MGC-24; Multi-glycosylated core protein 24 (MGC-24), sialomucin

    2. NM_001142402.3 → NP_001135874.1  sialomucin core protein 24 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001135874.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.
      Source sequence(s)
      AF299342, BM668503, DC402684
      Consensus CDS
      CCDS47465.1
      UniProtKB/Swiss-Prot
      Q04900
      Related
      ENSP00000314177.5, ENST00000324953.9
      Conserved Domains (1) summary
      pfam05283
      Location:60 → 178
      MGC-24; Multi-glycosylated core protein 24 (MGC-24), sialomucin

    3. NM_001142403.3 → NP_001135875.1  sialomucin core protein 24 isoform 4 precursor

      See identical proteins and their annotated locations for NP_001135875.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses alternate splice sites in the 3' coding region, compared to variant 1. It encodes isoform 4 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL359711
      Consensus CDS
      CCDS47463.1
      UniProtKB/Swiss-Prot
      Q04900
      Related
      ENSP00000402237.2, ENST00000413644.6
      Conserved Domains (1) summary
      pfam05283
      Location:60 → 174
      MGC-24; Multi-glycosylated core protein 24 (MGC-24), sialomucin

    4. NM_001142404.3 → NP_001135876.1  sialomucin core protein 24 isoform 5 precursor

      See identical proteins and their annotated locations for NP_001135876.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 5 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK298684, BM668503, BM830140, DC402684, EB388947
      Consensus CDS
      CCDS47462.1
      UniProtKB/TrEMBL
      B4DWV2
      Related
      ENSP00000427546.1, ENST00000512821.5
      Conserved Domains (1) summary
      pfam05283
      Location:60 → 130
      MGC-24; Multi-glycosylated core protein 24 (MGC-24), sialomucin

    5. NM_001346500.2 → NP_001333429.1  sialomucin core protein 24 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses an alternate translation start site compared to variant 1. The encoded isoform (6) has a shorter and distinct N-terminus, and lacks a predicted signal peptide compared to isoform 1.
      Source sequence(s)
      AL359711
      Consensus CDS
      CCDS87430.1
      UniProtKB/TrEMBL
      D6R9B4
      Related
      ENSP00000422999.1, ENST00000504373.2
      Conserved Domains (1) summary
      pfam05283
      Location:26 → 163
      MGC-24; Multi-glycosylated core protein 24 (MGC-24), sialomucin

    6. NM_006016.6 → NP_006007.2  sialomucin core protein 24 isoform 1 precursor

      See identical proteins and their annotated locations for NP_006007.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL359711
      Consensus CDS
      CCDS5073.1
      UniProtKB/Swiss-Prot
      B4DQ85, E1P5E7, E1P5E8, E1P5E9, O95413, Q04900, Q5JSU6, Q9BPV0, Q9NR26
      Related
      ENSP00000309376.4, ENST00000310786.10
      Conserved Domains (1) summary
      pfam05283
      Location:60 → 197
      MGC-24; Multi-glycosylated core protein 24 (MGC-24), sialomucin

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      109366514..109382467 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      110544551..110560504 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q04900.2 GenPept UniProtKB/Swiss-Prot:Q04900

    Gene LinkOut

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

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