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    SIGLEC1 sialic acid binding Ig like lectin 1 [ Homo sapiens (human) ]

    Gene ID: 6614, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SIGLEC1provided by HGNC
    Official Full Name
    sialic acid binding Ig like lectin 1provided by HGNC
    Primary source
    HGNC:HGNC:11127
    See related
    Ensembl:ENSG00000088827 MIM:600751; AllianceGenome:HGNC:11127
    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
    SN; CD169; SIGLEC-1
    Summary
    This gene encodes a member of the immunoglobulin superfamily. The encoded protein is a lectin-like adhesion molecule that binds glycoconjugate ligands on cell surfaces in a sialic acid-dependent manner. It is a type I transmembrane protein expressed only by a subpopulation of macrophages and is involved in mediating cell-cell interactions. The protein plays an important role in multiple human diseases and bacterial and viral infections has been shown to enhance SARS-CoV-2 infection. [provided by RefSeq, Dec 2021]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in SARS-CoV-2 infection.
    Expression
    Broad expression in placenta (RPKM 8.2), spleen (RPKM 6.4) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SIGLEC1 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (3686970..3712600, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (3717911..3743544, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (3667617..3693247, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12623 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:3647557-3648086 Neighboring gene GDNF family receptor alpha 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3651223-3651828 Neighboring gene ADAM metallopeptidase domain 33 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3657784-3658386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3658990-3659591 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3662082-3662975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3678505-3679004 Neighboring gene Sharpr-MPRA regulatory region 3812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12624 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3713394-3713973 Neighboring gene heat shock protein family A (Hsp70) member 12B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3722898-3723425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3725082-3725992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3729440-3729992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3729993-3730543 Neighboring gene adipose secreted signaling protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3747545-3748309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3748437-3749023

    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. Increased Siglec-1 expression in monocytes of patients with primary biliary cirrhosis. Bao G, et al. Immunol Invest, 2010. PMID 20653431
    2. Constitutive Siglec-1 expression confers susceptibility to HIV-1 infection of human dendritic cell precursors. Ruffin N, et al. Proc Natl Acad Sci U S A, 2019 Oct 22. PMID 31591213, Free PMC Article
    3. Siglec-1 inhibits RSV-induced interferon gamma production by adult T cells in contrast to newborn T cells. Jans J, et al. Eur J Immunol, 2018 Apr. PMID 29266251, Free PMC Article
    4. Sialic Acid-Binding Immunoglobulin-Like Lectin1 as a Novel Predictive Biomarker for Relapse in Graves' Disease: A Multicenter Study. Hashimoto K, et al. Thyroid, 2018 Jan. PMID 29037117
    5. Polymorphisms in SIGLEC1 contribute to susceptibility to pulmonary active tuberculosis possibly through the modulation of IL-1ß. Souza de Lima D, et al. Infect Genet Evol, 2017 Nov. PMID 28964857

    See all (77) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel subpopulation of monocytes with a strong interferon signature indicated by SIGLEC-1 is present in patients with in recent-onset type 1 diabetes.
      Title: A novel subpopulation of monocytes with a strong interferon signature indicated by SIGLEC-1 is present in patients with in recent-onset type 1 diabetes.
    2. CD169 expression on monocytes as a marker for assessing type I interferon status in pediatric inflammatory diseases.
      Title: CD169 expression on monocytes as a marker for assessing type I interferon status in pediatric inflammatory diseases.
    3. Sialoadhesin (CD169/Siglec-1) is an extended molecule that escapes inhibitory cis-interactions and synergizes with other macrophage receptors to promote phagocytosis.
      Title: Sialoadhesin (CD169/Siglec-1) is an extended molecule that escapes inhibitory cis-interactions and synergizes with other macrophage receptors to promote phagocytosis.
    4. The role of sialic acid-binding immunoglobulin-like-lectin-1 (siglec-1) in immunology and infectious disease.
      Title: The role of sialic acid-binding immunoglobulin-like-lectin-1 (siglec-1) in immunology and infectious disease.
    5. CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses.
      Title: CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses.
    6. The role of activated monocyte IFN/SIGLEC1 signalling in Graves' disease.
      Title: The role of activated monocyte IFN/SIGLEC1 signalling in Graves' disease.
    7. SIGLEC1 enables straightforward assessment of type I interferon activity in idiopathic inflammatory myopathies.
      Title: SIGLEC1 enables straightforward assessment of type I interferon activity in idiopathic inflammatory myopathies.
    8. Siglec-1 expression on monocytes is associated with the interferon signature in juvenile dermatomyositis and can predict treatment response.
      Title: Siglec-1 expression on monocytes is associated with the interferon signature in juvenile dermatomyositis and can predict treatment response.
    9. Prognostic value of CD169-positive macrophages in various tumors: a meta-analysis.
      Title: Prognostic value of CD169-positive macrophages in various tumors: a meta-analysis.
    10. Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles.
      Title: Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles.
    Submit: New GeneRIF Correction See all GeneRIFs (58)

    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

    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
    HIV-1 entry and replication require functional SIGLEC1 in monocyte derived macrophages; antibodies against SIGLEC1 inhibit replication PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 Env (gp120) V1/V2 loops bind to SIGLEC1 to enter monocyte derived macrophages PubMed
    env Interferon-alpha- and interferon-gamma-induced sialoadhesin-expressing monocytes adsorb HIV-1 through interaction with the sialic acid residues on the viral envelope glycoprotein gp120 PubMed
    Pr55(Gag) gag Co-localization of HIV-1 Gag virus-like particles in THP-1/CD169YF cells is reduced within CD81+ compartments, but enhanced within CD63+ or LAMP1+ compartments PubMed
    gag HIV-1 Gag co-localizes with Siglec-1 in the sac-like compartment PubMed
    capsid gag IFN-gamma-activated dendritic cells, monocytes, and macrophages have an enhanced ability to capture and trans-infect HIV-1 via Siglec-1 recognition of viral membrane gangliosides in terms of detected levels of p24 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

    • FLJ00051, FLJ00055, FLJ00073, FLJ00411, FLJ32150, DKFZp667F058

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables virion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-cell adhesion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cell-matrix adhesion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in clathrin-dependent endocytosis of virus by host cell IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in inflammatory response NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of type I interferon production IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in late endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sialoadhesin
    Names
    sialic acid binding Ig-like lectin 1, sialoadhesin
    sialic acid-binding immunoglobulin-like lectin 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.

    mRNA and Protein(s)

    1. NM_001367089.1 → NP_001354018.1  sialoadhesin isoform 2 precursor

      Status: REVIEWED

      Source sequence(s)
      AL109804
      UniProtKB/TrEMBL
      A5D8Z7
      Related
      ENSP00000516734.1, ENST00000707083.1
      Conserved Domains (8) summary
      smart00409
      Location:431 → 503
      IG; Immunoglobulin
      smart00410
      Location:715 → 792
      IG_like; Immunoglobulin like
      pfam08205
      Location:142 → 228
      C2-set_2; CD80-like C2-set immunoglobulin domain
      pfam13895
      Location:514 → 594
      Ig_2; Immunoglobulin domain
      pfam13927
      Location:242 → 309
      Ig_3; Immunoglobulin domain
      cd00096
      Location:1552 → 1627
      Ig; Immunoglobulin domain
      cl11960
      Location:21 → 136
      Ig; Immunoglobulin domain
      cl28434
      Location:898 → 980
      I-set; Immunoglobulin I-set domain

    2. NM_023068.4 → NP_075556.1  sialoadhesin isoform 1 precursor

      See identical proteins and their annotated locations for NP_075556.1

      Status: REVIEWED

      Source sequence(s)
      AF230073, AK024462, AL109804, AY927519, CD365566
      Consensus CDS
      CCDS13060.1
      UniProtKB/Swiss-Prot
      Q96DL4, Q9BZZ2, Q9GZS5, Q9H1H6, Q9H1H7, Q9H7L7
      UniProtKB/TrEMBL
      A5D8Z7
      Related
      ENSP00000341141.4, ENST00000344754.6
      Conserved Domains (8) summary
      cd00096
      Location:430 → 503
      Ig; Immunoglobulin domain
      smart00409
      Location:516 → 594
      IG; Immunoglobulin
      smart00410
      Location:247 → 323
      IG_like; Immunoglobulin like
      pfam07679
      Location:898 → 980
      I-set; Immunoglobulin I-set domain
      pfam00047
      Location:715 → 788
      ig; Immunoglobulin domain
      pfam08205
      Location:142 → 228
      C2-set_2; CD80-like C2-set immunoglobulin domain
      pfam13895
      Location:245 → 323
      Ig_2; Immunoglobulin domain
      cl11960
      Location:21 → 136
      Ig; Immunoglobulin domain

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      3686970..3712600 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      3717911..3743544 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZZ2.2 GenPept UniProtKB/Swiss-Prot:Q9BZZ2

    Gene LinkOut

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

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