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

Gene ID: 6614, updated on 5-Mar-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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Location:
20p13
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (3686970..3712600, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (3717911..3743544, complement)
105.20220307 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
  • 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. CD169 expression on monocytes as a marker for assessing type I interferon status in pediatric inflammatory diseases. Sakumura N, et al. Clin Immunol, 2023 May. PMID 37061149
  2. Sialoadhesin (CD169/Siglec-1) is an extended molecule that escapes inhibitory cis-interactions and synergizes with other macrophage receptors to promote phagocytosis. Klaas M, et al. Glycoconj J, 2023 Apr. PMID 36738392, Free PMC Article
  3. The role of activated monocyte IFN/SIGLEC1 signalling in Graves' disease. Wang Y, et al. J Endocrinol, 2022 Oct 1. PMID 35695299
  4. SIGLEC1 enables straightforward assessment of type I interferon activity in idiopathic inflammatory myopathies. Graf M, et al. RMD Open, 2022 Feb. PMID 35177553, Free PMC Article
  5. Prognostic value of CD169-positive macrophages in various tumors: a meta-analysis. Kong W, et al. Bioengineered, 2021 Dec. PMID 34607536, Free PMC Article

See all (75) 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_2023_10

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

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