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

Summary

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

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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
The role of activated monocyte IFN/SIGLEC1 signalling in Graves' disease.
Title: The role of activated monocyte IFN/SIGLEC1 signalling in Graves' disease.
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.
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.
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.
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)

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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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)

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
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