SIGLEC12 sialic acid binding Ig like lectin 12 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SIGLEC12provided by HGNC
Official Full Name: sialic acid binding Ig like lectin 12provided by HGNC
Primary source: HGNC:HGNC:15482
See related: Ensembl:ENSG00000254521 MIM:606094; AllianceGenome:HGNC:15482
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: S2V; SLG; SIGLECL1; Siglec-XII
Summary: Sialic acid-binding immunoglobulin-like lectins (SIGLECs) are a family of cell surface proteins belonging to the immunoglobulin superfamily. They mediate protein-carbohydrate interactions by selectively binding to different sialic acid moieties present on glycolipids and glycoproteins. This gene encodes a member of the SIGLEC3-like subfamily of SIGLECs. Members of this subfamily are characterized by an extracellular V-set immunoglobulin-like domain followed by two C2-set immunoglobulin-like domains, and the cytoplasmic tyrosine-based motifs ITIM and SLAM-like. The encoded protein, upon tyrosine phosphorylation, has been shown to recruit the Src homology 2 domain-containing protein-tyrosine phosphatases SHP1 and SHP2. It has been suggested that the protein is involved in the negative regulation of macrophage signaling by functioning as an inhibitory receptor. This gene is located in a cluster with other SIGLEC3-like genes on 19q13.4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Annotation information: Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Expression: Biased expression in spleen (RPKM 5.4), appendix (RPKM 3.1) and 9 other tissues See more
Orthologs: all
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Genomic context

Location:: 19q13.41

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (51491227..51501800, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (54579849..54590427, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (51994481..52005054, complement)

Chromosome 19 - NC_000019.10 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?

cardiovascular outcomes may differ based on SIGLEC12 genotype, and antihypertensive treatment strategy.
Title: Pharmacogenomic association of nonsynonymous SNPs in SIGLEC12, A1BG, and the selectin region and cardiovascular outcomes.
SIGLEC12, a human-specific segregating (pseudo)gene, encodes a signaling molecule expressed in prostate carcinomas.
Title: SIGLEC12, a human-specific segregating (pseudo)gene, encodes a signaling molecule expressed in prostate carcinomas.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.

Submit: New GeneRIF Correction

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sialic acid binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: sialic acid-binding Ig-like lectin 12

Names: SIGLEC-like 1; sialic acid-binding Ig-like lectin-like 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_001412258.1 → NP_001399187.1 sialic acid-binding Ig-like lectin 12 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses the same exon combination as variant 1 but represents the allele encoded by the T2T-CHM13v2.0 genome assembly. The encoded isoform (c) has a shorter and frameshifted N-terminus compared to isoform a.

Source sequence(s)

CP068259
NM_033329.2 → NP_201586.1 sialic acid-binding Ig-like lectin 12 isoform b precursor

See identical proteins and their annotated locations for NP_201586.1

Status: REVIEWED

Description

Transcript Variant: This variant (2), also known as SLG-Short (SLG-S), differs in the 5' UTR and uses an alternate segment in the 5' coding region compared to variant 1, resulting in the use of an alternate in-frame translation initiation codon. It encodes an isoform (b) with a different and shorter N-terminus compared to isoform a.

Source sequence(s)

AC020914

Consensus CDS

CCDS59416.1

UniProtKB/Swiss-Prot

Q96PQ1

Related

ENSP00000472873.1, ENST00000598614.1

Conserved Domains (2) summary

smart00410
Location:271 → 344

IG_like; Immunoglobulin like

cl11960
Location:33 → 151

Ig; Immunoglobulin domain
NM_053003.4 → NP_443729.1 sialic acid-binding Ig-like lectin 12 isoform a precursor

See identical proteins and their annotated locations for NP_443729.1

Status: REVIEWED

Description

Transcript Variant: This variant (1), also known as SLG-Long (SLG-L), encodes the longest isoform (a). Unlike other members of the SIGLEC3-like subfamily, which contain only one V-set immunoglobin-like domain, isoform a contains two. This variant uses the same exon combination as variant 3 but represents the allele encoded by the GRCh38 reference genome.

Source sequence(s)

AC020914, AY358140, BC035809, DA562082

Consensus CDS

CCDS12833.1

UniProtKB/Swiss-Prot

Q8IYH7, Q96PQ1

Related

ENSP00000291707.3, ENST00000291707.8

Conserved Domains (2) summary

smart00410
Location:389 → 462

IG_like; Immunoglobulin like

cl11960
Location:24 → 142

Ig; Immunoglobulin domain