SIGLEC10

sialic acid binding Ig like lectin 10, the group of V-set domain containing|C2-set domain containing|Sialic acid binding Ig like lectins

Basic information

Region (hg38): 19:51410020-51417803

Links

ENSG00000142512NCBI:89790OMIM:606091HGNC:15620Uniprot:Q96LC7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SIGLEC10 gene.

  • not_specified (108 variants)
  • not_provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033130.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
6
clinvar
2
clinvar
8
missense
83
clinvar
23
clinvar
1
clinvar
107
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 83 29 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SIGLEC10protein_codingprotein_codingENST00000356298 117783
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000006841.0012562701211257480.000481
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.003504070.8600.00002444423
Missense in Polyphen81103.980.779031262
Synonymous-0.3781851791.040.00001151472
Loss of Function3.231535.90.4180.00000214350

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001520.000152
Ashkenazi Jewish0.001590.00159
East Asian0.00005440.0000544
Finnish0.0004620.000462
European (Non-Finnish)0.0006720.000659
Middle Eastern0.00005440.0000544
South Asian0.0003930.000392
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. Preferentially binds to alpha-2,3- or alpha-2,6-linked sialic acid (By similarity). The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface. In the immune response, seems to act as an inhibitory receptor upon ligand induced tyrosine phosphorylation by recruiting cytoplasmic phosphatase(s) via their SH2 domain(s) that block signal transduction through dephosphorylation of signaling molecules (PubMed:11284738, PubMed:12163025). Involved in negative regulation of B-cell antigen receptor signaling. The inhibition of B cell activation is dependent on PTPN6/SHP-1 (By similarity). In association with CD24 may be involved in the selective suppression of the immune response to danger-associated molecular patterns (DAMPs) such as HMGB1, HSP70 and HSP90 (By similarity). In association with CD24 may regulate the immune repsonse of natural killer (NK) cells (PubMed:25450598). Plays a role in the control of autoimmunity (By similarity). During initiation of adaptive immune responses by CD8-alpha(+) dendritic cells inhibits cross-presentation by impairing the formation of MHC class I-peptide complexes. The function seems to implicate recruitment of PTPN6/SHP-1, which dephosphorylates NCF1 of the NADPH oxidase complex consequently promoting phagosomal acidification (By similarity). {ECO:0000250|UniProtKB:Q80ZE3, ECO:0000269|PubMed:11284738, ECO:0000269|PubMed:25450598, ECO:0000305|PubMed:12163025}.;
Pathway
Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

pRec
0.0813

Intolerance Scores

loftool
rvis_EVS
-0.24
rvis_percentile_EVS
36.31

Haploinsufficiency Scores

pHI
0.0817
hipred
N
hipred_score
0.403
ghis
0.489

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.353

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Siglecg
Phenotype
hematopoietic system phenotype; immune system phenotype;

Gene ontology

Biological process
adaptive immune response;cell adhesion;innate immune response;negative regulation of inflammatory response to wounding
Cellular component
extracellular region;plasma membrane;integral component of membrane
Molecular function
protein binding;phosphatase binding;carbohydrate binding;SH2 domain binding