SIGLEC10
Basic information
Region (hg38): 19:51410020-51417803
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 8 | |||||
missense | 83 | 23 | 107 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 83 | 29 | 3 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SIGLEC10 | protein_coding | protein_coding | ENST00000356298 | 11 | 7783 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000684 | 1.00 | 125627 | 0 | 121 | 125748 | 0.000481 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.00 | 350 | 407 | 0.860 | 0.0000244 | 4423 |
Missense in Polyphen | 81 | 103.98 | 0.77903 | 1262 | ||
Synonymous | -0.378 | 185 | 179 | 1.04 | 0.0000115 | 1472 |
Loss of Function | 3.23 | 15 | 35.9 | 0.418 | 0.00000214 | 350 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000152 | 0.000152 |
Ashkenazi Jewish | 0.00159 | 0.00159 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.000462 | 0.000462 |
European (Non-Finnish) | 0.000672 | 0.000659 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000393 | 0.000392 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
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