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

ENSG00000142512 ∙ NCBI:89790 ∙ OMIM:606091 ∙ HGNC:15620 ∙ Uniprot:Q96LC7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	3	6
missense			52	12	2	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	52	15	6

Variants in SIGLEC10

This is a list of pathogenic ClinVar variants found in the SIGLEC10 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-51411127-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-51411170-C-T		not specified	Uncertain significance (Mar 31, 2024)
19-51411187-G-A		not specified	Uncertain significance (Mar 13, 2023)
19-51411233-G-C		not specified	Uncertain significance (Dec 03, 2021)
19-51411235-G-A		not specified	Uncertain significance (Nov 06, 2023)
19-51411262-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-51411305-A-C		not specified	Uncertain significance (Jan 27, 2025)
19-51411331-C-T		not specified	Likely benign (Mar 28, 2024)
19-51411332-G-C		not specified	Uncertain significance (Apr 22, 2022)
19-51411338-T-C		not specified	Uncertain significance (Oct 12, 2022)
19-51411346-G-T		not specified	Likely benign (Jan 05, 2022)
19-51411371-C-T		not specified	Uncertain significance (May 10, 2022)
19-51413725-G-T			Benign (May 08, 2018)
19-51413732-C-T		not specified	Uncertain significance (May 15, 2024)
19-51413747-C-G		not specified	Uncertain significance (Jun 16, 2023)
19-51413754-C-T			Benign/Likely benign (Aug 01, 2022)
19-51413776-G-A		not specified	Uncertain significance (Dec 10, 2024)
19-51413798-T-C		not specified	Uncertain significance (Dec 28, 2023)
19-51413809-G-A		not specified	Uncertain significance (Mar 20, 2024)
19-51413822-T-C		not specified	Likely benign (Mar 15, 2024)
19-51413823-G-A		not specified	Likely benign (Jan 03, 2024)
19-51414447-G-A		not specified	Uncertain significance (Jun 10, 2024)
19-51414455-G-A		not specified	Likely benign (Mar 14, 2025)
19-51414480-C-T		not specified	Uncertain significance (Jun 06, 2023)
19-51414494-G-A		not specified	Uncertain significance (Sep 11, 2024)

GnomAD

Source: gnomAD

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: 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

• 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