SIGLEC11

sialic acid binding Ig like lectin 11, the group of V-set domain containing|C2-set domain containing|Sialic acid binding Ig like lectins|I-set domain containing

Basic information

Region (hg38): 19:49948985-49961172

Links

ENSG00000161640 ∙ NCBI:114132 ∙ OMIM:607157 ∙ HGNC:15622 ∙ Uniprot:Q96RL6 ∙ 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 SIGLEC11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC11 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				5	1	6
missense			74	9	5	88
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	74	14	6

Variants in SIGLEC11

This is a list of pathogenic ClinVar variants found in the SIGLEC11 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49950025-C-T		not specified	Uncertain significance (Apr 23, 2024)
19-49950049-A-C		not specified	Uncertain significance (Dec 13, 2022)
19-49950056-T-C		not specified	Uncertain significance (Dec 23, 2024)
19-49950094-G-A		not specified	Uncertain significance (Aug 10, 2021)
19-49950175-G-C		not specified	Uncertain significance (Sep 12, 2023)
19-49950190-G-A		not specified	Uncertain significance (Oct 03, 2023)
19-49950207-G-C		not specified	Uncertain significance (Jun 07, 2024)
19-49950215-C-T		not specified	Uncertain significance (Oct 20, 2023)
19-49951902-G-T		not specified	Uncertain significance (Sep 17, 2021)
19-49951927-C-T			Likely benign (Feb 07, 2018)
19-49951938-C-T		not specified	Uncertain significance (Oct 08, 2024)
19-49951945-G-A			Benign (Dec 31, 2019)
19-49951946-C-T		not specified	Uncertain significance (Feb 19, 2025)
19-49951947-G-A		not specified	Uncertain significance (Feb 05, 2025)
19-49952305-C-T		not specified	Likely benign (Oct 06, 2021)
19-49952338-C-T		not specified	Likely benign (Jun 11, 2021)
19-49952344-C-T		not specified	Uncertain significance (Mar 25, 2024)
19-49952382-T-C		not specified	Likely benign (Dec 07, 2021)
19-49958319-C-T		not specified	Uncertain significance (Mar 17, 2023)
19-49958324-A-G		not specified	Uncertain significance (Jan 22, 2024)
19-49958355-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-49958361-T-C		not specified	Uncertain significance (Apr 07, 2023)
19-49958372-T-G		not specified	Uncertain significance (Dec 13, 2023)
19-49958403-C-T		not specified	Uncertain significance (Mar 20, 2023)
19-49958418-T-A		not specified	Uncertain significance (Mar 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC11	protein_coding	protein_coding	ENST00000447370	11	12188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.81e-22	0.000251	125547	1	200	125748	0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.950	421	370	1.14	0.0000218	4415
Missense in Polyphen		101	99.245	1.0177		1336
Synonymous	-1.97	199	167	1.19	0.0000108	1459
Loss of Function	-0.718	30	26.0	1.15	0.00000141	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00185	0.00163
Ashkenazi Jewish	0.00	0.00
East Asian	0.00263	0.00261
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000681	0.000651
Middle Eastern	0.00263	0.00261
South Asian	0.00144	0.00121
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. Preferentially binds to alpha-2,8- linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface. In the immune response, may 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.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0827

Intolerance Scores

• loftool: 0.960
• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.48

Haploinsufficiency Scores

• pHI: 0.0754
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.515

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: multi organism cell adhesion;negative regulation of defense response to bacterium
• Cellular component: cell surface;integral component of membrane
• Molecular function: phosphatase binding;carbohydrate binding;sialic acid binding