SIGLEC7

sialic acid binding Ig like lectin 7, the group of V-set domain containing|CD molecules|Sialic acid binding Ig like lectins

Basic information

Region (hg38): 19:51142299-51153526

Previous symbols: [ "SIGLEC19P", "SIGLECP2" ]

Links

ENSG00000168995 ∙ NCBI:27036 ∙ OMIM:604410 ∙ HGNC:10876 ∙ Uniprot:Q9Y286 ∙ 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 SIGLEC7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC7 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						0
missense			36		1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	1

Variants in SIGLEC7

This is a list of pathogenic ClinVar variants found in the SIGLEC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51142411-G-C		not specified	Uncertain significance (Jan 20, 2025)
19-51142440-A-C		not specified	Uncertain significance (Nov 13, 2024)
19-51142497-A-C		not specified	Uncertain significance (Jul 26, 2021)
19-51142503-G-A		not specified	Uncertain significance (Dec 12, 2023)
19-51142515-C-G		not specified	Uncertain significance (Mar 14, 2023)
19-51142593-A-G		not specified	Uncertain significance (Nov 13, 2024)
19-51142598-C-T		not specified	Uncertain significance (Feb 09, 2025)
19-51142644-G-A		not specified	Uncertain significance (Jan 31, 2022)
19-51142658-C-T		not specified	Uncertain significance (Oct 04, 2022)
19-51142695-G-A		not specified	Uncertain significance (Feb 03, 2025)
19-51142722-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-51142796-G-A		not specified	Uncertain significance (Apr 06, 2022)
19-51144466-A-G		not specified	Uncertain significance (Jun 07, 2023)
19-51144480-G-A		not specified	Uncertain significance (Mar 31, 2023)
19-51144501-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-51144505-C-T		not specified	Uncertain significance (Jan 07, 2022)
19-51144513-A-G			Benign (Dec 11, 2017)
19-51144537-G-T		not specified	Uncertain significance (Apr 04, 2024)
19-51144564-C-T		not specified	Uncertain significance (Feb 09, 2025)
19-51144580-C-A		not specified	Uncertain significance (Jan 22, 2025)
19-51144602-C-G		not specified	Uncertain significance (Nov 25, 2024)
19-51144640-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-51144668-C-G		not specified	Uncertain significance (Jun 02, 2023)
19-51145866-C-A		not specified	Uncertain significance (Oct 19, 2024)
19-51145899-G-C		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC7	protein_coding	protein_coding	ENST00000317643	7	11228

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.39e-7	0.729	125625	1	121	125747	0.000485

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.859	221	260	0.850	0.0000140	2999
Missense in Polyphen		59	72.885	0.80949		942
Synonymous	-0.118	114	112	1.01	0.00000643	984
Loss of Function	1.27	13	18.9	0.686	9.64e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.00440	0.00441
Finnish	0.00	0.00
European (Non-Finnish)	0.000257	0.000193
Middle Eastern	0.00440	0.00441
South Asian	0.000369	0.000327
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- and alpha-2,6-linked sialic acid. Also binds disialogangliosides (disialogalactosyl globoside, disialyl lactotetraosylceramide and disialyl GalNAc lactotetraoslylceramide). 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. Mediates inhibition of natural killer cells cytotoxicity. May play a role in hemopoiesis. Inhibits differentiation of CD34+ cell precursors towards myelomonocytic cell lineage and proliferation of leukemic myeloid cells (in vitro). {ECO:0000269|PubMed:10611343}.
• Pathway: Microglia Pathogen Phagocytosis Pathway;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.860
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.0452
• hipred: N
• hipred_score: 0.139
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0708

Gene Damage Prediction

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

Gene ontology

• Biological process: cell adhesion;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: carbohydrate binding;signaling receptor activity