SIGLEC9

sialic acid binding Ig like lectin 9, the group of V-set domain containing|CD molecules|Sialic acid binding Ig like lectins

Basic information

Region (hg38): 19:51124906-51136651

Links

ENSG00000129450 ∙ NCBI:27180 ∙ OMIM:605640 ∙ HGNC:10878 ∙ Uniprot:Q9Y336 ∙ 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 SIGLEC9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC9 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				1	2	3
missense			30		1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	3

Variants in SIGLEC9

This is a list of pathogenic ClinVar variants found in the SIGLEC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51124992-G-A			Likely benign (Apr 01, 2023)
19-51125062-A-T		not specified	Uncertain significance (Dec 27, 2022)
19-51125063-C-T		not specified	Uncertain significance (Nov 03, 2023)
19-51125075-G-C		not specified	Uncertain significance (Dec 04, 2023)
19-51125086-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-51125117-A-G		not specified	Uncertain significance (Dec 19, 2023)
19-51125124-G-C		not specified	Uncertain significance (Feb 19, 2025)
19-51125125-A-G		not specified	Uncertain significance (Oct 21, 2021)
19-51125138-C-T		not specified	Uncertain significance (Mar 20, 2023)
19-51125173-A-G		not specified	Uncertain significance (Apr 07, 2022)
19-51125174-A-G		not specified	Uncertain significance (Dec 12, 2023)
19-51125210-C-T		not specified	Uncertain significance (Dec 31, 2023)
19-51125242-C-G		not specified	Uncertain significance (Jan 28, 2025)
19-51125333-G-A		not specified	Uncertain significance (Sep 30, 2021)
19-51125348-G-A			Benign (Dec 18, 2017)
19-51125638-G-C		not specified	Uncertain significance (Dec 12, 2024)
19-51125701-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-51125728-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-51125732-C-T		not specified	Uncertain significance (Aug 27, 2024)
19-51125750-C-T		not specified	Uncertain significance (Jan 20, 2025)
19-51125762-C-T		not specified	Uncertain significance (Dec 09, 2024)
19-51125848-A-G		not specified	Uncertain significance (Oct 04, 2024)
19-51126122-G-A		not specified	Uncertain significance (Feb 28, 2025)
19-51127186-C-T		not specified	Uncertain significance (Nov 15, 2024)
19-51127239-T-C		not specified	Uncertain significance (Dec 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC9	protein_coding	protein_coding	ENST00000440804	7	11744

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000253	0.927	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.612	250	279	0.897	0.0000154	3072
Missense in Polyphen		64	79.207	0.80801		964
Synonymous	0.503	112	119	0.941	0.00000698	1023
Loss of Function	1.67	10	17.5	0.570	8.34e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000352	0.000351
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000661	0.0000653
Other	0.00	0.00

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. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0795

Intolerance Scores

• loftool: 0.798
• rvis_EVS: 1.09
• rvis_percentile_EVS: 91.87

Haploinsufficiency Scores

• pHI: 0.0633
• hipred: N
• hipred_score: 0.112
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

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;cell surface receptor signaling pathway;neutrophil degranulation;regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane;secretory granule membrane
• Molecular function: protein binding;carbohydrate binding