SIGLEC15

sialic acid binding Ig like lectin 15, the group of V-set domain containing|Sialic acid binding Ig like lectins

Basic information

Region (hg38): 18:45825674-45844094

Previous symbols: [ "CD33L3" ]

Links

ENSG00000197046 ∙ NCBI:284266 ∙ OMIM:618105 ∙ HGNC:27596 ∙ Uniprot:Q6ZMC9 ∙ 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 SIGLEC15 gene.

• Inborn genetic diseases (21 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLEC15 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				2	1	3
missense			21	1	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	2

Variants in SIGLEC15

This is a list of pathogenic ClinVar variants found in the SIGLEC15 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-45825763-C-T		not specified	Likely benign (May 17, 2023)
18-45837066-C-G		not specified	Uncertain significance (Feb 16, 2023)
18-45837069-G-C		not specified	Uncertain significance (Sep 01, 2021)
18-45837513-G-T		not specified	Uncertain significance (May 31, 2023)
18-45837558-G-C		not specified	Uncertain significance (Jan 16, 2024)
18-45837570-G-A		not specified	Uncertain significance (Nov 08, 2022)
18-45837585-T-G		not specified	Uncertain significance (Jan 03, 2024)
18-45837590-T-G		not specified	Uncertain significance (Oct 12, 2021)
18-45837639-T-C		not specified	Uncertain significance (Jul 20, 2021)
18-45837693-C-T		not specified	Uncertain significance (Dec 11, 2023)
18-45837696-G-C		not specified	Uncertain significance (Mar 01, 2023)
18-45837733-C-G		not specified	Uncertain significance (Sep 06, 2022)
18-45837782-C-A		not specified	Uncertain significance (Oct 04, 2022)
18-45837788-G-C		not specified	Uncertain significance (Jul 26, 2022)
18-45837872-C-T		not specified	Uncertain significance (Apr 25, 2023)
18-45838724-C-G			Uncertain significance (Oct 01, 2023)
18-45838754-G-C		not specified	Uncertain significance (Oct 12, 2021)
18-45838756-C-G		not specified	Uncertain significance (Dec 14, 2022)
18-45838759-G-A		not specified	Uncertain significance (Jun 09, 2022)
18-45838772-G-A		not specified	Uncertain significance (Feb 06, 2023)
18-45838826-C-A		not specified	Uncertain significance (Aug 02, 2021)
18-45838827-G-A			Likely benign (Dec 01, 2022)
18-45838834-G-T		not specified	Uncertain significance (Mar 04, 2024)
18-45838852-G-A		not specified	Uncertain significance (Oct 20, 2021)
18-45838863-G-A			Benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLEC15	protein_coding	protein_coding	ENST00000389474	6	18569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.21e-9	0.0452	125731	0	11	125742	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.979	139	176	0.792	0.0000108	2003
Missense in Polyphen		32	34.373	0.93097		443
Synonymous	1.20	70	84.0	0.834	0.00000560	719
Loss of Function	-0.774	11	8.56	1.29	3.65e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000199	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.000109	0.000109
South Asian	0.000133	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds sialylated glycoproteins. {ECO:0000269|PubMed:17483134}.
• Pathway: DAP12 interactions;Innate Immune System;Immune System (Consensus)

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.367

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.181

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Siglec15
• Phenotype: immune system phenotype; renal/urinary system phenotype; skeleton phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: regulation of actin cytoskeleton organization;innate immune response;regulation of bone resorption;regulation of osteoclast development
• Cellular component: plasma membrane;integral component of membrane;protein-containing complex