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): 18:45825675-45844094

Previous symbols: [ "CD33L3" ]

Links

ENSG00000197046NCBI:284266OMIM:618105HGNC:27596Uniprot:Q6ZMC9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SIGLEC15 gene.

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
3
clinvar
1
clinvar
4
missense
25
clinvar
1
clinvar
1
clinvar
27
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 25 4 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
18-45825739-C-A not specified Uncertain significance (Jun 05, 2024)3318503
18-45825763-C-T not specified Likely benign (May 17, 2023)2514863
18-45837066-C-G not specified Uncertain significance (Feb 16, 2023)2466436
18-45837069-G-C not specified Uncertain significance (Sep 01, 2021)2248290
18-45837513-G-T not specified Uncertain significance (May 31, 2023)2553452
18-45837558-G-C not specified Uncertain significance (Jan 16, 2024)3162195
18-45837570-G-A not specified Uncertain significance (Nov 08, 2022)2324357
18-45837585-T-G not specified Uncertain significance (Jan 03, 2024)2379899
18-45837590-T-G not specified Uncertain significance (Oct 12, 2021)3162196
18-45837639-T-C not specified Uncertain significance (Jul 20, 2021)2356866
18-45837693-C-T not specified Uncertain significance (Dec 11, 2023)3162197
18-45837696-G-C not specified Uncertain significance (Mar 01, 2023)2473450
18-45837733-C-G not specified Uncertain significance (Sep 06, 2022)2364019
18-45837782-C-A not specified Uncertain significance (Oct 04, 2022)2224513
18-45837788-G-C not specified Uncertain significance (Jul 26, 2022)2303222
18-45837818-T-C not specified Uncertain significance (Apr 18, 2024)3318502
18-45837872-C-T not specified Uncertain significance (Apr 25, 2023)2539991
18-45837882-G-A not specified Uncertain significance (Apr 15, 2024)3318501
18-45838724-C-G Uncertain significance (Oct 01, 2023)2648697
18-45838754-G-C not specified Uncertain significance (Oct 12, 2021)2254539
18-45838756-C-G not specified Uncertain significance (Dec 14, 2022)2335055
18-45838759-G-A not specified Uncertain significance (Jun 09, 2022)2277904
18-45838772-G-A not specified Uncertain significance (Feb 06, 2023)2481227
18-45838826-C-A not specified Uncertain significance (Aug 02, 2021)2219431
18-45838827-G-A Likely benign (Dec 01, 2022)1879394

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SIGLEC15protein_codingprotein_codingENST00000389474 618569
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.21e-90.04521257310111257420.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9791391760.7920.00001082003
Missense in Polyphen3234.3730.93097443
Synonymous1.207084.00.8340.00000560719
Loss of Function-0.774118.561.293.65e-7112

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001990.000182
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.000008820.00000879
Middle Eastern0.0001090.000109
South Asian0.0001330.000131
Other0.000.00

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
ghis

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

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
Molecular function