SIGLEC15
Basic information
Region (hg38): 18:45825675-45844094
Previous symbols: [ "CD33L3" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 4 | |||||
missense | 25 | 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) | ||
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) | ||
18-45837818-T-C | not specified | Uncertain significance (Apr 18, 2024) | ||
18-45837872-C-T | not specified | Uncertain significance (Apr 25, 2023) | ||
18-45837882-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
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) |
GnomAD
Source:
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:
- 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
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
- Molecular function