CLEC5A
Basic information
Region (hg38): 7:141927357-141947007
Previous symbols: [ "CLECSF5" ]
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 CLEC5A 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in CLEC5A
This is a list of pathogenic ClinVar variants found in the CLEC5A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-141930133-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 7-141930186-G-C | not specified | Uncertain significance (Jul 25, 2024) | ||
| 7-141930200-C-G | not specified | Uncertain significance (Mar 16, 2022) | ||
| 7-141931768-C-T | not specified | Uncertain significance (Mar 26, 2024) | ||
| 7-141931769-G-A | not specified | Uncertain significance (Aug 11, 2024) | ||
| 7-141935833-A-G | not specified | Uncertain significance (Aug 17, 2022) | ||
| 7-141935837-T-C | not specified | Uncertain significance (Oct 27, 2022) | ||
| 7-141935897-A-T | not specified | Uncertain significance (Feb 16, 2023) | ||
| 7-141943898-G-T | not specified | Uncertain significance (May 18, 2023) | ||
| 7-141943902-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 7-141943919-A-G | not specified | Uncertain significance (Mar 16, 2024) | ||
| 7-141943940-G-A | not specified | Uncertain significance (Nov 17, 2023) | ||
| 7-141943945-G-T | not specified | Uncertain significance (Feb 10, 2022) | ||
| 7-141945358-G-T | not specified | Uncertain significance (Oct 27, 2023) | ||
| 7-141945385-T-C | not specified | Uncertain significance (May 29, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLEC5A | protein_coding | protein_coding | ENST00000546910 | 6 | 19651 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.126 | 0.853 | 125578 | 0 | 1 | 125579 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.236 | 94 | 101 | 0.934 | 0.00000500 | 1255 |
| Missense in Polyphen | 19 | 25.623 | 0.74151 | 328 | ||
| Synonymous | 0.193 | 32 | 33.4 | 0.957 | 0.00000178 | 315 |
| Loss of Function | 1.99 | 3 | 9.66 | 0.311 | 4.07e-7 | 120 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions as a positive regulator of osteoclastogenesis (By similarity). Cell surface receptor that signals via TYROBP (PubMed:10449773). Regulates inflammatory responses (By similarity). {ECO:0000250|UniProtKB:Q9R007, ECO:0000269|PubMed:10449773}.;
- Pathway
- Neutrophil degranulation;DAP12 interactions;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.0948
Intolerance Scores
- loftool
- 0.600
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 67.92
Haploinsufficiency Scores
- pHI
- 0.0997
- hipred
- N
- hipred_score
- 0.172
- ghis
- 0.416
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.137
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Clec5a
- Phenotype
- skeleton phenotype; immune system phenotype;
Gene ontology
- Biological process
- osteoblast development;cellular defense response;signal transduction;myeloid cell differentiation;negative regulation of myeloid cell apoptotic process;negative regulation of apoptotic process;neutrophil degranulation;innate immune response;viral entry into host cell;positive regulation of cytokine secretion
- Cellular component
- cytosol;plasma membrane;integral component of plasma membrane;cell surface;specific granule membrane;tertiary granule membrane
- Molecular function
- virus receptor activity;protein binding;carbohydrate binding