CD300A
Basic information
Region (hg38): 17:74466399-74484798
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (49 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD300A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007261.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 41 | 47 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 8 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD300A | protein_coding | protein_coding | ENST00000360141 | 7 | 18379 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000115 | 0.589 | 125729 | 0 | 17 | 125746 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.229 | 157 | 165 | 0.950 | 0.00000850 | 1910 |
| Missense in Polyphen | 39 | 41.427 | 0.94142 | 525 | ||
| Synonymous | 0.494 | 66 | 71.3 | 0.926 | 0.00000425 | 615 |
| Loss of Function | 0.939 | 11 | 14.9 | 0.738 | 7.20e-7 | 159 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000125 | 0.000123 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000368 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibitory receptor which may contribute to the down- regulation of cytolytic activity in natural killer (NK) cells, and to the down-regulation of mast cell degranulation (PubMed:10746781, PubMed:16339535, PubMed:9701027). Negatively regulates the Toll-like receptor (TLR) signaling mediated by MYD88 but not TRIF through activation of PTPN6 (PubMed:22043923). {ECO:0000269|PubMed:10746781, ECO:0000269|PubMed:16339535, ECO:0000269|PubMed:22043923, ECO:0000269|PubMed:9701027}.;
- Pathway
- Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Intolerance Scores
- loftool
- 0.854
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.99
Haploinsufficiency Scores
- pHI
- 0.283
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.515
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.00480
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd300a
- Phenotype
- homeostasis/metabolism phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype;
Gene ontology
- Biological process
- cell adhesion;negative regulation of B cell proliferation;positive regulation of phosphoprotein phosphatase activity;negative regulation of mast cell activation involved in immune response;negative regulation of MyD88-dependent toll-like receptor signaling pathway;negative regulation of mast cell degranulation;neutrophil degranulation;negative regulation of MAP kinase activity;negative regulation of fibroblast proliferation;regulation of immune response;regulation of T cell receptor signaling pathway;negative regulation of B cell receptor signaling pathway;negative regulation of NK T cell activation;negative regulation of phagocytosis, engulfment;negative regulation of neutrophil activation;negative regulation of eosinophil activation;negative regulation of activation of Janus kinase activity;negative regulation of eosinophil migration
- Cellular component
- plasma membrane;membrane;integral component of membrane;extracellular exosome;tertiary granule membrane;ficolin-1-rich granule membrane
- Molecular function
- phosphatidylserine binding;protein binding;phosphatidylethanolamine binding;signaling receptor activity