CD300A
protein-codingCD300a molecule, the group of V-set domain containing|CD molecules
Gene summary
This gene encodes a member of the CD300 glycoprotein family of cell surface proteins found on leukocytes involved in immune response signaling pathways. This gene is located on chromosome 17 in a cluster with all but one of the other family members. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CD300A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007261.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 45 | 6 | 51 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 46 | 8 | 0 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_009192.2 | 7 | MANE Select | |
| Ensembl | ENSP00000353259.3 | 7 | MANE Select | |
| RefSeq | NP_001243770.1 | 6 | Standard | |
| RefSeq | NP_001317385.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ebola Virus Pathway on Host
- Ebola Virus Pathway on Host
- Neutrophil degranulation
- Innate Immune System
- Immune System
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
Molecular Function
- phosphatidylserine binding
- protein binding
- phosphatidylethanolamine binding
- signaling receptor activity
Cellular Component
- plasma membrane
- membrane
- integral component of membrane
- extracellular exosome
- tertiary granule membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000360141
- Coding exons
- 7
- Length
- 18379
- Individuals with no LoFs
- 125729
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 17
- Defined
- 125746
- p
- 0.0000676
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.229 | 157 | 165 | 0.950 | 0.00000850 | 1910 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00013 | 0.00012 | rare |
| South Asian | 0.000037 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Intolerance Scores
- LoFtool
- 0.854
- RVIS EVS
- -0.25
- RVIS percentile EVS
- 35.99
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.00480
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |