CD69
Basic information
Region (hg38): 12:9752486-9760901
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 CD69 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 | 1 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 1 |
Variants in CD69
This is a list of pathogenic ClinVar variants found in the CD69 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-9753550-T-C | Benign (Aug 07, 2018) | |||
| 12-9754627-G-A | not specified | Uncertain significance (Jul 14, 2021) | ||
| 12-9755093-G-A | not specified | Uncertain significance (Nov 22, 2021) | ||
| 12-9755217-A-G | not specified | Uncertain significance (Oct 04, 2024) | ||
| 12-9756389-C-T | not specified | Likely benign (Nov 17, 2022) | ||
| 12-9756418-A-C | not specified | Uncertain significance (Oct 26, 2021) | ||
| 12-9760783-G-A | not specified | Uncertain significance (Nov 18, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD69 | protein_coding | protein_coding | ENST00000228434 | 5 | 8416 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0297 | 0.929 | 124493 | 0 | 2 | 124495 | 0.00000803 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.259 | 112 | 105 | 1.07 | 0.00000502 | 1322 |
| Missense in Polyphen | 16 | 25.393 | 0.6301 | 341 | ||
| Synonymous | 1.05 | 28 | 36.0 | 0.777 | 0.00000180 | 349 |
| Loss of Function | 1.75 | 4 | 9.98 | 0.401 | 5.21e-7 | 113 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets.;
- Pathway
- IL-3 Signaling Pathway
(Consensus)
Recessive Scores
- pRec
- 0.396
Intolerance Scores
- loftool
- 0.724
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.76
Haploinsufficiency Scores
- pHI
- 0.135
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.494
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.513
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd69
- Phenotype
- cellular phenotype; immune system phenotype; skeleton phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- cellular response to drug
- Cellular component
- integral component of plasma membrane;external side of plasma membrane;protein-containing complex
- Molecular function
- transmembrane signaling receptor activity;calcium ion binding;protein binding;carbohydrate binding;protein homodimerization activity