CD200
CD200 molecule, the group of Immunoglobulin like domain containing|CD molecules
Basic information
Region (hg38): 3:112332235-112363181
Previous symbols: [ "MOX1", "MOX2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 CD200 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 9 | 1 | 0 |
Variants in CD200
This is a list of pathogenic ClinVar variants found in the CD200 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-112333220-G-C | not specified | Uncertain significance (Jul 11, 2023) | ||
| 3-112336011-T-A | not specified | Uncertain significance (Nov 29, 2021) | ||
| 3-112340957-C-T | not specified | Uncertain significance (Oct 06, 2023) | ||
| 3-112340974-A-G | not specified | Likely benign (Jul 12, 2023) | ||
| 3-112345048-A-G | not specified | Uncertain significance (Aug 21, 2024) | ||
| 3-112345081-C-T | not specified | Uncertain significance (Nov 25, 2024) | ||
| 3-112345110-C-A | not specified | Uncertain significance (Nov 22, 2022) | ||
| 3-112345282-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 3-112347589-C-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 3-112347606-A-G | not specified | Uncertain significance (Apr 19, 2024) | ||
| 3-112347701-C-A | not specified | Uncertain significance (Mar 29, 2023) | ||
| 3-112347809-T-G | not specified | Uncertain significance (Jul 09, 2024) | ||
| 3-112349730-C-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 3-112349799-G-A | not specified | Uncertain significance (Feb 28, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD200 | protein_coding | protein_coding | ENST00000473539 | 7 | 30466 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.414 | 0.585 | 125735 | 0 | 10 | 125745 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.656 | 138 | 161 | 0.855 | 0.00000837 | 1903 |
| Missense in Polyphen | 32 | 46.733 | 0.68474 | 599 | ||
| Synonymous | -0.0777 | 65 | 64.2 | 1.01 | 0.00000327 | 600 |
| Loss of Function | 2.70 | 3 | 13.9 | 0.217 | 5.88e-7 | 160 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000547 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000547 | 0.0000544 |
| South Asian | 0.000294 | 0.000294 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Costimulates T-cell proliferation. May regulate myeloid cell activity in a variety of tissues.;
- Pathway
- Vitamin D Receptor Pathway;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.167
Intolerance Scores
- loftool
- 0.490
- rvis_EVS
- 0.48
- rvis_percentile_EVS
- 79.25
Haploinsufficiency Scores
- pHI
- 0.312
- hipred
- N
- hipred_score
- 0.212
- ghis
- 0.429
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.737
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd200
- Phenotype
- hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- negative regulation of leukocyte activation;negative regulation of cell population proliferation;negative regulation of NF-kappaB transcription factor activity;positive regulation of CREB transcription factor activity;heterotypic cell-cell adhesion;negative regulation of macrophage activation;regulation of immune response;positive regulation of transforming growth factor beta production;cell-cell adhesion;positive regulation of arginase activity;positive regulation of protein-glutamine gamma-glutamyltransferase activity;regulation of neuroinflammatory response;negative regulation of neuroinflammatory response;negative regulation of interleukin-6 secretion;negative regulation of neuron death;negative regulation of matrix metallopeptidase secretion;negative regulation of macrophage migration;negative regulation of T cell migration
- Cellular component
- plasma membrane;integral component of plasma membrane;cell surface;membrane;axon;neuron projection;neuronal cell body;cell body
- Molecular function
- protein binding;protein binding involved in heterotypic cell-cell adhesion;glycosylated region protein binding