CD200R1
Basic information
Region (hg38): 3:112921205-112975103
Previous symbols: [ "MOX2R" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD200R1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138806.4. 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 | 0 | |||||
| missense | 37 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 37 | 4 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD200R1 | protein_coding | protein_coding | ENST00000308611 | 8 | 53914 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.31e-9 | 0.205 | 125719 | 0 | 9 | 125728 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.703 | 157 | 184 | 0.854 | 0.00000915 | 2263 |
| Missense in Polyphen | 64 | 72.171 | 0.88678 | 900 | ||
| Synonymous | 0.112 | 70 | 71.2 | 0.983 | 0.00000407 | 651 |
| Loss of Function | 0.467 | 14 | 16.0 | 0.874 | 6.74e-7 | 208 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000672 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000219 | 0.000218 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.000219 | 0.000218 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibitory receptor for the CD200/OX2 cell surface glycoprotein. Limits inflammation by inhibiting the expression of proinflammatory molecules including TNF-alpha, interferons, and inducible nitric oxide synthase (iNOS) in response to selected stimuli. Also binds to HHV-8 K14 viral CD200 homolog with identical affinity and kinetics as the host CD200. {ECO:0000269|PubMed:12960329}.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.0947
Intolerance Scores
- loftool
- 0.969
- rvis_EVS
- 0.82
- rvis_percentile_EVS
- 87.95
Haploinsufficiency Scores
- pHI
- 0.0396
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.393
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.671
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd200r4
- Phenotype
Gene ontology
- Biological process
- signal transduction;viral process;heterotypic cell-cell adhesion;intracellular signal transduction;Fc receptor signaling pathway;regulation of immune response;regulation of neuroinflammatory response;negative regulation of neuroinflammatory response;negative regulation of interleukin-6 secretion;negative regulation of neuron death;negative regulation of macrophage migration;negative regulation of T cell migration
- Cellular component
- extracellular region;plasma membrane;external side of plasma membrane;cell surface;integral component of membrane;receptor complex
- Molecular function
- protein binding;immunoglobulin receptor activity;signaling receptor activity;glycosylated region protein binding