CD200R1

CD200 receptor 1, the group of C2-set domain containing

Basic information

Region (hg38): 3:112921205-112975103

Previous symbols: [ "MOX2R" ]

Links

ENSG00000163606 ∙ NCBI:131450 ∙ OMIM:607546 ∙ HGNC:24235 ∙ Uniprot:Q8TD46 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD200R1 gene.

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.

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			15	2	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	1

Variants in CD200R1

This is a list of pathogenic ClinVar variants found in the CD200R1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-112923721-C-G			Benign (Feb 23, 2021)
3-112925176-A-G		not specified	Uncertain significance (May 18, 2022)
3-112928819-G-A		not specified	Uncertain significance (Jan 04, 2024)
3-112928876-C-T		not specified	Uncertain significance (Sep 27, 2022)
3-112928891-G-A		not specified	Uncertain significance (Oct 06, 2021)
3-112928903-G-T		not specified	Uncertain significance (Dec 16, 2023)
3-112928924-C-T		not specified	Uncertain significance (Apr 23, 2024)
3-112928962-T-C		not specified	Uncertain significance (Oct 27, 2023)
3-112928963-C-T		not specified	Uncertain significance (Nov 30, 2021)
3-112929213-C-T		not specified	Likely benign (May 20, 2024)
3-112929225-C-T		not specified	Uncertain significance (Jun 06, 2023)
3-112929282-C-T		not specified	Likely benign (Jul 06, 2021)
3-112929310-G-A		not specified	Uncertain significance (Feb 15, 2023)
3-112929328-T-G		not specified	Uncertain significance (Aug 04, 2023)
3-112929487-T-C		not specified	Uncertain significance (Dec 16, 2023)
3-112931123-G-A		not specified	Uncertain significance (Aug 28, 2023)
3-112931136-T-C		not specified	Uncertain significance (Mar 04, 2024)
3-112947915-C-T		not specified	Uncertain significance (Feb 22, 2023)
3-112947921-G-A		not specified	Uncertain significance (Jun 10, 2022)
3-112974806-T-C		not specified	Likely benign (Aug 17, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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