CD200R1

protein-coding

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

Gene summary

This gene encodes a receptor for the OX-2 membrane glycoprotein. Both the receptor and substrate are cell surface glycoproteins containing two immunoglobulin-like domains. This receptor is restricted to the surfaces of myeloid lineage cells and the receptor-substrate interaction may function as a myeloid downregulatory signal. Mouse studies of a related gene suggest that this interaction may control myeloid function in a tissue-specific manner. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

Previous symbols:

MOX2R

MANE transcript

NM_138806.4

Inheritance

—

ClinVar variants

U:44B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr3:112,921,205-112,975,103

External References & Databases

Ensembl (ENSG00000163606)

Transcript & Mutation Effects

hg38 • Region Span ~53.9 kb

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GenCC 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 CD200R1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138806.4. 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						0
missense			44 clinvar	4 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	4	0	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138806.4	RefSeq	NP_620161.1	8	MANE Select
ENST00000308611.8	Ensembl	ENSP00000311035.3	8	MANE Select
NM_138939.3	RefSeq	NP_620385.1	4	Standard
NM_138940.3	RefSeq	NP_620386.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

signal transduction
viral process
heterotypic cell-cell adhesion
intracellular signal transduction
Fc receptor signaling pathway

Molecular Function

protein binding
immunoglobulin receptor activity
signaling receptor activity
glycosylated region protein binding

Cellular Component

extracellular region
plasma membrane
external side of plasma membrane
cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308611
Coding exons: 8
Length: 53914
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125728
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.703	157	184	0.854	0.00000915	2263
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000067	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0947

Intolerance Scores

LoFtool: 0.969
RVIS EVS: 0.82
RVIS percentile EVS: 87.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.671

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium