CD200R1

Summary

CD200R1 (CD200 receptor 1, HGNC:24235) is a protein-coding gene on chromosome 3q13.2, encoding Cell surface glycoprotein CD200 receptor 1 (Q8TD46). Inhibitory receptor for the CD200/OX2 cell surface glycoprotein.

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.

Source: NCBI Gene 131450 — RefSeq curated summary.

At a glance

• GWAS associations: 30
• Clinical variants (ClinVar): 113 total
• MANE Select transcript: NM_138806

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24235
Approved symbol	CD200R1
Name	CD200 receptor 1
Location	3q13.2
Locus type	gene with protein product
Status	Approved
Aliases	OX2R, HCRTR2, CD200R
Ensembl gene	ENSG00000163606
Ensembl biotype	protein_coding
OMIM	607546
Entrez	131450

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000295863, ENST00000308611, ENST00000440122, ENST00000471858, ENST00000490004

RefSeq mRNA: 4 — MANE Select: NM_138806 NM_138806, NM_138939, NM_138940, NM_170780

CCDS: CCDS2969, CCDS2970, CCDS46889, CCDS54623

Canonical transcript exons

ENST00000308611 — 8 exons

Exon	Start	End
ENSE00001076486	112924490	112924535
ENSE00001076487	112925085	112925193
ENSE00001076488	112928816	112929064
ENSE00001076489	112931106	112931171
ENSE00001076493	112929190	112929507
ENSE00001175354	112921205	112923799
ENSE00001199958	112947856	112947924
ENSE00001824878	112974791	112975103

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 82.83.

FANTOM5 (CAGE): breadth broad, TPM avg 2.6297 / max 207.1146, expressed in 262 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
43823	2.2128	243
43819	0.1546	41
43821	0.1213	47
43820	0.1095	37
43818	0.0210	5
43822	0.0106	5

Top tissues by expression

242 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.83	gold quality
epithelium of nasopharynx	UBERON:0001951	80.34	gold quality
nasal cavity epithelium	UBERON:0005384	77.92	gold quality
bone marrow cell	CL:0002092	76.70	gold quality
granulocyte	CL:0000094	74.38	gold quality
leukocyte	CL:0000738	73.13	gold quality
monocyte	CL:0000576	72.47	gold quality
lymph node	UBERON:0000029	72.42	gold quality
bone marrow	UBERON:0002371	71.55	gold quality
vermiform appendix	UBERON:0001154	71.07	gold quality
superficial temporal artery	UBERON:0001614	70.28	gold quality
spleen	UBERON:0002106	69.11	gold quality
gall bladder	UBERON:0002110	68.33	gold quality
rectum	UBERON:0001052	68.25	gold quality
caecum	UBERON:0001153	67.47	gold quality
upper leg skin	UBERON:0004262	66.94	gold quality
germinal epithelium of ovary	UBERON:0001304	66.93	gold quality
esophagus mucosa	UBERON:0002469	66.62	gold quality
mucosa of paranasal sinus	UBERON:0005030	66.32	gold quality
gingival epithelium	UBERON:0001949	66.27	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	66.11	gold quality
nasal cavity mucosa	UBERON:0001826	65.96	gold quality
skin of hip	UBERON:0001554	65.45	gold quality
blood	UBERON:0000178	65.15	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	65.05	gold quality
smooth muscle tissue	UBERON:0001135	64.86	gold quality
tonsil	UBERON:0002372	63.89	gold quality
calcaneal tendon	UBERON:0003701	63.85	gold quality
placenta	UBERON:0001987	63.81	gold quality
oral cavity	UBERON:0000167	63.44	silver quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-9801	yes	4.36
E-ANND-3	no	3.89
E-CURD-112	no	2.96

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CEBPB, IRF6

miRNA regulators (miRDB)

81 targeting CD200R1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-186-5P	99.99	70.83	3707
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-124-3P	99.89	73.74	3043

Literature-anchored findings (GeneRIF, showing 40)

• The CD200 receptor gene family resembles the signal regulatory proteins and killer Ig-related receptors in having receptor family members with potential activatory and inhibitory functions that may play important roles in immune regulation and balance. (PMID:12960329)
• Human Herpesvirus-8 K14 protein interacts with human CD200R during the lytic cycle. Despite sharing only 40% primary sequence identity, K14 and CD200 interacts with CD200R with an almost identical and low affinity (K(D) = 0.5 microM) (PMID:15220441)
• CD200R represents a novel and potent inhibitory receptor that can be targeted in vivo to regulate mast cell-dependent pathologies. (PMID:15661892)
• Human CD200R is an important regulatory molecule of basophil activation. (PMID:16177086)
• Reactions with CD200 antigen modulate immunomodulation for prevention of undesired immune responses of the skin. (PMID:16354172)
• In human tonsils, CD200R is differentially expressed on B cells, with high expression on memory cells and plasmablasts. (PMID:17714785)
• Review highlights the close correlation between CD200-CD200 receptor (CD200R), microglia activation, and Parkinson’s disease. (PMID:18040859)
• The CD200-CD200R pathway seems of critical relevance for macrophage-mediated damage in autoimmune inflammation of the CNS. (PMID:18164423)
• CD200-mediated immune suppression may occur not only via neuron-microglia interactions, but also via glia-glia interactions, especially in inflammatory conditions in which an immune-suppressive environment needs to be restored. (PMID:19151626)
• CD200R inhibits the activation of human myeloid cells through direct recruitment of Dok2 and subsequent activation of RAS p21 protein activator 1. (PMID:19786546)
• results suggest an intrinsic abnormality in the CD200-CD200R signaling in monocyte-derived macrophages during aging and, especially, in Parkinson disease (PMID:19924532)
• Dok1 negatively regulates Dok2-mediated CD200R signaling through the recruitment of CrkL. (PMID:21078907)
• The role of the CD200-CD200R axis in bone marrow-derived mesenchymal stem cell mediated immunosuppression was studied using THP-1 human macrophages. (PMID:22363701)
• Mechanistically, Kaposi’s sarcoma-associated herpesvirus viral OX2 protein and CD200 expression on antigen presenting cells suppressed the phosphorylation of ERK1/2 mitogen-activated protein kinase in responding T cells. (PMID:22491458)
• these results indicate a role of CD200R:CD200 in T cell responses to helminths which has diagnostic and prognostic relevance as a marker of infection for chronic schistosomiasis in mouse and man. (PMID:22496920)
• Mesenchymal stromal cells are able to modulate the expression of both CD200 and CD200R on some T-cells. (PMID:22575528)
• CD200 and CD200R1 expression and function are abnormal in systemic lupus erythematosus (PMID:22621248)
• The expression of CD200R as well as B7-H4 co-stimulatory molecules on CD14(+) cells were significantly higher in cord blood when compared with peripheral blood. (PMID:23066977)
• blocking CD200 on tumor cells may have opposite effects on tumor proliferation depending on the “affinity” of the macrophages to form the CD200-CD200R-complex with tumor cells. (PMID:23541619)
• in cutaneous squamous cell carcinoma, CD200 expression on local blood vessels may promote tumor progression by suppressing CD200R myeloid cells during diapedesis (PMID:23560298)
• The expression of CD200 and its receptor, CD200R, on CD83+ monocyte-derived dendritic cells (Mo-DCs), pulsed or not with autologous tumor cell lysates (aTCL) in patients who suffer from laryngeal carcinoma, were examined. (PMID:23690219)
• Mesenchymal stem cells, through the expression of CD200, play a major role in the regulation of bone resorption and bone physiology and the CD200-CD200R couple could be a new target to control bone diseases. (PMID:23940819)
• Measurement of sCD200 and/or sCD200R1 may prove a useful and rapid means of monitoring subjects at risk of bone loss. (PMID:24333170)
• [review] CD200R1 is comparable to other pathogen-targeted inhibitory receptors; its signaling pathway is utilized by a diverse number of pathogens and represents a novel targeting strategy for infectiouis diseases. (PMID:24388216)
• We demonstrate a significant correlation between CD200R1 positive cells and disease severity in rheumatoid arthritis (RA) patients, thus indicating the relevance of the CD200/CD200R1 signaling pathway potential involvement in the pathogenesis of RA. (PMID:24496593)
• The mechanism underlying ESA might be associated with enhanced expression of CD200 and CD200R in the trophoblast, leading to an upregulation of the immune response during the first trimester of pregnancy. (PMID:25145957)
• The proportion of CD200R1+ cells in PBMCs, peripheral CD14+ cells and CD4+ T cells was significantly lower in rheumatoid arthritis patients compared to controls. (PMID:25261692)
• data show that the expression of CD200R, CD95 and CD95L was influenced by cardiac surgery and imply the role of these membrane molecules in cell regulation-inhibition and apoptosis following cardiac surgery. (PMID:25404054)
• This is the first report of CD200R1 expression by human epithelial tumor cells, and specifically, early-stage human breast cancer cells. It is also the first report of CD200R1 expression by term placental villous trophoblasts. (PMID:26011475)
• CD200-CD200R1 signaling may be required for human pregnancy success. (PMID:26123445)
• The authors showed that the viral orthologues e127 from rat cytomegalovirus and K14 from human herpesvirus 8 do not bind the activating CD200R-like proteins from their respective species, although they do bind the inhibitory receptors. (PMID:26538068)
• Inflammatory Bowel Disease patients showed a significant decrease in the percentage of plasmacytoid dendritic cells and myeloid dendritic cells expressing CD200R1 compared to that of the control group. (PMID:26690123)
• Constitutively expressed Siglec-9 inhibits LPS-induced CCR7, but enhances IL-4-induced CD200R expression in human macrophages. (PMID:26923638)
• we revealed a critical role for CD200R signaling in limiting the growth and metastasis of CD200(+) tumors. (PMID:27385779)
• Our findings suggest a promising role of CD200R as a prognostic marker in predicting elevated recurrence and reduced survival, and a potential therapeutic target in treating hepatocellular carcinoma. (PMID:27562325)
• Reduced expression of monocyte CD200R is associated with enhanced proinflammatory cytokine production in sarcoidosis (PMID:27929051)
• we demonstrated for the first time that CD200R is highly expressed on cells involved in type 2 immune responses, namely on Th2, Tc2, ILC2, and basophils. All these cell types play a role in type 2 inflammation. (PMID:28106273)
• Residual CD200 activity may prevent completion of abortions via induction of Treg cells. In chronic histiocytic intervillositis, infiltrating maternal effector T cells may block Treg induction. An autocrine role for CD200-CD200R interaction versus inhibition of soluble CD200 by soluble CD200R is discussed. (PMID:28326648)
• Coexpression of CD200R-CD28 enhances function in WT1-specific T-cell receptor - transduced human primary T cells. (PMID:29042364)
• MMP12-producing monocyte-derived cells in gingival tissue of periodontitis patients also had reduced CD200R surface levels. Treatment with a CD200R ligand reduced CSF2-induced MMP12 production in these cells. This novel association of the CD200/CD200R pathway with MMP12 production by monocyte-derived cells may play a key role in PD progression. (PMID:29101312)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cd200r1	ENSMUSG00000022667
mus_musculus	Cd200r3	ENSMUSG00000036172
mus_musculus	Cd200r4	ENSMUSG00000062082
mus_musculus	Cd200r2	ENSMUSG00000090176
rattus_norvegicus	Cd200r1l	ENSRNOG00000002046
rattus_norvegicus	Cd200r1	ENSRNOG00000039048

Paralogs (1): CD200R1L (ENSG00000206531)

Protein

Protein identifiers

Cell surface glycoprotein CD200 receptor 1 — Q8TD46 (reviewed: Q8TD46)

Alternative names: CD200 cell surface glycoprotein receptor, Cell surface glycoprotein OX2 receptor 1

All UniProt accessions (2): Q8TD46, H9KV32

UniProt curated annotations — full annotation on UniProt →

Function. Inhibitory receptor for the CD200/OX2 cell surface glycoprotein. Limits inflammation by inhibiting the expression of pro-inflammatory molecules including TNF, 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.

Subunit / interactions. CD200 and CD200R1 interact via their respective N-terminal Ig-like domains. Interacts with Human herpesvirus 8 vOX2 protein. (Microbial infection) Interacts with human herpesvirus 8/HHV-8 protein vOX2/K14.

Subcellular location. Cell membrane Cell membrane Secreted Secreted.

Tissue specificity. Expressed in granulocytes, monocytes, most T-cells, neutrophils, basophils and a subset of NK, NKT and B-cells (at protein level). Expressed in bone marrow, lymph nodes, spleen, lung, liver, spinal cord, kidney. Expressed in monocyte-derived dendritic and mast cells.

Similarity. Belongs to the CD200R family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8TD46-4	4	yes
Q8TD46-1	1
Q8TD46-2	2
Q8TD46-3	3

RefSeq proteins (4): NP_620161, NP_620385, NP_620386, NP_740750 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007110	Ig-like_dom	Domain
IPR013162	CD80_C2-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR040012	CD200R	Family

Pfam: PF08205

UniProt features (27 total): glycosylation site 9, disulfide bond 4, sequence variant 4, splice variant 3, topological domain 2, signal peptide 1, chain 1, sequence conflict 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
9GWT	X-RAY DIFFRACTION	2.89

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TD46-F1	74.74	0.45

Antibody-complex structures (SAbDab): 1 — 9GWT

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (4): 83–155, 107–123, 190–239, 209–227

Glycosylation sites (9): 122, 185, 218, 233, 247, 31, 60, 69, 116

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-1280218	Adaptive Immune System
R-HSA-168256	Immune System

MSigDB gene sets: 304 (showing top): GOBP_CIRCADIAN_RHYTHM, GOBP_BEHAVIOR, GOBP_MYELOID_LEUKOCYTE_MIGRATION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_INFLAMMATORY_RESPONSE, GOCC_CELL_SURFACE, GOBP_REGULATION_OF_LEUKOCYTE_MIGRATION, MORF_RAD51L3, GOBP_CELL_CELL_SIGNALING, GOBP_NEGATIVE_REGULATION_OF_INTERLEUKIN_6_PRODUCTION, GOBP_REGULATION_OF_MONONUCLEAR_CELL_MIGRATION, GOBP_REGULATION_OF_CIRCADIAN_RHYTHM, GOBP_CELL_CELL_ADHESION, GOBP_LEUKOCYTE_MIGRATION, REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS

GO Biological Process (9): signal transduction (GO:0007165), negative regulation of interleukin-6 production (GO:0032715), heterotypic cell-cell adhesion (GO:0034113), intracellular signal transduction (GO:0035556), regulation of neuroinflammatory response (GO:0150077), negative regulation of neuroinflammatory response (GO:0150079), negative regulation of macrophage migration (GO:1905522), negative regulation of T cell migration (GO:2000405), Fc receptor signaling pathway (GO:0038093)

GO Molecular Function (4): immunoglobulin receptor activity (GO:0019763), signaling receptor activity (GO:0038023), glycosylated region protein binding (GO:0140081), protein binding (GO:0005515)

GO Cellular Component (6): extracellular region (GO:0005576), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), cell surface (GO:0009986), signaling receptor complex (GO:0043235), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Adaptive Immune System	1
Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
neuroinflammatory response	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
negative regulation of cytokine production	1
interleukin-6 production	1
regulation of interleukin-6 production	1
cell-cell adhesion	1
intracellular anatomical structure	1
signal transduction	1
regulation of inflammatory response	1
negative regulation of inflammatory response	1
regulation of neuroinflammatory response	1
negative regulation of mononuclear cell migration	1
macrophage migration	1
regulation of macrophage migration	1
T cell migration	1
negative regulation of lymphocyte migration	1
regulation of T cell migration	1
immune response-regulating cell surface receptor signaling pathway	1
transmembrane signaling receptor activity	1
immunoglobulin binding	1
Fc receptor signaling pathway	1
immune receptor activity	1
molecular transducer activity	1
protein binding	1
carbohydrate derivative binding	1
binding	1
membrane	1
cell periphery	1
plasma membrane	1
cell surface	1
side of membrane	1
protein-containing complex	1

Protein interactions and networks

STRING

1246 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CD200R1	CD200	P41217	999
CD200R1	CD47	Q08722	990
CD200R1	CX3CL1	P78423	972
CD200R1	DOK2	O60496	943
CD200R1	CD22	P20273	934
CD200R1	SIRPA	P78324	861
CD200R1	CX3CR1	P49238	790
CD200R1	CD274	Q9NZQ7	779
CD200R1	TREM2	Q9NZC2	696
CD200R1	CD276	Q5ZPR3	615
CD200R1	CD27	P26842	602
CD200R1	TNFRSF11A	Q9Y6Q6	602
CD200R1	CD70	P32970	594
CD200R1	MRC1	P22897	575
CD200R1	CD86	P42081	555

IntAct

12 interactions, top by confidence:

A	B	Type	Score
CD200R1	CD200	psi-mi:“MI:0915”(physical association)	0.710
CD200	CD200R1	psi-mi:“MI:0915”(physical association)	0.710
CD200R1	CD200	psi-mi:“MI:0407”(direct interaction)	0.710
MAGEB3	PPP1R7	psi-mi:“MI:0914”(association)	0.560
CD200R1	SCN2B	psi-mi:“MI:0915”(physical association)	0.400
CD200R1	PVR	psi-mi:“MI:0914”(association)	0.350
CD200R1	KIF2A	psi-mi:“MI:0914”(association)	0.350
MAGEB3	MYH7B	psi-mi:“MI:0914”(association)	0.350

BioGRID (26): MBOAT7 (Affinity Capture-MS), TNPO2 (Affinity Capture-MS), NCR3LG1 (Affinity Capture-MS), POMT2 (Affinity Capture-MS), FUT8 (Affinity Capture-MS), COL1A1 (Affinity Capture-MS), TCP10L2 (Affinity Capture-MS), CD200R1 (Reconstituted Complex), CD200R1 (Two-hybrid), CD200R1 (Two-hybrid), CD200R1 (Two-hybrid), CLDN19 (Two-hybrid), SFTPC (Two-hybrid), ADIPOQ (Two-hybrid), PTCH1 (Two-hybrid)

ESM2 similar proteins: A0A0E4BZH1, A4QPC6, A5D7V5, A7TZE6, A7TZF0, A7TZF3, A7XUX6, A7XV04, A7XV07, A8K4G0, A8MVZ5, O70355, P08508, P18892, P24071, P31994, P55803, P78410, P79391, Q13410, Q16653, Q29ZQ1, Q3KPI0, Q58DF9, Q5R7W8, Q5R960, Q5R996, Q61885, Q62556, Q63345, Q6Q8B3, Q6UXZ3, Q6XJV4, Q6XJV6, Q7KYR7, Q7TST0, Q7YR73, Q8BTP3, Q8K249, Q8TD46

Diamond homologs: A5D7V5, Q2YHT5, Q2YHT7, Q5R412, Q5UKY4, Q6Q8B3, Q6XJV4, Q6XJV6, Q7Z3B1, Q80Z24, Q8BTP3, Q8TD46, Q9ES57, Q9ES58, Q9W6V2, Q9Z0J8, A2AJ76, Q8NDA2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

113 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	88
Likely benign	9
Benign	7

Top pathogenic / likely-pathogenic (0)

SpliceAI

2774 predictions. Top by Δscore:

Variant	Effect	Δscore
3:112928810:A:AC	donor_gain	1.0000
3:112928811:C:CC	donor_gain	1.0000
3:112929503:GTTAA:G	acceptor_gain	1.0000
3:112929504:TTAA:T	acceptor_gain	1.0000
3:112929505:TAA:T	acceptor_gain	1.0000
3:112929507:AC:A	acceptor_loss	1.0000
3:112929508:C:CA	acceptor_loss	1.0000
3:112929508:C:CC	acceptor_gain	1.0000
3:112929513:CA:C	acceptor_gain	1.0000
3:112929514:A:AC	acceptor_gain	1.0000
3:112929514:A:C	acceptor_gain	1.0000
3:112947943:A:C	acceptor_gain	1.0000
6:55248632:A:AG	acceptor_gain	1.0000
6:55248633:A:G	acceptor_gain	1.0000
6:55248637:A:AG	acceptor_gain	1.0000
6:55248637:AGTT:A	acceptor_loss	1.0000
6:55248638:G:GA	acceptor_gain	1.0000
6:55248638:GT:G	acceptor_gain	1.0000
6:55248638:GTT:G	acceptor_gain	1.0000
6:55248638:GTTT:G	acceptor_gain	1.0000
6:55255131:TCTAG:T	acceptor_loss	1.0000
6:55255132:CTAG:C	acceptor_loss	1.0000
6:55255133:TA:T	acceptor_loss	1.0000
6:55255134:A:AG	acceptor_gain	1.0000
6:55255134:AGACC:A	acceptor_gain	1.0000
6:55255135:G:GG	acceptor_gain	1.0000
6:55255135:GA:G	acceptor_gain	1.0000
6:55255135:GAC:G	acceptor_gain	1.0000
6:55255135:GACC:G	acceptor_gain	1.0000
6:55255135:GACCG:G	acceptor_gain	1.0000

AlphaMissense

2280 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000055881 (3:112974220 G>A), RS1000070854 (3:112966139 G>T), RS1000080573 (3:112925451 G>A), RS1000137894 (3:112959492 G>A), RS1000298278 (3:112944708 T>A), RS1000302182 (3:112937726 A>G), RS1000413942 (3:112945076 T>A), RS1000419485 (3:112952656 G>A), RS1000438085 (3:112966718 T>C), RS1000470763 (3:112973045 A>G), RS1000521311 (3:112972618 A>C), RS1000632940 (3:112937430 C>T), RS1000684429 (3:112932254 T>C), RS1000882422 (3:112957752 T>C), RS1000924026 (3:112957745 A>C,G)

Disease associations

OMIM: gene MIM:607546 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

30 associations (top):

Study	Trait	p-value
GCST000549_28	HIV-1 control	1.000000e-07
GCST001519_4	Economic and political preferences	6.000000e-06
GCST002541_22	Menarche (age at onset)	1.000000e-12
GCST003429_33	Morning vs. evening chronotype	4.000000e-09
GCST003837_6	Chronotype	8.000000e-13
GCST003838_6	Morning vs. evening chronotype	2.000000e-07
GCST003979_13	Excessive daytime sleepiness	5.000000e-06
GCST003982_6	Sleep traits (multi-trait analysis)	4.000000e-10
GCST004172_4	Rheumatoid arthritis	5.000000e-08
GCST004174_4	Rheumatoid arthritis (rheumatoid factor and/or anti-cyclic citrullinated peptide seropositive)	4.000000e-07
GCST004606_115	Eosinophil count	1.000000e-11
GCST004624_49	Sum eosinophil basophil counts	3.000000e-10
GCST005929_6	Severity of nausea and vomiting of pregnancy	6.000000e-09
GCST006585_324	Blood protein levels	9.000000e-17
GCST007559_20	Sleep duration (short sleep)	2.000000e-08
GCST007565_208	Morning person	2.000000e-31
GCST007565_54	Morning person	6.000000e-19
GCST007565_97	Morning person	3.000000e-48
GCST007576_295	Chronotype	3.000000e-48
GCST008062_125	Blood urea nitrogen levels	3.000000e-08
GCST008478_14	Neurological blood protein biomarker levels	2.000000e-30
GCST008478_15	Neurological blood protein biomarker levels	3.000000e-16
GCST008504_1	Fasting glucose change (long-term)	3.000000e-07
GCST009597_79	Multiple sclerosis	3.000000e-09
GCST010042_123	Asthma	1.000000e-08
GCST010043_113	Asthma	4.000000e-10
GCST011494_30	Daytime nap	6.000000e-52
GCST90000047_121	Age at first sexual intercourse	3.000000e-08
GCST90002381_182	Eosinophil count	2.000000e-22
GCST90002382_577	Eosinophil percentage of white cells	9.000000e-23

EFO canonical traits (14, from GWAS)

EFO ID	Trait name
EFO:0000180	HIV-1 infection
EFO:0004827	economic and social preference
EFO:0004703	age at menarche
EFO:0007875	excessive daytime sleepiness measurement
EFO:0007876	insomnia measurement
EFO:0007791	rheumatoid factor seropositivity measurement
EFO:0007837	anti-citrullinated protein antibody seropositivity
EFO:0004842	eosinophil count
EFO:0005090	basophil count
EFO:0009265	nausea and vomiting of pregnancy severity measurement
EFO:0008328	chronotype measurement
EFO:0007828	daytime rest measurement
EFO:0009749	age at first sexual intercourse measurement
EFO:0007991	eosinophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	3
Benzo(a)pyrene	increases methylation, affects methylation, decreases expression	2
daidzein	affects cotreatment, increases expression	1
daidzin	affects cotreatment, increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression	1
genistin	affects cotreatment, increases expression	1
glycitein	increases expression, affects cotreatment	1
CGP 52608	affects binding, increases reaction	1
glycitin	affects cotreatment, increases expression	1
(+)-JQ1 compound	increases expression	1
Air Pollutants, Occupational	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Nickel	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Genistein	increases expression, affects cotreatment	1

Cellosaurus cell lines

2 cell lines: 2 spontaneously immortalized cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E6PA	Genomeditech CHO-K1 H_CD200R1	Spontaneously immortalized cell line	Female
CVCL_KA25	CHO-K1/CD200 R1	Spontaneously immortalized cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.