CD200R1L

protein-coding

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

Gene summary

Predicted to enable signaling receptor activity. Predicted to be involved in regulation of neuroinflammatory response. Predicted to be located in cell surface and membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001199215.3

Inheritance

—

ClinVar variants

U:41B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr3:112,815,709-112,846,864

External References & Databases

Ensembl (ENSG00000206531)

Transcript & Mutation Effects

hg38 • Region Span ~31.2 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 CD200R1L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 42

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001199215.3. 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			40 clinvar	2 clinvar		42
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	2	0	43

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001199215.3	RefSeq	NP_001186144.1	5	MANE Select
ENST00000488794.6	Ensembl	ENSP00000418413.1	5	MANE Select
NM_001008784.4	RefSeq	NP_001008784.2	6	Standard
NM_001370552.3	RefSeq	NP_001357481.1	5	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)

Biological Process

regulation of neuroinflammatory response

Molecular Function

signaling receptor activity

Cellular Component

external side of plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398214
Coding exons: 6
Length: 31148
Individuals with no LoFs: 124970
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 124975
p: 0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.414	160	146	1.10	0.00000718	1745
Missense (PolyPhen)		45	36.882	1.2201		452
Synonymous	-1.86	71	53.7	1.32	0.00000283	539
Loss of Function	1.73	6	12.6	0.474	5.33e-7	163

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a receptor for the CD200/OX2 cell surface glycoprotein. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.698
RVIS EVS: -0.05
RVIS percentile EVS: 50.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0518

Gene Damage Prediction

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