CD200R1L

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

Basic information

Region (hg38): 3:112815709-112846864

Links

ENSG00000206531 ∙ NCBI:344807 ∙ ∙ HGNC:24665 ∙ Uniprot:Q6Q8B3 ∙ 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 CD200R1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD200R1L 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in CD200R1L

This is a list of pathogenic ClinVar variants found in the CD200R1L region.

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

Position	Type	Phenotype	Significance	ClinVar
3-112819778-T-C		not specified	Uncertain significance (Feb 10, 2023)
3-112819827-C-T		not specified	Uncertain significance (Jun 21, 2023)
3-112819829-A-G		not specified	Uncertain significance (Aug 02, 2021)
3-112819833-G-C		not specified	Uncertain significance (Nov 06, 2023)
3-112819877-G-C		not specified	Uncertain significance (Nov 17, 2022)
3-112819889-C-T		not specified	Uncertain significance (Jun 27, 2022)
3-112819893-G-A		not specified	Uncertain significance (Jun 03, 2022)
3-112827008-C-T		not specified	Likely benign (Feb 06, 2024)
3-112827029-T-A		not specified	Uncertain significance (Feb 15, 2023)
3-112827030-C-G		not specified	Uncertain significance (Nov 17, 2022)
3-112827055-G-A		not specified	Uncertain significance (Mar 17, 2023)
3-112827067-C-A		not specified	Uncertain significance (Jun 06, 2023)
3-112827188-C-T		not specified	Uncertain significance (Nov 10, 2023)
3-112827391-G-A		not specified	Uncertain significance (Feb 01, 2023)
3-112827396-A-C		not specified	Uncertain significance (Mar 23, 2022)
3-112827435-C-T		not specified	Uncertain significance (Sep 29, 2022)
3-112827447-G-A		not specified	Likely benign (Dec 15, 2023)
3-112827453-A-C		not specified	Uncertain significance (Mar 28, 2024)
3-112827460-G-A		not specified	Uncertain significance (Nov 20, 2024)
3-112827472-C-G		not specified	Uncertain significance (Jul 20, 2021)
3-112827504-A-C		not specified	Uncertain significance (Mar 19, 2024)
3-112827537-T-C		not specified	Uncertain significance (Jun 17, 2024)
3-112827555-T-C		not specified	Uncertain significance (Jan 22, 2024)
3-112827625-C-T		not specified	Uncertain significance (Nov 12, 2021)
3-112827627-A-G		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD200R1L	protein_coding	protein_coding	ENST00000398214	6	31148

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00304	0.949	124970	0	5	124975	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.414	160	146	1.10	0.00000718	1745
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000882
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a receptor for the CD200/OX2 cell surface glycoprotein. {ECO:0000250}.
• Pathway: Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.698
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.387

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0518

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: regulation of neuroinflammatory response
• Cellular component: external side of plasma membrane;integral component of membrane
• Molecular function: signaling receptor activity