CNR2

cannabinoid receptor 2, the group of Cannabinoid receptors

Basic information

Region (hg38): 1:23870514-23913362

Links

ENSG00000188822 ∙ NCBI:1269 ∙ OMIM:605051 ∙ HGNC:2160 ∙ Uniprot:P34972 ∙ 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 CNR2 gene.

• Inborn genetic diseases (16 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNR2 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				1	1	2
missense			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	2

Variants in CNR2

This is a list of pathogenic ClinVar variants found in the CNR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-23874594-C-A		not specified	Uncertain significance (Jan 23, 2023)
1-23874617-C-A		not specified	Uncertain significance (Jan 24, 2023)
1-23874635-G-A		not specified	Uncertain significance (May 15, 2023)
1-23874661-C-G		not specified	Uncertain significance (Nov 08, 2021)
1-23874679-G-A			Benign (Jul 04, 2018)
1-23874713-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-23875023-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-23875061-A-T		not specified	Uncertain significance (Nov 22, 2023)
1-23875143-C-A		not specified	Uncertain significance (Sep 22, 2023)
1-23875288-A-C		not specified	Uncertain significance (Sep 29, 2023)
1-23875327-G-A			Likely benign (Mar 29, 2018)
1-23875401-T-A		not specified	Uncertain significance (Apr 13, 2023)
1-23875410-A-G		not specified	Uncertain significance (Nov 04, 2022)
1-23875421-C-T			Benign (Dec 31, 2019)
1-23875437-A-G		not specified	Uncertain significance (Nov 09, 2021)
1-23875496-G-A		not specified	Uncertain significance (Jun 03, 2022)
1-23875529-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-23875552-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-23875554-T-C		not specified	Uncertain significance (Jun 22, 2021)
1-23875558-G-T		not specified	Uncertain significance (Aug 14, 2023)
1-23875575-C-A		not specified	Uncertain significance (Jun 10, 2022)
1-23875580-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-23875580-G-C		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNR2	protein_coding	protein_coding	ENST00000536471	1	88534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000654	0.287	125628	0	119	125747	0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.681	173	200	0.864	0.0000104	2316
Missense in Polyphen		53	73.413	0.72194		906
Synonymous	-0.314	88	84.3	1.04	0.00000430	785
Loss of Function	0.0786	8	8.24	0.970	5.21e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000363	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.00266	0.00267
Finnish	0.000881	0.000878
European (Non-Finnish)	0.000249	0.000246
Middle Eastern	0.00266	0.00267
South Asian	0.000491	0.000392
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Heterotrimeric G protein-coupled receptor for endocannabinoid 2-arachidonoylglycerol mediating inhibition of adenylate cyclase. May function in inflammatory response, nociceptive transmission and bone homeostasis. {ECO:0000269|PubMed:10051546, ECO:0000269|PubMed:12663043, ECO:0000269|PubMed:12711605, ECO:0000269|PubMed:18692962}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Small Ligand GPCRs;Cannabinoid receptor signaling;Gastric ulcer formation;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;metabolism of anandamide an endogenous cannabinoid;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.452

Intolerance Scores

• loftool: 0.727
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.208
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnr2
• Phenotype: hematopoietic system phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: cnr2
• Affected structure: hepatocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: response to amphetamine;inflammatory response;immune response;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;sensory perception of pain;leukocyte chemotaxis;negative regulation of synaptic transmission, GABAergic;response to lipopolysaccharide;negative regulation of mast cell activation;cannabinoid signaling pathway;negative regulation of action potential;negative regulation of inflammatory response;negative regulation of nitric-oxide synthase activity
• Cellular component: plasma membrane;integral component of plasma membrane;dendrite;extrinsic component of cytoplasmic side of plasma membrane;perikaryon
• Molecular function: cannabinoid receptor activity