GRM2

glutamate metabotropic receptor 2, the group of Glutamate metabotropic receptors

Basic information

Region (hg38): 3:51707068-51718613

Links

ENSG00000164082 ∙ NCBI:2912 ∙ OMIM:604099 ∙ HGNC:4594 ∙ Uniprot:Q14416 ∙ 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 GRM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRM2 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				4	3	7
missense			63	2	1	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	63	6	4

Variants in GRM2

This is a list of pathogenic ClinVar variants found in the GRM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-51709032-G-A		not specified	Uncertain significance (May 08, 2024)
3-51709080-G-A		not specified	Uncertain significance (Jan 27, 2022)
3-51709113-G-A		not specified	Uncertain significance (Jul 15, 2021)
3-51709116-G-A		not specified	Uncertain significance (Apr 12, 2022)
3-51709272-C-T		not specified	Uncertain significance (Jul 09, 2024)
3-51709352-C-T			Likely benign (Mar 29, 2018)
3-51709357-C-A		not specified	Uncertain significance (Nov 03, 2022)
3-51709389-A-G		not specified	Uncertain significance (Dec 30, 2024)
3-51709403-T-C			Likely benign (Jun 20, 2018)
3-51709413-T-G		not specified	Uncertain significance (Dec 07, 2023)
3-51712582-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-51712611-G-C		not specified	Uncertain significance (Jan 24, 2023)
3-51712621-G-A		not specified	Uncertain significance (Jul 25, 2023)
3-51712625-C-G		not specified	Uncertain significance (Dec 15, 2022)
3-51712665-G-A		not specified	Uncertain significance (Aug 04, 2024)
3-51712758-A-G		not specified	Uncertain significance (Nov 21, 2023)
3-51712762-G-A		not specified	Uncertain significance (Feb 20, 2025)
3-51712765-C-T			Likely benign (Jul 18, 2018)
3-51712803-C-G		not specified	Uncertain significance (Sep 27, 2024)
3-51712832-C-T			Benign (Jul 04, 2018)
3-51712833-C-T		not specified	Uncertain significance (Mar 28, 2024)
3-51712839-G-A		not specified	Uncertain significance (Aug 07, 2024)
3-51712846-C-T		not specified	Uncertain significance (Sep 02, 2024)
3-51712864-C-T		not specified	Uncertain significance (Oct 26, 2021)
3-51712910-T-C			Likely benign (Jun 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRM2	protein_coding	protein_coding	ENST00000395052	5	11544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.120	0.880	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.37	423	584	0.724	0.0000398	5616
Missense in Polyphen		151	252.8	0.59732		2632
Synonymous	1.00	218	238	0.917	0.0000152	1909
Loss of Function	3.58	7	27.1	0.258	0.00000141	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.0000977	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: G-protein coupled receptor for glutamate. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors, such as adenylate cyclase. Signaling inhibits adenylate cyclase activity. May mediate suppression of neurotransmission or may be involved in synaptogenesis or synaptic stabilization. {ECO:0000269|PubMed:18297054, ECO:0000269|PubMed:22300836, ECO:0000269|PubMed:23129762, ECO:0000269|PubMed:7620613}.
• Pathway: Glutamatergic synapse - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Cocaine addiction - Homo sapiens (human);GPCRs, Class C Metabotropic glutamate, pheromone;Signaling by GPCR;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Class C/3 (Metabotropic glutamate/pheromone receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;G alpha (i) signalling events;GPCR signaling-G alpha i;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• loftool: 0.0683
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.54

Haploinsufficiency Scores

• pHI: 0.874
• hipred: Y
• hipred_score: 0.768
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.117

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grm2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;negative regulation of adenylate cyclase activity;adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway;G protein-coupled glutamate receptor signaling pathway;chemical synaptic transmission;glutamate secretion;regulation of synaptic transmission, glutamatergic;glutamate homeostasis
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;axon;dendrite;presynaptic membrane;integral component of postsynaptic membrane
• Molecular function: group II metabotropic glutamate receptor activity;G protein-coupled receptor activity;calcium channel regulator activity;protein binding;glutamate receptor activity