GRM3

glutamate metabotropic receptor 3, the group of Glutamate metabotropic receptors

Basic information

Region (hg38): 7:86643909-86864879

Links

ENSG00000198822 ∙ NCBI:2913 ∙ OMIM:601115 ∙ HGNC:4595 ∙ Uniprot:Q14832 ∙ 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 GRM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRM3 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				6	2	8
missense			19		2	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	6	4

Variants in GRM3

This is a list of pathogenic ClinVar variants found in the GRM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-86765277-G-A			Benign (Dec 31, 2019)
7-86765334-C-A		not specified	Uncertain significance (Aug 08, 2023)
7-86765537-C-T		not specified	Uncertain significance (Dec 20, 2023)
7-86786404-C-G		not specified	Uncertain significance (Nov 21, 2023)
7-86786408-C-T		not specified	Uncertain significance (Feb 22, 2023)
7-86786442-C-A		not specified	Uncertain significance (May 14, 2024)
7-86786491-A-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
7-86786530-G-A			Likely benign (Feb 09, 2018)
7-86786583-T-C		not specified	Uncertain significance (Dec 04, 2023)
7-86786591-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-86786608-G-C			Likely benign (Mar 29, 2018)
7-86786679-C-G		not specified	Uncertain significance (Jan 03, 2024)
7-86786945-G-A		not specified	Uncertain significance (Apr 04, 2023)
7-86787053-G-A		not specified	Uncertain significance (Nov 22, 2023)
7-86838938-G-A			Benign (May 01, 2022)
7-86838980-C-A		not specified	Uncertain significance (Aug 26, 2022)
7-86838987-G-A			Likely benign (Apr 11, 2018)
7-86838998-A-C		not specified	Uncertain significance (Feb 06, 2024)
7-86839013-C-T		not specified	Uncertain significance (Jun 24, 2022)
7-86839280-T-C		not specified	Uncertain significance (May 09, 2024)
7-86839354-C-T		not specified	Uncertain significance (Mar 18, 2024)
7-86839392-C-T			Likely benign (Aug 14, 2018)
7-86839402-T-A		not specified	Uncertain significance (Aug 17, 2021)
7-86839434-C-T			Likely benign (May 29, 2018)
7-86839525-G-A		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRM3	protein_coding	protein_coding	ENST00000361669	5	220971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.785	0.215	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.20	323	530	0.609	0.0000323	5782
Missense in Polyphen		109	244.47	0.44586		2681
Synonymous	0.784	205	220	0.933	0.0000147	1738
Loss of Function	4.21	6	31.5	0.191	0.00000169	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000260	0.000260
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000165	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. Signaling inhibits adenylate cyclase activity. {ECO:0000269|PubMed:8840013}.
• 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: 0.255

Intolerance Scores

• loftool: 0.0728
• rvis_EVS: -1.29
• rvis_percentile_EVS: 5.08

Haploinsufficiency Scores

• pHI: 0.494
• hipred: Y
• hipred_score: 0.800
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grm3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal 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); 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;regulation of synaptic transmission, glutamatergic
• Cellular component: plasma membrane;integral component of plasma membrane;postsynaptic density;axon;dendritic spine;glutamatergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
• Molecular function: group II metabotropic glutamate receptor activity;G protein-coupled receptor activity;calcium channel regulator activity;glutamate receptor activity