GRM4
Basic information
Region (hg38): 6:34018643-34155622
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (104 variants)
- not_provided (12 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRM4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000841.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | |||||
| missense | 106 | 107 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 106 | 1 | 8 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GRM4 | protein_coding | protein_coding | ENST00000538487 | 10 | 133772 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.993 | 0.00693 | 125720 | 0 | 26 | 125746 | 0.000103 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.68 | 447 | 638 | 0.701 | 0.0000443 | 5933 |
| Missense in Polyphen | 179 | 296.3 | 0.60412 | 2805 | ||
| Synonymous | 1.03 | 251 | 273 | 0.921 | 0.0000204 | 1892 |
| Loss of Function | 4.86 | 5 | 36.9 | 0.136 | 0.00000194 | 380 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000630 | 0.0000615 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000523 | 0.000523 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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:7617140, ECO:0000269|PubMed:8738157, ECO:0000269|PubMed:9473604}.;
- Pathway
- Glutamatergic synapse - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Taste transduction - 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
- 0.198
Intolerance Scores
- loftool
- 0.0353
- rvis_EVS
- -2.48
- rvis_percentile_EVS
- 0.96
Haploinsufficiency Scores
- pHI
- 0.270
- hipred
- Y
- hipred_score
- 0.755
- ghis
- 0.691
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.453
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Grm4
- 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);
Gene ontology
- Biological process
- activation of MAPK activity;G protein-coupled receptor signaling pathway;adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway;G protein-coupled glutamate receptor signaling pathway;chemical synaptic transmission;neurotransmitter secretion;positive regulation of MAPK cascade;regulation of neuron apoptotic process;regulation of synaptic transmission, glutamatergic
- Cellular component
- plasma membrane;integral component of plasma membrane;cytoplasmic vesicle;presynaptic membrane
- Molecular function
- G protein-coupled receptor activity;glutamate receptor activity