GRIK3

glutamate ionotropic receptor kainate type subunit 3, the group of Glutamate ionotropic receptor kainate type subunits

Basic information

Region (hg38): 1:36795526-37034515

Links

ENSG00000163873 ∙ NCBI:2899 ∙ OMIM:138243 ∙ HGNC:4581 ∙ Uniprot:Q13003 ∙ 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 GRIK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRIK3 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	7	11
missense			39	2	1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	39	6	8

Variants in GRIK3

This is a list of pathogenic ClinVar variants found in the GRIK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36801940-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-36802011-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-36802021-C-T		not specified	Uncertain significance (Sep 22, 2023)
1-36802033-T-G		not specified	Uncertain significance (Dec 20, 2023)
1-36802044-C-T		not specified	Uncertain significance (Feb 13, 2023)
1-36804959-T-C			Likely benign (Feb 01, 2024)
1-36805006-T-C		not specified	Uncertain significance (May 26, 2024)
1-36805096-T-C		not specified	Uncertain significance (Sep 01, 2015)
1-36805145-T-C		not specified	Uncertain significance (May 17, 2023)
1-36805150-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-36805163-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-36805223-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-36805228-T-A		not specified	Uncertain significance (Apr 09, 2024)
1-36806096-T-A			Likely benign (Dec 31, 2019)
1-36806227-T-C		not specified	Uncertain significance (Jun 13, 2024)
1-36806252-G-A			Likely benign (Sep 01, 2022)
1-36817164-C-T		not specified	Uncertain significance (Dec 14, 2022)
1-36817166-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-36817238-A-G		not specified	Uncertain significance (Oct 20, 2023)
1-36819805-C-T		not specified	Uncertain significance (May 15, 2024)
1-36825812-G-A			Likely benign (Nov 01, 2022)
1-36841741-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-36841757-C-A		not specified	Uncertain significance (Jan 06, 2023)
1-36841856-T-C			Benign (Dec 31, 2019)
1-36841879-C-T		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRIK3	protein_coding	protein_coding	ENST00000373091	16	238603

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000239	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.01	386	592	0.652	0.0000380	6031
Missense in Polyphen		105	231.2	0.45415		2430
Synonymous	-0.400	264	256	1.03	0.0000185	1821
Loss of Function	5.86	4	47.6	0.0840	0.00000275	467

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. The postsynaptic actions of Glu are mediated by a variety of receptors that are named according to their selective agonists. This receptor binds domoate > kainate >> L-glutamate = quisqualate >> AMPA = NMDA.
• Pathway: Glutamatergic synapse - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Activation of Ca-permeable Kainate Receptor;Ionotropic activity of kainate receptors;Presynaptic function of Kainate receptors;Activation of kainate receptors upon glutamate binding;Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.00441
• rvis_EVS: -1.68
• rvis_percentile_EVS: 2.68

Haploinsufficiency Scores

• pHI: 0.202
• hipred: Y
• hipred_score: 0.768
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grik3
• 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)

Gene ontology

• Biological process: adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway;glutamate receptor signaling pathway;G protein-coupled glutamate receptor signaling pathway;ion transmembrane transport;ionotropic glutamate receptor signaling pathway;synaptic transmission, glutamatergic;regulation of membrane potential;modulation of chemical synaptic transmission;negative regulation of synaptic transmission, glutamatergic;regulation of presynaptic membrane potential
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;axon;dendrite;dendrite cytoplasm;kainate selective glutamate receptor complex;presynaptic membrane;terminal bouton;perikaryon;postsynaptic membrane;glutamatergic synapse
• Molecular function: adenylate cyclase inhibiting G protein-coupled glutamate receptor activity;G protein-coupled receptor binding;ionotropic glutamate receptor activity;glutamate receptor activity;kainate selective glutamate receptor activity;ligand-gated ion channel activity involved in regulation of presynaptic membrane potential;transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential