GRIK4

glutamate ionotropic receptor kainate type subunit 4, the group of Glutamate ionotropic receptor kainate type subunits

Basic information

Region (hg38): 11:120511746-120988906

Previous symbols: [ "GRIK" ]

Links

ENSG00000149403 ∙ NCBI:2900 ∙ OMIM:600282 ∙ HGNC:4582 ∙ Uniprot:Q16099 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Response to antidepressant treatment with citalopram	AD	Pharmacogenomic	The choice of medications may be affected by the presence of variants	General	17671280; 18370842; 19924111

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GRIK4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRIK4 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				7	7	14
missense			52		5	57
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1	1	2
Total	0	0	53	8	13

Variants in GRIK4

This is a list of pathogenic ClinVar variants found in the GRIK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-120660333-G-T			Likely benign (Dec 31, 2019)
11-120660335-C-T		not specified	Uncertain significance (Aug 08, 2023)
11-120660338-C-T		not specified	Uncertain significance (May 09, 2022)
11-120660356-C-T		not specified	Uncertain significance (Aug 28, 2021)
11-120660364-G-A		not specified	Uncertain significance (Dec 19, 2022)
11-120660373-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-120660387-C-G			Benign (Dec 31, 2019)
11-120792654-T-C		not specified	Benign (Mar 09, 2018)
11-120802734-C-T		not specified	Uncertain significance (Jan 08, 2024)
11-120802742-C-T			Likely benign (Jul 19, 2018)
11-120802773-G-A		not specified	Uncertain significance (May 05, 2022)
11-120802816-T-G		not specified	Uncertain significance (May 03, 2023)
11-120802838-G-A			Benign (Aug 09, 2018)
11-120815415-C-G			Benign (Dec 31, 2019)
11-120819909-C-G			Benign (Dec 31, 2019)
11-120819915-C-A		not specified	Uncertain significance (Jan 26, 2022)
11-120831888-T-G		not specified	Uncertain significance (Feb 15, 2023)
11-120831942-C-T		not specified	Uncertain significance (Dec 03, 2021)
11-120831962-C-T		not specified	Uncertain significance (Sep 27, 2022)
11-120831976-C-T			Likely benign (Dec 31, 2019)
11-120831994-C-T			Benign (Dec 31, 2019)
11-120836782-G-A			Likely benign (Dec 21, 2018)
11-120861998-C-G		not specified	Uncertain significance (Jul 05, 2022)
11-120862007-A-G			Benign (Dec 31, 2019)
11-120862072-C-G		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRIK4	protein_coding	protein_coding	ENST00000527524	19	477146

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.111	0.889	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.04	436	574	0.760	0.0000347	6211
Missense in Polyphen		154	241.31	0.63818		2606
Synonymous	-0.191	242	238	1.02	0.0000157	1884
Loss of Function	4.65	11	44.5	0.247	0.00000208	510

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.000218	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for glutamate. 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.
• Pathway: Glutamatergic synapse - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Activation of Ca-permeable Kainate Receptor;Ionotropic activity 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: 0.161

Intolerance Scores

• loftool: 0.208
• rvis_EVS: -0.55
• rvis_percentile_EVS: 20

Haploinsufficiency Scores

• pHI: 0.259
• hipred: Y
• hipred_score: 0.623
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.103

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grik4
• Phenotype: homeostasis/metabolism 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: glutamate receptor signaling pathway;chemical synaptic transmission;ion transmembrane transport;ionotropic glutamate receptor signaling pathway;synaptic transmission, glutamatergic;modulation of chemical synaptic transmission
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;kainate selective glutamate receptor complex;presynaptic membrane;postsynaptic membrane;hippocampal mossy fiber to CA3 synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
• Molecular function: glutamate receptor activity;kainate selective glutamate receptor activity;transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential