GRIK1

glutamate ionotropic receptor kainate type subunit 1, the group of Glutamate ionotropic receptor kainate type subunits

Basic information

Region (hg38): 21:29536933-29940033

Previous symbols: [ "GLUR5" ]

Links

ENSG00000171189 ∙ NCBI:2897 ∙ OMIM:138245 ∙ HGNC:4579 ∙ Uniprot:P39086 ∙ 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 GRIK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRIK1 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				10	2	12
missense			56	1	1	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	56	11	3

Variants in GRIK1

This is a list of pathogenic ClinVar variants found in the GRIK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-29537234-G-T		not specified	Uncertain significance (May 04, 2022)
21-29537258-C-A		not specified	Uncertain significance (Mar 01, 2023)
21-29537297-T-C		not specified	Uncertain significance (Jun 16, 2024)
21-29537303-T-C		not specified	Uncertain significance (Oct 03, 2022)
21-29553686-C-T		not specified	Uncertain significance (Feb 14, 2023)
21-29553695-A-G		not specified	Uncertain significance (Nov 18, 2022)
21-29553703-G-A			Benign (Dec 31, 2019)
21-29553704-C-A		not specified	Uncertain significance (Sep 20, 2023)
21-29555094-T-A			Benign (Nov 15, 2018)
21-29555098-A-G		not specified	Uncertain significance (Jun 11, 2024)
21-29555141-T-C		not specified	Uncertain significance (Jan 18, 2022)
21-29555179-G-A		not specified	Uncertain significance (May 28, 2024)
21-29555198-C-T		not specified	Uncertain significance (Dec 15, 2023)
21-29555248-C-T		not specified	Uncertain significance (Mar 04, 2024)
21-29561642-C-T		not specified	Uncertain significance (Nov 23, 2021)
21-29561691-T-G		not specified	Uncertain significance (Jan 17, 2024)
21-29561728-A-G		not specified	Uncertain significance (Dec 15, 2022)
21-29561809-A-G		not specified	Uncertain significance (Nov 22, 2022)
21-29576980-G-A		not specified	Uncertain significance (Nov 23, 2021)
21-29576988-A-C		not specified	Uncertain significance (Nov 14, 2023)
21-29576997-C-T			Likely benign (Jun 13, 2018)
21-29576999-C-T		not specified	Uncertain significance (Aug 02, 2023)
21-29577012-C-T			Likely benign (Dec 14, 2018)
21-29577040-G-A		not specified	Uncertain significance (Feb 23, 2023)
21-29577052-G-A		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRIK1	protein_coding	protein_coding	ENST00000399907	17	403098

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-9	0.999	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	440	510	0.862	0.0000274	6019
Missense in Polyphen		139	203.49	0.68308		2395
Synonymous	-0.497	210	201	1.04	0.0000119	1755
Loss of Function	3.03	22	43.6	0.504	0.00000204	536

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000660	0.000633
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000109	0.000109
South Asian	0.000137	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L- glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. May be involved in the transmission of light information from the retina to the hypothalamus.
• 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;Activation of Na-permeable kainate receptors;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.550

Intolerance Scores

• loftool: 0.227
• rvis_EVS: -1.64
• rvis_percentile_EVS: 2.84

Haploinsufficiency Scores

• pHI: 0.177
• hipred: Y
• hipred_score: 0.602
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grik1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region 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)

Gene ontology

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