GRIK5

glutamate ionotropic receptor kainate type subunit 5, the group of Glutamate ionotropic receptor kainate type subunits

Basic information

Region (hg38): 19:41998320-42070206

Previous symbols: [ "GRIK2" ]

Links

ENSG00000105737 ∙ NCBI:2901 ∙ OMIM:600283 ∙ HGNC:4583 ∙ Uniprot:Q16478 ∙ 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 GRIK5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRIK5 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				9	1	10
missense			49	3	1	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	49	13	2

Variants in GRIK5

This is a list of pathogenic ClinVar variants found in the GRIK5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41998880-C-A		not specified	Uncertain significance (Feb 02, 2024)
19-41998893-C-T		not specified	Uncertain significance (Feb 06, 2024)
19-41998984-C-T		not specified	Uncertain significance (Dec 13, 2022)
19-41998989-A-C		not specified	Uncertain significance (Dec 03, 2021)
19-41998998-A-C		not specified	Uncertain significance (Dec 03, 2021)
19-41999005-G-C		not specified	Uncertain significance (Feb 21, 2024)
19-41999026-C-A		not specified	Uncertain significance (Apr 23, 2024)
19-41999037-G-T		not specified	Uncertain significance (Nov 10, 2022)
19-41999044-G-A		not specified	Uncertain significance (Aug 28, 2023)
19-41999108-C-A			Likely benign (Mar 01, 2022)
19-41999226-C-G		not specified	Uncertain significance (Jul 11, 2023)
19-41999247-C-A		not specified	Uncertain significance (Apr 01, 2024)
19-41999247-C-T		not specified	Uncertain significance (Mar 20, 2024)
19-41999249-G-C		not specified	Uncertain significance (Feb 27, 2023)
19-41999253-G-C		not specified	Uncertain significance (Apr 01, 2024)
19-41999254-A-T		not specified	Uncertain significance (Apr 01, 2024)
19-41999293-C-G		not specified	Uncertain significance (Aug 28, 2023)
19-41999293-C-T		not specified	Uncertain significance (Apr 12, 2024)
19-42002424-C-T			Likely benign (Dec 01, 2022)
19-42002448-G-C		GRIK5-related disorder	Likely benign (Apr 08, 2019)
19-42003351-C-A		GRIK5-related disorder	Benign (Dec 31, 2019)
19-42003588-G-A		GRIK5-related disorder	Uncertain significance (Jul 24, 2023)
19-42003593-C-T		not specified	Uncertain significance (Jan 12, 2024)
19-42003594-C-G		not specified	Uncertain significance (Dec 07, 2021)
19-42003651-T-C		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRIK5	protein_coding	protein_coding	ENST00000262895	19	71178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00575	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.36	358	587	0.609	0.0000395	6255
Missense in Polyphen		127	253.68	0.50063		2590
Synonymous	0.0562	252	253	0.996	0.0000181	2081
Loss of Function	5.34	7	46.2	0.152	0.00000247	479

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000123
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

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. This receptor binds kainate > quisqualate > domoate > L- glutamate >> AMPA >> NMDA = 1S,3R-ACPD.
• 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: 0.144
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.52

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.671
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.704

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grik5
• 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein retention in ER lumen;regulation of synaptic vesicle fusion to presynaptic active zone membrane;ion transmembrane transport;ionotropic glutamate receptor signaling pathway;synaptic transmission, glutamatergic;receptor clustering;positive regulation of neuron apoptotic process;modulation of chemical synaptic transmission;establishment of localization in cell;excitatory postsynaptic potential;cellular response to glucose stimulus
• Cellular component: nucleus;endoplasmic reticulum;plasma membrane;cell junction;dendrite;kainate selective glutamate receptor complex;presynaptic membrane;terminal bouton;perikaryon;postsynaptic membrane;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse;integral component of presynaptic membrane;integral component of postsynaptic density membrane
• Molecular function: glutamate receptor activity;kainate selective glutamate receptor activity;SH3 domain binding;PDZ domain binding;identical protein binding;transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential