GRID1

glutamate ionotropic receptor delta type subunit 1, the group of Glutamate ionotropic receptor delta type subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:85599551-86366795

Links

ENSG00000182771 ∙ NCBI:2894 ∙ OMIM:610659 ∙ HGNC:4575 ∙ Uniprot:Q9ULK0 ∙ 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 GRID1 gene.

• Inborn genetic diseases (35 variants)
• GRID1-associated neurodevelopmental disorder (32 variants)
• not provided (3 variants)
• Gestational diabetes mellitus uncontrolled (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRID1 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						0
missense	1		60		2	63
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	61	0	2

Variants in GRID1

This is a list of pathogenic ClinVar variants found in the GRID1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-85602319-C-T		not specified	Uncertain significance (Mar 29, 2022)
10-85602353-G-A		GRID1-associated neurodevelopmental disorder	Uncertain significance (May 08, 2023)
10-85602364-G-A		not specified	Uncertain significance (Jul 25, 2023)
10-85602448-G-A		GRID1-associated neurodevelopmental disorder	Uncertain significance (May 08, 2023)
10-85602550-C-T		not specified	Uncertain significance (Mar 22, 2023)
10-85602613-G-A		GRID1-associated neurodevelopmental disorder	Uncertain significance (May 08, 2023)
10-85602667-C-T			Uncertain significance (Jan 13, 2022)
10-85613411-T-C		not specified	Uncertain significance (Aug 26, 2022)
10-85613417-G-A		not specified	Uncertain significance (Feb 28, 2023)
10-85613433-G-A		not specified	Uncertain significance (Oct 06, 2022)
10-85613478-G-C		not specified	Uncertain significance (Nov 14, 2023)
10-85613559-C-T		GRID1-associated neurodevelopmental disorder	Uncertain significance (May 08, 2023)
10-85619901-G-A		not specified	Uncertain significance (Dec 28, 2022)
10-85619957-G-A		not specified	Uncertain significance (Jan 30, 2024)
10-85619972-G-A		GRID1-associated neurodevelopmental disorder	Uncertain significance (May 08, 2023)
10-85647243-C-A		not specified	Uncertain significance (Feb 05, 2024)
10-85647249-C-T		GRID1-associated neurodevelopmental disorder • not specified	Uncertain significance (May 08, 2023)
10-85647275-T-C		GRID1-associated neurodevelopmental disorder	Uncertain significance (May 08, 2023)
10-85647339-C-T		not specified	Uncertain significance (Aug 28, 2023)
10-85647345-C-G		GRID1-associated neurodevelopmental disorder	Uncertain significance (May 08, 2023)
10-85723052-C-T		GRID1-associated neurodevelopmental disorder	Pathogenic (May 08, 2023)
10-85723089-C-A		not specified	Uncertain significance (Sep 29, 2022)
10-85723106-T-G		not specified	Uncertain significance (Aug 15, 2023)
10-85723109-G-T		not specified	Uncertain significance (Apr 26, 2023)
10-85723127-C-T		not specified	Uncertain significance (Oct 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRID1	protein_coding	protein_coding	ENST00000327946	16	766939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000691	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.62	509	622	0.818	0.0000385	6642
Missense in Polyphen		204	287.61	0.7093		3044
Synonymous	-0.369	272	264	1.03	0.0000180	2000
Loss of Function	5.37	5	43.1	0.116	0.00000193	477

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
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. 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: Neuroactive ligand-receptor interaction - Homo sapiens (human);MECP2 and Associated Rett Syndrome (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.108
• rvis_EVS: -2.1
• rvis_percentile_EVS: 1.55

Haploinsufficiency Scores

• pHI: 0.403
• hipred: Y
• hipred_score: 0.685
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.351

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grid1
• Phenotype: growth/size/body region 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); hearing/vestibular/ear phenotype; skeleton phenotype

Gene ontology

• Biological process: ion transmembrane transport;social behavior;ionotropic glutamate receptor signaling pathway;synaptic transmission, glutamatergic;modulation of chemical synaptic transmission
• Cellular component: plasma membrane;cell junction;postsynaptic membrane;extracellular exosome;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: ionotropic glutamate receptor activity;glutamate receptor activity;transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential