GRID1

protein-coding

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

Gene summary

This gene encodes a subunit of glutamate receptor channels. These channels mediate most of the fast excitatory synaptic transmission in the central nervous system and play key roles in synaptic plasticity.[provided by RefSeq, Jan 2009]

MANE transcript

NM_017551.3

Inheritance

—

ClinVar variants

P:1U:151B:4

Top phenotype

GRID1-associated neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr10:85,599,552-86,366,795

External References & Databases

Ensembl (ENSG00000182771)

Transcript & Mutation Effects

hg38 • Region Span ~767.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GRID1 variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 121

GRID1-associated neurodevelopmental disorderTotal: 32

GRID1-related disorderTotal: 3

Abnormality of neuronal migrationTotal: 2

not providedTotal: 1

Prostate cancerTotal: 1

Gestational diabetes mellitus uncontrolledTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017551.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense	1 clinvar		147 clinvar	1 clinvar	2 clinvar	151
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	151	2	2	156

Highest pathogenic variant AF is 6.848424e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017551.3	RefSeq	NP_060021.1	16	MANE Select
ENST00000327946.12	Ensembl	ENSP00000330148.7	16	MANE Select
ENST00000464741.2	Ensembl	ENSP00000433064.1	14	Standard
ENST00001110659.1	Ensembl	ENSP00000780464.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuroactive ligand-receptor interaction - Homo sapiens (human)
MECP2 and Associated Rett Syndrome

Biological Process

ion transmembrane transport
social behavior
ionotropic glutamate receptor signaling pathway
synaptic transmission, glutamatergic
modulation of chemical synaptic transmission

Molecular Function

ionotropic glutamate receptor activity
glutamate receptor activity
transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential

Cellular Component

plasma membrane
cell junction
postsynaptic membrane
extracellular exosome
glutamatergic synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000327946
Coding exons: 16
Length: 766939
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125748
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.62	509	622	0.818	0.0000385	6642
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.108
RVIS EVS: -2.1
RVIS percentile EVS: 1.55

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.351

Gene Damage Prediction

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