GRIA2

Chr 4AD

glutamate ionotropic receptor AMPA type subunit 2

Also known as: GLUR2, GLURB, GluA2, GluR-K2, HBGR2, NEDLIB, gluR-2, gluR-B

NCBI Gene: 2891 ENSG00000120251 UniProt: P42262 OMIM: 138247

The protein functions as the GRIA2 subunit of AMPA glutamate receptors, which are ligand-activated cation channels that mediate excitatory neurotransmission in the brain and undergo RNA editing to become impermeable to calcium. Mutations cause autosomal dominant neurodevelopmental disorder with language impairment and behavioral abnormalities. The pathogenic mechanism likely involves disrupted excitatory neurotransmission due to altered AMPA receptor function.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated in a variety of normal neurophysiologic processes. This gene product belongs to a family of glutamate receptors that are sensitive to alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA), and function as ligand-activated cation channels. These channels are assembled from 4 related subunits, GRIA1-4. The subunit encoded by this gene (GRIA2) is subject to RNA editing (CAG->CGG; Q->R) within the second transmembrane domain, which is thought to render the channel impermeable to Ca(2+). Human and animal studies suggest that pre-mRNA editing is essential for brain function, and defective GRIA2 RNA editing at the Q/R site may be relevant to amyotrophic lateral sclerosis (ALS) etiology. Alternative splicing, resulting in transcript variants encoding different isoforms, (including the flip and flop isoforms that vary in their signal transduction properties), has been noted for this gene. [provided by RefSeq, Jul 2008]

GeneReviews OMIM ResearchGenerating clinical summary…

LOFmechanismADLOEUF 0.251 OMIM phenotype

Clinical Summary— GRIA2

🧬

Gene-Disease Validity (ClinGen)

neurodevelopmental disorder with language impairment and behavioral abnormalities · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡

Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

📋

ClinVar Variants

42 unique Pathogenic / Likely Pathogenic· 154 VUS of 242 total submissions

Explore recent and relevant literature in Research Assistant →

📖

GeneReview available — GRIA2

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.25LOEUF

pLI 0.999

Z-score 5.33

OE 0.12 (0.06–0.25)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

4.56Z-score

OE missense 0.41 (0.37–0.47)

197 obs / 477.1 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.12 (0.06–0.25)

0≤0.351.4

Missense OE?0.41 (0.37–0.47)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 5 / 42.5Missense obs/exp: 197 / 477.1Syn Z: 0.57

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

strongGRIA2-related developmental disorderLOFAD

This gene — mechanism propensity

0.5378th %ile

GOF

0.6735th %ile

LOF

0.59top 25%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function, gain-of-function and dominant-negative). The Badonyi & Marsh model scores gain-of-function highest among its predictions, but genomic evidence (constraint, ClinVar variant spectrum, and literature) most strongly supports loss-of-function (haploinsufficiency). Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOF1 literature citation · 31% of P/LP variants are LoF · LOEUF 0.25

GOFprediction above median

DN1 literature citation

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Literature Evidence

DNWe assume that either haploinsufficiency of GRIA2 or a GLRB/GRIA2 fusion gene leading to a protein with dominant-negative properties is causing the phenotype of the patient.1

LOFWe assume that either haploinsufficiency of GRIA2 or a GLRB/GRIA2 fusion gene leading to a protein with dominant-negative properties is causing the phenotype of the patient.1

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

References

1.PMID 22669415 ↗

ClinVar Variant Classifications

242 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic12

Likely Pathogenic30

VUS154

Likely Benign28

Benign9

Conflicting2

Pathogenic

Likely Pathogenic

154

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	7	5	0	0	12
Likely Pathogenic	6	24	0	0	30
VUS	4	141	9	0	154
Likely Benign	0	5	8	15	28
Benign	0	3	1	5	9
Conflicting	—				2
Total	17	178	18	20	235

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

33 pathogenic / likely-pathogenic (of 37) ClinVar copy-number / structural variants overlap GRIA2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →