GRIK2

Chr 6ARAD

glutamate ionotropic receptor kainate type subunit 2

Also known as: EAA4, GLR6, GLUK6, GLUR6, GluK2, MRT6, NEDLAS

This protein functions as an ionotropic glutamate receptor that forms cation-permeable channels gated by L-glutamate and kainic acid, serving as an excitatory neurotransmitter receptor in the central nervous system. Mutations cause intellectual developmental disorder and neurodevelopmental disorder with impaired language and ataxia with or without seizures, inherited in autosomal recessive or autosomal dominant patterns. The gene is highly constrained against loss-of-function variants, indicating intolerance to protein-disrupting mutations.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismAR/ADLOEUF 0.262 OMIM phenotypes
Clinical SummaryGRIK2
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Gene-Disease Validity (ClinGen)
complex neurodevelopmental disorder · ARModerate

Moderate evidence — consider for supplementary testing

2 total gene-disease associations curated

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.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.26LOEUF
pLI 0.998
Z-score 5.41
OE 0.13 (0.070.26)
Highly constrained

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

Missense Constraint
2.91Z-score
OE missense 0.64 (0.580.70)
319 obs / 502.3 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.13 (0.070.26)
00.351.4
Missense OE0.64 (0.580.70)
00.61.4
Synonymous OE1.05
01.21.6
LoF obs/exp: 6 / 45.2Missense obs/exp: 319 / 502.3Syn Z: -0.50
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveGRIK2-related intellectual developmental disorderLOFAR
strongGRIK2-related intellectual disability and hypomyelinationOTHERAD
DN
0.5771th %ile
GOF
0.7030th %ile
LOF
0.53top 25%

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and loss-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median · 1 literature citation
LOFLOEUF 0.26

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

GOFA gain-of-function mutation in the GRIK2 gene causes neurodevelopmental deficits.PMID:28180184

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

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

GRIK2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
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