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Intellectual disability

Gene: GRIN2D

Green List (high evidence)
GRIN2D (glutamate ionotropic receptor NMDA type subunit 2D)
EnsemblGeneIds (GRCh38): ENSG00000105464
EnsemblGeneIds (GRCh37): ENSG00000105464
OMIM: 602717, Gene2Phenotype
GRIN2D is in 4 panels

2 reviews

Louise Daugherty (Genomics England Curator)

Comment on list classification: New gene added by external expert and reviewed by curation team, enough evidence to support gene-disease association and relevance to this panel to rate this gene Green
Created: 7 Jan 2019, 11:57 a.m.
Created: 7 Jan 2019, 11:57 a.m.

Panel version: 2.589

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Heterozygous pathogenic variants in GRIN2D cause Epileptic encephalopathy, early infantile, 46 (MIM 617162).

PMID: 27616483 is the first report on 2 unrelated individuals with severe epileptic encephalopathy (onset of seizures at the age of 2 and 4 months). Severe DD with ID was noted in both.

Each of these individuals were heterozygous for the same missense variant (NM_000836.2:c.1999G>A or p.Val667Ile) as a de novo event. Functional studies demonstrated a gain-of-function effect.

GRIN2D encodes for an NMDA receptor subunit, and the gain-of-function effect shown for this variant suggests that NMDAR antagonists might be useful as adjuvant therapy for individuals with such variants (some improvement noted in both individuals).

[The mode of pathogenicity selected here may be modified as more evidence on further variants becomes available. GRIN2D appears to be intolerant also to LoF mutations with a pLI of 1. Both LoF and GoF mutations have been described for genes encoding other NMDAR subunits].

PMID: 30280376 reports on 3 additional unrelated patients with developmental and epileptic encephalopathy and pathogenic or likely pathogenic missense variants in GRIN2D.

Three additional missense variants are reported (Met681Ile, Ser694Arg, Asp449Asn). Parental studies were possible only for the patient with Met681Ile (de novo) as well as for the individual with Ser694Arg (only one parent available though).

Significant developmental delay was evident in all prior to the onset of seizures (1m/2y/3y respectively) and subsequent developmental stagnation/regression with ID.

The phenotype of these 3 individuals as well as of the 2 previously described is summarized in table 1 of the latter article.

GRIN2D is a probable DD gene in G2P and is included in gene panels for ID offered by diagnostic laboratories.

Several other genes for NMDA receptor subunits (eg. GRIN2A, GRIN2B, GRIN1) and relevant/similar phenotypes are included in this panel as green.

As a result, this gene can be considered for inclusion in the ID panel as green (or amber).
Sources: Literature
Created: 6 Dec 2018, 2 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Epileptic encephalopathy, early infantile, 46 (MIM 617162)

Publications

Variants in this GENE are reported as part of current diagnostic practice

Created: 6 Dec 2018, 2 p.m.

Panel version: 2.576

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
Phenotypes
  • Epileptic encephalopathy, early infantile, 46, 617162
  • intellectual disability
OMIM
602717
Clinvar variants
Variants in GRIN2D
Penetrance
unknown
Publications
Panels with this gene

History Filter Activity

7 Jan 2019, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: GRIN2D were changed from Epileptic encephalopathy, early infantile, 46 (MIM 617162) to Epileptic encephalopathy, early infantile, 46, 617162; intellectual disability

7 Jan 2019, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: grin2d has been classified as Green List (High Evidence).

6 Dec 2018, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: GRIN2D was added gene: GRIN2D was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: GRIN2D was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: GRIN2D were set to 27616483; 30280376 Phenotypes for gene: GRIN2D were set to Epileptic encephalopathy, early infantile, 46 (MIM 617162) Penetrance for gene: GRIN2D were set to unknown Review for gene: GRIN2D was set to GREEN gene: GRIN2D was marked as current diagnostic