NM_001134407.3(GRIN2A):c.2077A>G (p.Asn693Asp) AND Landau-Kleffner syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 16, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001290247.1

Allele description

NM_001134407.3(GRIN2A):c.2077A>G (p.Asn693Asp)

Gene:

GRIN2A:glutamate ionotropic receptor NMDA type subunit 2A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.2

Genomic location:

Preferred name:

NM_001134407.3(GRIN2A):c.2077A>G (p.Asn693Asp)

HGVS:

NC_000016.10:g.9822355T>C
NG_011812.2:g.365400A>G
NM_000833.5:c.2077A>G
NM_001134407.3:c.2077A>GMANE SELECT
NM_001134408.2:c.2077A>G
NP_000824.1:p.Asn693Asp
NP_001127879.1:p.Asn693Asp
NP_001127880.1:p.Asn693Asp
NC_000016.9:g.9916212T>C
NG_011812.1:g.365400A>G
NM_000833.4:c.2077A>G

Protein change:

N693D

Links:

dbSNP: rs2042303226

NCBI 1000 Genomes Browser:

rs2042303226

Molecular consequence:

NM_000833.5:c.2077A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001134407.3:c.2077A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001134408.2:c.2077A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Landau-Kleffner syndrome (FESD)
Synonyms:: Acquired aphasia with convulsive disorder; Acquired epileptiform aphasia; APHASIA, ACQUIRED, WITH EPILEPSY; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009509; MedGen: C0282512; Orphanet: 1945; Orphanet: 725; Orphanet: 98818; OMIM: 245570

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001477290	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 16, 2020)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001477290

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 16, 2020)

de novo

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001477290.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		not provided	not provided	not provided	clinical testing	PubMed (1)

Description

We identified the variant c.2077A>G, p.Asn693Asp in the gene GRIN2A in heterozygous state. The variant could not be detected in DNA from leukocytes of the patientâ€™s parents, so we assume that it originated de novo. It is not yet described in the databases for disease-causing changes (HGMD, ClinVar, DECIPHER) and in the literature and is located in a mutational hot spot. The variant allele was not identified in control chromosomes (gnomAD). The in silico tools we use mostly assess the change as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic according to the ACMG classification system (Richards et al., 2015, PMID: 25741868). PS2_Moderate, PM1, PM2, PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 5, 2023

ClinVar

Relating variation to medicine