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NM_001134407.3(GRIN2A):c.806del (p.Pro269fs) AND Landau-Kleffner syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 6, 2023
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:
RCV003582243.2

Allele description [Variation Report for NM_001134407.3(GRIN2A):c.806del (p.Pro269fs)]

NM_001134407.3(GRIN2A):c.806del (p.Pro269fs)

Gene:
GRIN2A:glutamate ionotropic receptor NMDA type subunit 2A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16p13.2
Genomic location:
Preferred name:
NM_001134407.3(GRIN2A):c.806del (p.Pro269fs)
HGVS:
  • NC_000016.10:g.9938162del
  • NG_011812.2:g.249595del
  • NM_000833.5:c.806del
  • NM_001134407.3:c.806delMANE SELECT
  • NM_001134408.2:c.806del
  • NP_000824.1:p.Pro269fs
  • NP_001127879.1:p.Pro269fs
  • NP_001127880.1:p.Pro269fs
  • NC_000016.9:g.10032017del
  • NC_000016.9:g.10032019del
Protein change:
P269fs
Molecular consequence:
  • NM_000833.5:c.806del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001134407.3:c.806del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001134408.2:c.806del - frameshift variant - [Sequence Ontology: SO:0001589]

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004254657Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Dec 6, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in GRIN2A cause idiopathic focal epilepsy with rolandic spikes.

Lemke JR, Lal D, Reinthaler EM, Steiner I, Nothnagel M, Alber M, Geider K, Laube B, Schwake M, Finsterwalder K, Franke A, Schilhabel M, Jähn JA, Muhle H, Boor R, Van Paesschen W, Caraballo R, Fejerman N, Weckhuysen S, De Jonghe P, Larsen J, Møller RS, et al.

Nat Genet. 2013 Sep;45(9):1067-72. doi: 10.1038/ng.2728. Epub 2013 Aug 11.

PubMed [citation]
PMID:
23933819

GRIN2A mutations in acquired epileptic aphasia and related childhood focal epilepsies and encephalopathies with speech and language dysfunction.

Lesca G, Rudolf G, Bruneau N, Lozovaya N, Labalme A, Boutry-Kryza N, Salmi M, Tsintsadze T, Addis L, Motte J, Wright S, Tsintsadze V, Michel A, Doummar D, Lascelles K, Strug L, Waters P, de Bellescize J, Vrielynck P, de Saint Martin A, Ville D, Ryvlin P, et al.

Nat Genet. 2013 Sep;45(9):1061-6. doi: 10.1038/ng.2726. Epub 2013 Aug 11.

PubMed [citation]
PMID:
23933820
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004254657.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Pro269Glnfs*24) in the GRIN2A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GRIN2A are known to be pathogenic (PMID: 23933819, 23933820). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GRIN2A-related conditions. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024