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NM_001134407.3(GRIN2A):c.1007+1G>A AND Landau-Kleffner syndrome

Germline classification:
Pathogenic/Likely pathogenic (6 submissions)
Last evaluated:
Jan 26, 2025
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000074386.45

Allele description [Variation Report for NM_001134407.3(GRIN2A):c.1007+1G>A]

NM_001134407.3(GRIN2A):c.1007+1G>A

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.1007+1G>A
HGVS:
  • NC_000016.10:g.9937958C>T
  • NG_011812.2:g.249797G>A
  • NM_000833.5:c.1007+1G>A
  • NM_001134407.3:c.1007+1G>AMANE SELECT
  • NM_001134408.2:c.1007+1G>A
  • NC_000016.9:g.10031815C>T
  • NM_000833.3:c.1007+1G>A
  • NM_000833.4:c.1007+1G>A
  • NM_000833.5:c.1007+1G>A
  • NM_001134407.2:c.1007+1G>A
Nucleotide change:
IVS4DS, G-A, +1
Links:
OMIM: 138253.0005; dbSNP: rs397518465
NCBI 1000 Genomes Browser:
rs397518465
Molecular consequence:
  • NM_000833.5:c.1007+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001134407.3:c.1007+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001134408.2:c.1007+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Landau-Kleffner syndrome (FESD)
Synonyms:
EPILEPSY, FOCAL, WITH SPEECH DISORDER AND WITH OR WITHOUT MENTAL RETARDATION; Acquired aphasia with convulsive disorder; Acquired epileptiform aphasia; 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
SCV000105996OMIM
no assertion criteria provided
Pathogenic
(Sep 1, 2013)
germlineliterature only

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

SCV000320740GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000761171Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 26, 2025)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV002026172Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 1, 2019)
unknownresearch

PubMed (2)
[See all records that cite these PMIDs]

SCV002767349Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 6, 2021)
germlineclinical testing

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

SCV005418560Juno Genomics, Hangzhou Juno Genomics, Inc
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing, literature only
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedresearch

Citations

PubMed

Autosomal dominant rolandic epilepsy and speech dyspraxia: a new syndrome with anticipation.

Scheffer IE, Jones L, Pozzebon M, Howell RA, Saling MM, Berkovic SF.

Ann Neurol. 1995 Oct;38(4):633-42.

PubMed [citation]
PMID:
7574460

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (10)

Details of each submission

From OMIM, SCV000105996.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In affected members of a family with autosomal dominant rolandic epilepsy, mental retardation, and speech dyspraxia (FESD; 245570), originally reported by Scheffer et al. (1995), Carvill et al. (2013) identified a heterozygous G-to-A transition in intron 4 of the GRIN2A gene (c.1007+1G-A), predicted to result in the skipping of exon 4 and premature termination (Phe139IlefsTer15). The mutation was not found in 6,500 control exomes. The same heterozygous mutation was also found in a father and son with epileptic encephalopathy with continuous spike and wave in slow-wave sleep. Analysis of patient cells showed that the mutant transcript underwent nonsense-mediate mRNA decay. Both of the families were of European descent, and haplotype analysis indicated a founder effect. The findings suggested that GRIN2A mutations can cause a spectrum of epilepsy-aphasia phenotypes.

Lemke et al. (2013) identified a heterozygous c.1007+1G-A in 7 affected individuals from 3 unrelated families and in a singleton individual, all with variable manifestations of epilepsy, including Landau-Kleffner syndrome, continuous spike and waves during slow-wave sleep, atypical benign partial epilepsy, and benign epilepsy with centrotemporal spikes. Lemke et al. (2013) suggested that additional modifying factors might explain the phenotypic variability.

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

From GeneReviews, SCV000320740.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000761171.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change affects a donor splice site in intron 4 of the GRIN2A gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and 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). Disruption of this splice site has been observed in individuals with Landau-Kleffner syndrome, atypical benign partial epilepsy, benign epilepsy with centrotemporal spikes, and focal epilepsy (PMID: 23933818, 23933819, 28102150). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 88727). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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

From Institute of Human Genetics, University of Leipzig Medical Center, SCV002026172.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767349.1

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

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function, dominant negative and gain of function are known mechanisms of disease in this gene and are associated with focal epilepsy with speech disorder and with or without mental retardation (MIM#245570). Haploinsufficiency of GRIN2A is known to result in disease, and some variants have also been shown to act antagonistically to the wild type allele when two homologous subunits are incorporated into the same protein complex. Furthermore, the overall effect of these variants on complex activity results in a gain of function of the NMDA receptor (OMIM). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. Some carriers of familial variants are unaffected (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity. Disease presentation and severity is known to vary, even amongst family members carrying the same variant (OMIM). (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0704 - Another canonical splice site variant comparable to the one identified in this case has limited previous evidence for pathogenicity. An alternate change to thymine at the same nucleotide has previously been reported in individuals with epilepsy (ClinVar, PMID: 23933819). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has previously been reported in more the five unrelated individuals with variable phenotypes on the epilepsy-aphasia spectrum (ClinVar, PMID: 23933819, PMID: 29124671). (SP) 0901 - This variant has strong evidence for segregation with disease. The variant has previously been shown to segregate with disease in at least two families (PMID: 23933819). (SP) 1206 - This variant has been shown to be paternally inherited. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

From Juno Genomics, Hangzhou Juno Genomics, Inc, SCV005418560.1

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

Description

PM2_Supporting+PVS1+PS4_Moderate+PS2_Supporting

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

Last Updated: Apr 20, 2025