VCV000208479.2 - ClinVar

NC_000010.11:g.(93704377_?)_(?_93785620)del

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000010.11:g.(93704377_?)_(?_93785620)del

Variation ID: 208479 Accession: VCV000208479.2

Type and length

Deletion, 81,244 bp

Location

Cytogenetic: 10q23.33 10: 93704377-93785620 (GRCh38) [ NCBI UCSC ] 10: 95464133-95545376 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 5, 2015	Oct 3, 2016	Aug 27, 2015

HGVS

Nucleotide	Protein	Molecular consequence
NC_000010.11:g.(93704377_?)_(?_93785620)del
NC_000010.10:g.(95464133_?)_(?_95545376)del

Protein change

Other names

81-KB DEL

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

OMIM: 604619.0012 VarSome

Comment on variant

Approximately 81kb genomic deletion beginning 3'-of the LGI1 gene and spanning the first four exons, ending in intron 4.

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
LGI1		-	-	GRCh38 GRCh37	483	507

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Epilepsy, familial temporal lobe, 1	Pathogenic (2)	no assertion criteria provided	Aug 27, 2015	RCV000194261.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Aug 27, 2015)	no assertion criteria provided Method: literature only	Epilepsy, lateral temporal lobe, autosomal dominant Affected status: yes Allele origin: germline	GeneReviews Accession: SCV000245374.1 First in ClinVar: Oct 05, 2015 Last updated: Oct 05, 2015 Comment: Deletes exons 1-4 and maps between rs11187602 and rs7099034 [Fanciulli et al 2012 (PMID:22496201)]	Publications: PubMed (1) PubMed: 22496201 Other databases http://www.ncbi.nlm.nih.gov/book… http://www.ncbi.nlm.nih.gov/books/NBK1537/
Pathogenic (Apr 24, 2012)	no assertion criteria provided Method: literature only	EPILEPSY, LATERAL TEMPORAL LOBE, AUTOSOMAL DOMINANT Affected status: not provided Allele origin: germline	OMIM Accession: SCV000057085.2 First in ClinVar: Apr 04, 2013 Last updated: Oct 03, 2016	Publications: PubMed (1) PubMed: 22496201 Comment on evidence: In affected members of a 3-generation Italian family with ADLTE (600512), Fanciulli et al. (2012) identified a heterozygous 81-kb deletion encompassing part of the upstream … (more) In affected members of a 3-generation Italian family with ADLTE (600512), Fanciulli et al. (2012) identified a heterozygous 81-kb deletion encompassing part of the upstream region and the first 4 exons of the LGI1 gene, predicted to result in a loss of function. The deletion was found by CNV analysis after exon sequencing of the gene failed to identify a point mutation. The deletion was not found in several large databases. There were 8 affected individuals. Most patients had onset of seizures in the second decade, although 2 had onset as adults. Six had tonic-clonic seizures with focal onset, and most experienced accompanying auditory features. Brain imaging was unremarkable in all patients who were studied, and EEG showed mild abnormalities only in 3 patients. Patients showed a good response to antiepileptic medication. Two unaffected family members, aged 24 and 17 years, also carried the deletion, consistent with later onset of the disorder or incomplete penetrance. (less)

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Autosomal Dominant Epilepsy with Auditory Features.	Adam MP	-	2024	PMID: 20301709
LGI1 microdeletion in autosomal dominant lateral temporal epilepsy.	Fanciulli M	Neurology	2012	PMID: 22496201

Text-mined citations for this variant ...

Record last updated Sep 24, 2022

ClinVar Genomic variation as it relates to human health

NC_000010.11:g.(93704377_?)_(?_93785620)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...