VCV000833358.3 - ClinVar

NC_000002.12:g.(?_165112865)_(166311776_?)dup

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.

Uncertain significance

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000002.12:g.(?_165112865)_(166311776_?)dup

Variation ID: 833358 Accession: VCV000833358.3

Type and length

Duplication, 1,198,912 bp

Location

Cytogenetic: 2q24.3 2: 165969375-167168286 (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	Apr 15, 2020	Mar 22, 2021	Sep 27, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NC_000002.11:g.(?_165969375)_(167168286_?)dup

Protein change

Other names

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

VarSome

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.
SCN1A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2231	4609
SCN2A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2587	2662
CSRNP3		-	-	GRCh38 GRCh37	36	100
GALNT3		-	-	GRCh38 GRCh37	433	496
SCN3A		-	-	GRCh38 GRCh37	1692	1746
SCN9A		-	-	GRCh38 GRCh37	448	2664
TTC21B		-	-	GRCh38 GRCh37	1123	1326

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.
not provided	Uncertain significance (1)	criteria provided, single submitter	Sep 27, 2019	RCV001346192.3
Early infantile epileptic encephalopathy with suppression bursts	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV001033802.5

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.
Uncertain significance (Sep 27, 2019)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001540368.1 First in ClinVar: Mar 22, 2021 Last updated: Mar 22, 2021	Publications: PubMed (2) PubMed: 23016767‚ 21416599 Comment: This variant results in a copy number gain of the genomic region encompassing exons 1-21 of the SCN3A gene, which includes the initiator codon. The … (more) This variant results in a copy number gain of the genomic region encompassing exons 1-21 of the SCN3A gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 21 of the SCN3A gene. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. Isolated whole-gene copy number gains of SCN3A have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 23016767,21416599). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
Uncertain significance (Oct 03, 2019)	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV001197109 appears to (...more) Source: NCBI	Early infantile epileptic encephalopathy with suppression bursts Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001197109.1 First in ClinVar: Apr 15, 2020 Last updated: Apr 15, 2020	Publications: PubMed (5) PubMed: 23016767‚ 21416599‚ 23184456‚ 21692795‚ 26068938 Comment: This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the SCN1A gene. The boundaries of this … (more) This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the SCN1A gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. Isolated whole-gene duplications of the SCN1A gene have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 23016767, 26068938, 21416599, 23184456, 21692795). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more

Comment:

This variant results in a copy number gain of the genomic region encompassing exons 1-21 of the SCN3A gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 21 of the SCN3A gene. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. Isolated whole-gene copy number gains of SCN3A have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 23016767,21416599). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Comment:

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the SCN1A gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. Isolated whole-gene duplications of the SCN1A gene have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 23016767, 26068938, 21416599, 23184456, 21692795). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy.	Epilepsy Phenome/Genome Project Epi4K Consortium	Annals of neurology	2015	PMID: 26068938
Epilepsy with cognitive deficit and autism spectrum disorders: prospective diagnosis by array CGH.	Nicholl J	American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics	2013	PMID: 23184456
Duplication of the sodium channel gene cluster on 2q24 in children with early onset epilepsy.	Goeggel Simonetti B	Epilepsia	2012	PMID: 23016767
Refractory neonatal epilepsy with a de novo duplication of chromosome 2q24.2q24.3.	Okumura A	Epilepsia	2011	PMID: 21692795
An interstitial duplication at 2q24.3 involving the SCN1A, SCN2A, SCN3A genes associated with infantile epilepsy.	Raymond G	American journal of medical genetics. Part A	2011	PMID: 21416599

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NC_000002.12:g.(?_165112865)_(166311776_?)dup

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...