NC_000003.11:g.(?_50513539)_(50540854_?)del AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 16, 2022
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:: RCV001972525.5

Allele description [Variation Report for NC_000003.11:g.(?_50513539)_(50540854_?)del]

NC_000003.11:g.(?_50513539)_(50540854_?)del

Gene:: CACNA2D2:calcium voltage-gated channel auxiliary subunit alpha2delta 2 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 3p21.31
Genomic location:: Chr3: 50513539 - 50540854 (on Assembly GRCh37)
Preferred name:: NC_000003.11:g.(?_50513539)_(50540854_?)del
HGVS:: NC_000003.11:g.(?_50513539)_(50540854_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Synonyms:: Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
Identifiers:: MONDO: MONDO:0100062; MedGen: C0393706; Orphanet: 1934; OMIM: PS308350

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002245829	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 16, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24358150, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002245829

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 16, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A novel null homozygous mutation confirms CACNA2D2 as a gene mutated in epileptic encephalopathy.

Pippucci T, Parmeggiani A, Palombo F, Maresca A, Angius A, Crisponi L, Cucca F, Liguori R, Valentino ML, Seri M, Carelli V.

PLoS One. 2013;8(12):e82154. doi: 10.1371/journal.pone.0082154.

PubMed [citation]

PMID:: 24358150
PMCID:: PMC3864908

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002245829.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 1-2 of the CACNA2D2 gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CACNA2D2 are known to be pathogenic (PMID: 24358150). This variant has not been reported in the literature in individuals affected with CACNA2D2-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 11, 2023

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