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NC_000003.11:g.(?_49547968)_(50685477_?)del AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 17, 2021
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:
RCV001970206.4

Allele description

NC_000003.11:g.(?_49547968)_(50685477_?)del

Genes:
  • CAMKV:CaM kinase like vesicle associated [Gene - OMIM - HGNC]
  • GNAI2:G protein subunit alpha i2 [Gene - OMIM - HGNC]
  • GNAT1:G protein subunit alpha transducin 1 [Gene - OMIM - HGNC]
  • GMPPB:GDP-mannose pyrophosphorylase B [Gene - OMIM - HGNC]
  • HEMK1:HemK methyltransferase family member 1 [Gene - OMIM - HGNC]
  • MAPKAPK3:MAPK activated protein kinase 3 [Gene - OMIM - HGNC]
  • MON1A:MON1 homolog A, secretory trafficking associated [Gene - OMIM - HGNC]
  • NAA80:N-alpha-acetyltransferase 80, NatH catalytic subunit [Gene - OMIM - HGNC]
  • NPRL2:NPR2 like, GATOR1 complex subunit [Gene - OMIM - HGNC]
  • RBM5:RNA binding motif protein 5 [Gene - OMIM - HGNC]
  • RBM6:RNA binding motif protein 6 [Gene - OMIM - HGNC]
  • RASSF1:Ras association domain family member 1 [Gene - OMIM - HGNC]
  • SEMA3F-AS1:SEMA3F antisense RNA 1 [Gene - HGNC]
  • TRAIP:TRAF interacting protein [Gene - OMIM - HGNC]
  • APEH:acylaminoacyl-peptide hydrolase [Gene - OMIM - HGNC]
  • AMIGO3:adhesion molecule with Ig like domain 3 [Gene - OMIM - HGNC]
  • BSN:bassoon presynaptic cytomatrix protein [Gene - OMIM - HGNC]
  • CDHR4:cadherin related family member 4 [Gene - HGNC]
  • CACNA2D2:calcium voltage-gated channel auxiliary subunit alpha2delta 2 [Gene - OMIM - HGNC]
  • C3orf18:chromosome 3 open reading frame 18 [Gene - HGNC]
  • CYB561D2:cytochrome b561 family member D2 [Gene - OMIM - HGNC]
  • CISH:cytokine inducible SH2 containing protein [Gene - OMIM - HGNC]
  • DAG1:dystroglycan 1 [Gene - OMIM - HGNC]
  • HYAL1:hyaluronidase 1 [Gene - OMIM - HGNC]
  • HYAL2:hyaluronidase 2 [Gene - OMIM - HGNC]
  • HYAL3:hyaluronidase 3 [Gene - OMIM - HGNC]
  • INKA1:inka box actin regulator 1 [Gene - OMIM - HGNC]
  • IP6K1:inositol hexakisphosphate kinase 1 [Gene - OMIM - HGNC]
  • IFRD2:interferon related developmental regulator 2 [Gene - OMIM - HGNC]
  • LSMEM2:leucine rich single-pass membrane protein 2 [Gene - HGNC]
  • MST1R:macrophage stimulating 1 receptor [Gene - OMIM - HGNC]
  • MST1:macrophage stimulating 1 [Gene - OMIM - HGNC]
  • RNF123:ring finger protein 123 [Gene - OMIM - HGNC]
  • SEMA3B:semaphorin 3B [Gene - OMIM - HGNC]
  • SEMA3F:semaphorin 3F [Gene - OMIM - HGNC]
  • SLC38A3:solute carrier family 38 member 3 [Gene - OMIM - HGNC]
  • TMEM115:transmembrane protein 115 [Gene - OMIM - HGNC]
  • TUSC2:tumor suppressor 2, mitochondrial calcium regulator [Gene - OMIM - HGNC]
  • UBA7:ubiquitin like modifier activating enzyme 7 [Gene - OMIM - HGNC]
  • ZMYND10:zinc finger MYND-type containing 10 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3p21.31-21.2
Genomic location:
Chr3: 49547968 - 50685477 (on Assembly GRCh37)
Preferred name:
NC_000003.11:g.(?_49547968)_(50685477_?)del
HGVS:
NC_000003.11:g.(?_49547968)_(50685477_?)del

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002243085Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 17, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002243085.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the CACNA2D2 gene has been identified. Loss-of-function variants in CACNA2D2 are known to be pathogenic (PMID: 24358150). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. 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.

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

Last Updated: Nov 11, 2023