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NM_001271.4(CHD2):c.2882del (p.Asn961fs) AND Developmental and epileptic encephalopathy 94

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 15, 2023
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:
RCV003741930.1

Allele description

NM_001271.4(CHD2):c.2882del (p.Asn961fs)

Genes:
LOC126862230:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93523977-93525176 [Gene]
CHD2:chromodomain helicase DNA binding protein 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
15q26.1
Genomic location:
Preferred name:
NM_001271.4(CHD2):c.2882del (p.Asn961fs)
HGVS:
  • NC_000015.10:g.92980820del
  • NG_012826.2:g.85500del
  • NG_086728.1:g.174del
  • NM_001271.4:c.2882delMANE SELECT
  • NP_001262.3:p.Asn961fs
  • LRG_1425t1:c.2882del
  • LRG_1425:g.85500del
  • LRG_1425p1:p.Asn961fs
  • NC_000015.9:g.93524048del
  • NC_000015.9:g.93524050del
Protein change:
N961fs
Molecular consequence:
  • NM_001271.4:c.2882del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Developmental and epileptic encephalopathy 94 (DEE94)
Synonyms:
Epileptic encephalopathy, childhood-onset
Identifiers:
MONDO: MONDO:0014150; MedGen: C3809278; Orphanet: 1942; Orphanet: 2382; OMIM: 615369

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004422873Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 15, 2023) 		germlineclinical testing

PubMed (3)
[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

Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1.

Carvill GL, Heavin SB, Yendle SC, McMahon JM, O'Roak BJ, Cook J, Khan A, Dorschner MO, Weaver M, Calvert S, Malone S, Wallace G, Stanley T, Bye AM, Bleasel A, Howell KB, Kivity S, Mackay MT, Rodriguez-Casero V, Webster R, Korczyn A, Afawi Z, et al.

Nat Genet. 2013 Jul;45(7):825-30. doi: 10.1038/ng.2646. Epub 2013 May 26.

PubMed [citation]
PMID:
23708187
PMCID:
PMC3704157

De novo loss-of-function mutations in CHD2 cause a fever-sensitive myoclonic epileptic encephalopathy sharing features with Dravet syndrome.

Suls A, Jaehn JA, Kecskés A, Weber Y, Weckhuysen S, Craiu DC, Siekierska A, Djémié T, Afrikanova T, Gormley P, von Spiczak S, Kluger G, Iliescu CM, Talvik T, Talvik I, Meral C, Caglayan HS, Giraldez BG, Serratosa J, Lemke JR, Hoffman-Zacharska D, Szczepanik E, et al.

Am J Hum Genet. 2013 Nov 7;93(5):967-75. doi: 10.1016/j.ajhg.2013.09.017. Epub 2013 Oct 24.

PubMed [citation]
PMID:
24207121
PMCID:
PMC3824114
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004422873.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CHD2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asn961Ilefs*8) in the CHD2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CHD2 are known to be pathogenic (PMID: 23708187, 24207121).

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

Last Updated: Feb 28, 2024