NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del) AND Early infantile epileptic encephalopathy 18

Clinical significance:Uncertain significance (Last evaluated: Dec 3, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001004920.2

Allele description [Variation Report for NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)]

NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)

Gene:
SZT2:SZT2 subunit of KICSTOR complex [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p34.2
Genomic location:
Preferred name:
NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)
HGVS:
  • NC_000001.11:g.43437256_43437258del
  • NG_029091.1:g.52372_52374del
  • NM_001365999.1:c.6120_6122delMANE SELECT
  • NM_015284.4:c.5949_5951del
  • NP_001352928.1:p.Val2041del
  • NP_056099.3:p.Val1984del
  • NC_000001.10:g.43902925_43902927del
  • NC_000001.10:g.43902927_43902929del
  • NM_015284.3:c.5949_5951del
  • NM_015284.3:c.5949_5951delTGT
  • p.Val1984del
Protein change:
V1984del
Links:
dbSNP: rs746200792
NCBI 1000 Genomes Browser:
rs746200792
Molecular consequence:
  • NM_001365999.1:c.6120_6122del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_015284.4:c.5949_5951del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Early infantile epileptic encephalopathy 18 (DEE18)
Synonyms:
DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 18
Identifiers:
MONDO: MONDO:0014201; MedGen: C3809624; Orphanet: 369894; OMIM: 615476

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001164430Broad Institute Rare Disease Group, Broad Institutecriteria provided, single submitter
Uncertain significance
(Dec 3, 2018)
germlineresearch

PubMed (1)
[See all records that cite this PMID]

SCV001423312GenomeConnect, ClinGenno assertion providednot providedpaternal, unknownphenotyping only

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch
not providedunknownunknown1not providednot provided1not providedphenotyping only
not providedpaternalyes1not providednot provided1not providedphenotyping only

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Broad Institute Rare Disease Group, Broad Institute, SCV001164430.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)

Description

The heterozygous p.Val1984del variant was identifed by our study in the compound heterozygous state, with another VUS, in one individual with early infantile epileptic encephalopathy. This variant has been identified in 0.08865% (9/10152) of Ashkenazi Jewish chromosomes chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs756197807). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant is predicted to change the protein length with the in-frame deletion of Valine (Val) at position 1984. In summary, the clinical significance of the p.Val1984del variant is uncertain. ACMG/AMP Criteria applied: PM2, PM4, PP3 (Richards 2015).

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

From GenomeConnect, ClinGen, SCV001423312.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedphenotyping onlynot provided
2not provided1not providednot providedphenotyping onlynot provided

Description

Variant interpretted as Likely pathogenic and reported on 06-02-2016 by Lab or GTR ID 506013. Variant also interpretted as Likley pathogenic and reported on 08-22-2019 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyes1not providedvalidation1not providednot providednot provided
2unknownunknown1not providednot provided1not providednot providednot provided

Last Updated: Apr 12, 2021

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