NM_001323289.2(CDKL5):c.1675C>T (p.Arg559Ter) AND Early infantile epileptic encephalopathy 2

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Oct 14, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000145521.6

Allele description [Variation Report for NM_001323289.2(CDKL5):c.1675C>T (p.Arg559Ter)]

NM_001323289.2(CDKL5):c.1675C>T (p.Arg559Ter)

Gene:
CDKL5:cyclin dependent kinase like 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.13
Genomic location:
Preferred name:
NM_001323289.2(CDKL5):c.1675C>T (p.Arg559Ter)
Other names:
p.R559*:CGA>TGA
HGVS:
  • NC_000023.11:g.18604599C>T
  • NG_008475.1:g.183995C>T
  • NM_001037343.1:c.1675C>T
  • NM_001037343.2:c.1675C>T
  • NM_001323289.2:c.1675C>TMANE SELECT
  • NM_003159.2:c.1675C>T
  • NM_003159.3:c.1675C>T
  • NP_001032420.1:p.Arg559Ter
  • NP_001032420.1:p.Arg559Ter
  • NP_001310218.1:p.Arg559Ter
  • NP_003150.1:p.Arg559Ter
  • NP_003150.1:p.Arg559Ter
  • NC_000023.10:g.18622719C>T
Protein change:
R559*
Links:
RettBASE (CDKL5): 86; dbSNP: rs267608395
NCBI 1000 Genomes Browser:
rs267608395
Molecular consequence:
  • NM_001037343.1:c.1675C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001037343.2:c.1675C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001323289.2:c.1675C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_003159.2:c.1675C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_003159.3:c.1675C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Early infantile epileptic encephalopathy 2 (DEE2)
Synonyms:
INFANTILE SPASM SYNDROME, X-LINKED 2
Identifiers:
MONDO: MONDO:0010396; MedGen: C4750718; Orphanet: 1934; Orphanet: 3451; OMIM: 300672

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000192609Genetic Services Laboratory,University of Chicagocriteria provided, single submitter
Pathogenic
(Feb 8, 2013)
germlineclinical testing

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

SCV000222316RettBASEno assertion criteria providedPathogenic
(Mar 13, 2014)
unknowncuration

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

SCV000611255Fulgent Genetics,Fulgent Geneticscriteria provided, single submitter
Pathogenic
(May 18, 2017)
unknownclinical testing

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

SCV001164147Génétique des Maladies du Développement, Hospices Civils de Lyoncriteria provided, single submitter
Pathogenic
(Jul 11, 2017)
somaticclinical testing

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

SCV001428707Institute of Human Genetics, University of Leipzig Medical Centercriteria provided, single submitter
Likely pathogenic
(Oct 14, 2019)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedsomaticyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownyes1not providednot provided1not providedcuration
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]
PMID:
18414213

CDKL5 alterations lead to early epileptic encephalopathy in both genders.

Liang JS, Shimojima K, Takayama R, Natsume J, Shichiji M, Hirasawa K, Imai K, Okanishi T, Mizuno S, Okumura A, Sugawara M, Ito T, Ikeda H, Takahashi Y, Oguni H, Imai K, Osawa M, Yamamoto T.

Epilepsia. 2011 Oct;52(10):1835-42. doi: 10.1111/j.1528-1167.2011.03174.x. Epub 2011 Jul 19.

PubMed [citation]
PMID:
21770923
See all PubMed Citations (4)

Details of each submission

From Genetic Services Laboratory,University of Chicago, SCV000192609.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From RettBASE, SCV000222316.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedcuration PubMed (1)

Description

"Not Rett syndrome - epileptic encephalopathy"
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided

From Fulgent Genetics,Fulgent Genetics, SCV000611255.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Génétique des Maladies du Développement, Hospices Civils de Lyon, SCV001164147.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1somaticyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001428707.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

This variant was identified as hemizygous

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 20, 2021

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