NM_001323289.2(CDKL5):c.1675C>T (p.Arg559Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Aug 4, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000133328.5

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]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000191066GeneDxcriteria provided, single submitter
Pathogenic
(Aug 4, 2020)
germlineclinical testing

Citation Link,

SCV000778216Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantesno assertion criteria providedPathogenic
(Sep 26, 2016)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000191066.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 27823948, 22670135, 22779007, 23064044, 25525159, 19161156, 27770071, 28837158, 27081548, 23583054, 30928302, 30460546, 31313283, 22872100, 21770923)

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

From Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes, SCV000778216.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 20, 2021

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