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NM_001323289.2(CDKL5):c.1546del (p.Tyr516fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 7, 2017
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:
RCV000598749.1

Allele description [Variation Report for NM_001323289.2(CDKL5):c.1546del (p.Tyr516fs)]

NM_001323289.2(CDKL5):c.1546del (p.Tyr516fs)

Gene:
CDKL5:cyclin dependent kinase like 5 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp22.13
Genomic location:
Preferred name:
NM_001323289.2(CDKL5):c.1546del (p.Tyr516fs)
HGVS:
  • NC_000023.11:g.18604470del
  • NG_008475.1:g.183866del
  • NM_001037343.2:c.1546del
  • NM_001323289.2:c.1546delMANE SELECT
  • NM_003159.3:c.1546del
  • NP_001032420.1:p.Tyr516fs
  • NP_001310218.1:p.Tyr516fs
  • NP_003150.1:p.Tyr516fs
  • NC_000023.10:g.18622590del
  • NM_003159.2:c.1546delT
Protein change:
Y516fs
Links:
dbSNP: rs1555952063
NCBI 1000 Genomes Browser:
rs1555952063
Molecular consequence:
  • NM_001037343.2:c.1546del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001323289.2:c.1546del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003159.3:c.1546del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000710130GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Dec 7, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000710130.2

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

Description

The c.1546delT pathogenic variant causes a frameshift starting with codon Tyrosine 516, changes this amino acid to a Threonine residue and creates a premature Stop codon at position 7 of the newreading frame, denoted p.Tyr516ThrfsX7. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1546delT variant is not observed in large population cohorts (Lek et al., 2016). Although this variant has not been previously reported to our knowledge, other loss-of-function variants in CDKL5 have been reported in the Human Gene Mutation Database in association with CDKL5-related disorders (Stenson et al., 2014). The presence of c.1546delT is consistent with the diagnosis of a CDKL5-related disorder in this individual.

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

Last Updated: Apr 23, 2022