NM_001323289.2(CDKL5):c.155_156del (p.Glu52fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 2, 2019
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:: RCV001822814.4

Allele description [Variation Report for NM_001323289.2(CDKL5):c.155_156del (p.Glu52fs)]

NM_001323289.2(CDKL5):c.155_156del (p.Glu52fs)

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.155_156del (p.Glu52fs)

HGVS:

NC_000023.11:g.18575363_18575364del
NG_008475.1:g.154759_154760del
NM_001037343.2:c.155_156del
NM_001323289.2:c.155_156delMANE SELECT
NM_003159.3:c.155_156del
NP_001032420.1:p.Glu52fs
NP_001310218.1:p.Glu52fs
NP_003150.1:p.Glu52fs
NC_000023.10:g.18593483_18593484del
NM_003159.2:c.155_156del

Protein change:

E52fs

Links:

dbSNP: rs2147139532

NCBI 1000 Genomes Browser:

rs2147139532

Molecular consequence:

NM_001037343.2:c.155_156del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001323289.2:c.155_156del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003159.3:c.155_156del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002072024	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 2, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002072024

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 2, 2019)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

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 Genetic Services Laboratory, University of Chicago, SCV002072024.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

DNA sequence analysis of the CDKL5 gene demonstrated a two base pair deletion in exon 5, c.155_156del. This pathogenic sequence change results in an amino acid frameshift and creates a premature stop codon nine amino acids downstream of the mutation, p.Glu52Glyfs*10. This pathogenic sequence change is present in ~13% of Next Generation Sequencing reads, and Sanger sequencing supports the mosaic nature of this sequence change. This sequence change is absent from large population databases such as ExAC and gnomAD. This pathogenic sequence change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated CDKL5 protein with potentially abnormal function.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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