NM_001323289.2(CDKL5):c.108_110del (p.His36_Glu37delinsGln) AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 20, 2021
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:: RCV001975877.4

Allele description [Variation Report for NM_001323289.2(CDKL5):c.108_110del (p.His36_Glu37delinsGln)]

NM_001323289.2(CDKL5):c.108_110del (p.His36_Glu37delinsGln)

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.108_110del (p.His36_Glu37delinsGln)

HGVS:

NC_000023.11:g.18564485_18564487del
NG_008475.1:g.143881_143883del
NM_001037343.2:c.108_110del
NM_001323289.2:c.108_110delMANE SELECT
NM_003159.3:c.108_110del
NP_001032420.1:p.His36_Glu37delinsGln
NP_001310218.1:p.His36_Glu37delinsGln
NP_003150.1:p.His36_Glu37delinsGln
NC_000023.10:g.18582604_18582606del
NC_000023.10:g.18582605_18582607del

Links:

dbSNP: rs2147132235

NCBI 1000 Genomes Browser:

rs2147132235

Molecular consequence:

NM_001037343.2:c.108_110del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001323289.2:c.108_110del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_003159.3:c.108_110del - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

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

Name:: Angelman syndrome-like
Identifiers:: MedGen: CN128785

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PREDICTED: Homo sapiens bridging integrator 3 (BIN3), transcript variant X2, mRN...
PREDICTED: Homo sapiens bridging integrator 3 (BIN3), transcript variant X2, mRNA
gi|2462620231|ref|XM_054360844.1|

Nucleotide
bridging integrator 3 isoform X1 [Homo sapiens]
bridging integrator 3 isoform X1 [Homo sapiens]
gi|2217372575|ref|XP_047277951.1|

Protein
Human mRNA 3'-fragment for glycogen phosphorylase (aa 673-840)
Human mRNA 3'-fragment for glycogen phosphorylase (aa 673-840)
gi|35457|emb|X03031.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002255359	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Oct 20, 2021)	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

SCV002255359

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Oct 20, 2021)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002255359.3

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

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant has been observed in individual(s) with clinical features of CDKL5-related conditions (Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (ExAC no frequency). This variant, c.108_110del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the CDKL5 protein (p.His36_Glu37delinsGln).

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

Last Updated: Sep 29, 2024

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