NM_001323289.2(CDKL5):c.1296_1298del (p.Lys432_Tyr433delinsAsn) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 31, 2022
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:: RCV002524164.2

Allele description

NM_001323289.2(CDKL5):c.1296_1298del (p.Lys432_Tyr433delinsAsn)

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.1296_1298del (p.Lys432_Tyr433delinsAsn)

HGVS:

NC_000023.11:g.18604220_18604222del
NG_008475.1:g.183616_183618del
NM_001037343.2:c.1296_1298del
NM_001323289.2:c.1296_1298delMANE SELECT
NM_003159.3:c.1296_1298del
NP_001032420.1:p.Lys432_Tyr433delinsAsn
NP_001310218.1:p.Lys432_Tyr433delinsAsn
NP_003150.1:p.Lys432_Tyr433delinsAsn
NP_003150.1:p.Lys432_Tyr433delinsAsn
NC_000023.10:g.18622339_18622341del
NC_000023.10:g.18622340_18622342del
NC_000023.11:g.18604220_18604222delGTA
NM_003159.2(CDKL5):c.1296_1298del
NM_003159.2:c.1296_1298del
p.Lys432_Tyr433delinsAsn

Links:

dbSNP: rs1555951997

NCBI 1000 Genomes Browser:

rs1555951997

Molecular consequence:

NM_001037343.2:c.1296_1298del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001323289.2:c.1296_1298del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_003159.3:c.1296_1298del - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003208841	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 31, 2022)	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

SCV003208841

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 31, 2022)

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 Invitae, SCV003208841.2

#	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 available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 434662). This variant has not been reported in the literature in individuals affected with CDKL5-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.1296_1298del, results in the deletion of one amino acid(s) of the CDKL5 protein (p.Lys432_Tyr433delinsAsn), but otherwise preserves the integrity of the reading frame.

#	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: Aug 4, 2024

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