NM_003718.5(CDK13):c.1152del (p.Ser385fs) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 20, 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:: RCV000599056.1

Allele description [Variation Report for NM_003718.5(CDK13):c.1152del (p.Ser385fs)]

NM_003718.5(CDK13):c.1152del (p.Ser385fs)

Gene:

CDK13:cyclin dependent kinase 13 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7p14.1

Genomic location:

Preferred name:

NM_003718.5(CDK13):c.1152del (p.Ser385fs)

HGVS:

NC_000007.14:g.39951793del
NG_052965.1:g.6434del
NM_003718.5:c.1152delMANE SELECT
NM_031267.3:c.1152del
NP_003709.3:p.Ser385fs
NP_112557.2:p.Ser385fs
NC_000007.13:g.39991392del
NM_003718.4:c.1152delT

Protein change:

S385fs

Links:

dbSNP: rs1554317470

NCBI 1000 Genomes Browser:

rs1554317470

Molecular consequence:

NM_003718.5:c.1152del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_031267.3:c.1152del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Chain p, tube
Chain p, tube
gi|1938941864|pdb|3J9Q|p

Protein
LOC6547312 [Drosophila erecta]
LOC6547312 [Drosophila erecta]
Gene ID:6547312

Gene
BioAssay by Target (List) for Gene (Select 23157) (13)
PubChem BioAssay
Zhonghua 6 (R)
Zhonghua 6 (R)

biosample
SAMN03952832 (1)
BioSample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000710297	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Dec 20, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000710297

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Dec 20, 2017)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000710297.2

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

Description

The c.1152delTvariant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1152delT variant is not observed in large population cohorts (Lek et al., 2016). The c.1152delT variant causes a frameshift starting with codon Serine 385, changes this amino acid to a Valine residue, and creates a premature Stop codon at position 59 of the new reading frame, denoted p.Ser385ValfsX59. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. However, CDK13 is a gene for which loss-of-function is not a known mechanism of disease. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#	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: Apr 23, 2022

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