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NM_003718.5(CDK13):c.181del (p.Leu61fs) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 16, 2023
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:
RCV000623626.4

Allele description [Variation Report for NM_003718.5(CDK13):c.181del (p.Leu61fs)]

NM_003718.5(CDK13):c.181del (p.Leu61fs)

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.181del (p.Leu61fs)
HGVS:
  • NC_000007.14:g.39950822del
  • NG_052965.1:g.5463del
  • NM_003718.5:c.181delMANE SELECT
  • NM_031267.3:c.181del
  • NP_003709.3:p.Leu61fs
  • NP_112557.2:p.Leu61fs
  • NC_000007.13:g.39990421del
  • NM_003718.4:c.180delC
  • NM_003718.4:c.181delC
  • p.Leu61TrpfsTer80
Protein change:
L61fs
Links:
dbSNP: rs1554317002
NCBI 1000 Genomes Browser:
rs1554317002
Molecular consequence:
  • NM_003718.5:c.181del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_031267.3:c.181del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000741641Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Aug 16, 2023) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Diagnostic utility of transcriptome sequencing for rare Mendelian diseases.

Lee H, Huang AY, Wang LK, Yoon AJ, Renteria G, Eskin A, Signer RH, Dorrani N, Nieves-Rodriguez S, Wan J, Douine ED, Woods JD, Dell'Angelica EC, Fogel BL, Martin MG, Butte MJ, Parker NH, Wang RT, Shieh PB, Wong DA, Gallant N, Singh KE, et al.

Genet Med. 2020 Mar;22(3):490-499. doi: 10.1038/s41436-019-0672-1. Epub 2019 Oct 14.

PubMed [citation]
PMID:
31607746
PMCID:
PMC7405636

Details of each submission

From Ambry Genetics, SCV000741641.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.181delC (p.L61Wfs*80) alteration, located in exon 1 (coding exon 1) of the CDK13 gene, consists of a deletion of one nucleotide at position 181, causing a translational frameshift with a predicted alternate stop codon after 80 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been determined to be the result of a de novo mutation in one individual with features consistent with CDK13-related neurodevelopmental disorder (Lee, 2020). Based on the available evidence, this alteration is classified as pathogenic.

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

Last Updated: May 1, 2024