NM_003718.5:c.70G>T
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PM2
The NM_003718.5(CDK13):c.70G>T(p.Glu24*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CDK13
NM_003718.5 stop_gained
NM_003718.5 stop_gained
Scores
3
2
2
Clinical Significance
Conservation
PhyloP100: 0.876
Publications
0 publications found
Genes affected
CDK13 (HGNC:1733): (cyclin dependent kinase 13) The protein encoded by this gene is a member of the cyclin-dependent serine/threonine protein kinase family. Members of this family are well known for their essential roles as master switches in cell cycle control. The exact function of this protein has not yet been determined, but it may play a role in mRNA processing and may be involved in regulation of hematopoiesis. Alternatively spliced transcript variants have been described.[provided by RefSeq, Dec 2009]
CDK13 Gene-Disease associations (from GenCC):
- congenital heart defects, dysmorphic facial features, and intellectual developmental disorderInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Illumina
- syndromic intellectual disabilityInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 10 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 89 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CDK13 | NM_003718.5 | c.70G>T | p.Glu24* | stop_gained | Exon 1 of 14 | ENST00000181839.10 | NP_003709.3 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1301072Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 640068
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1301072
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
640068
African (AFR)
AF:
AC:
0
AN:
26084
American (AMR)
AF:
AC:
0
AN:
22398
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22002
East Asian (EAS)
AF:
AC:
0
AN:
28338
South Asian (SAS)
AF:
AC:
0
AN:
69354
European-Finnish (FIN)
AF:
AC:
0
AN:
34228
Middle Eastern (MID)
AF:
AC:
0
AN:
3856
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1040930
Other (OTH)
AF:
AC:
0
AN:
53882
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder Uncertain:1
Oct 13, 2022
Baylor Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
PhyloP100
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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