chr7-39950766-C-CGCTCCTGCAGCCGCA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003718.5(CDK13):c.135_149dup(p.Gln47_Pro51dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000302 in 1,324,282 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000030 ( 0 hom. )
Consequence
CDK13
NM_003718.5 inframe_insertion
NM_003718.5 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.38
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK13 | NM_003718.5 | c.135_149dup | p.Gln47_Pro51dup | inframe_insertion | 1/14 | ENST00000181839.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK13 | ENST00000181839.10 | c.135_149dup | p.Gln47_Pro51dup | inframe_insertion | 1/14 | 1 | NM_003718.5 | P3 | |
CDK13 | ENST00000340829.10 | c.135_149dup | p.Gln47_Pro51dup | inframe_insertion | 1/14 | 1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000125 AC: 1AN: 79836Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 45656
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GnomAD4 exome AF: 0.00000302 AC: 4AN: 1324282Hom.: 0 Cov.: 33 AF XY: 0.00000306 AC XY: 2AN XY: 652974
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2023 | This variant, c.135_149dup, results in the insertion of 5 amino acid(s) of the CDK13 protein (p.Gln47_Pro51dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CDK13-related conditions. ClinVar contains an entry for this variant (Variation ID: 2576177). 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Oct 25, 2022 | PM4, PM2_SUP - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at