rs1554335512
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PP3_StrongPP5
The NM_003718.5(CDK13):c.2716G>A(p.Glu906Lys) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003718.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDK13 | NM_003718.5 | c.2716G>A | p.Glu906Lys | missense_variant | Exon 9 of 14 | ENST00000181839.10 | NP_003709.3 | |
CDK13 | NM_031267.3 | c.2716G>A | p.Glu906Lys | missense_variant | Exon 9 of 14 | NP_112557.2 | ||
CDK13 | XM_017012750.3 | c.2806G>A | p.Glu936Lys | missense_variant | Exon 10 of 15 | XP_016868239.1 | ||
CDK13 | XM_017012751.3 | c.2806G>A | p.Glu936Lys | missense_variant | Exon 10 of 15 | XP_016868240.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152092Hom.: 0 Cov.: 31 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461404Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 727032
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152092Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74288
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Inborn genetic diseases Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at