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GeneBe

7-39950790-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_003718.5(CDK13):c.149A>C(p.Gln50Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CDK13
NM_003718.5 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.348
Variant links:
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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.11612034).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDK13NM_003718.5 linkuse as main transcriptc.149A>C p.Gln50Pro missense_variant 1/14 ENST00000181839.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDK13ENST00000181839.10 linkuse as main transcriptc.149A>C p.Gln50Pro missense_variant 1/141 NM_003718.5 P3Q14004-1
CDK13ENST00000340829.10 linkuse as main transcriptc.149A>C p.Gln50Pro missense_variant 1/141 A1Q14004-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxMay 08, 2023Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.093
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.56
Cadd
Uncertain
24
Dann
Benign
0.95
DEOGEN2
Benign
0.11
T;.
Eigen
Benign
-0.59
Eigen_PC
Benign
-0.46
FATHMM_MKL
Benign
0.047
N
LIST_S2
Benign
0.54
T;T
M_CAP
Pathogenic
0.30
D
MetaRNN
Benign
0.12
T;T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
0.0
N;N
MutationTaster
Benign
0.98
N;N
PrimateAI
Pathogenic
0.93
D
PROVEAN
Benign
-0.69
N;N
REVEL
Benign
0.043
Sift
Pathogenic
0.0
D;D
Sift4G
Benign
0.25
T;T
Polyphen
0.0
B;B
Vest4
0.33
MutPred
0.21
Gain of glycosylation at Q50 (P = 0.0023);Gain of glycosylation at Q50 (P = 0.0023);
MVP
0.27
MPC
2.0
ClinPred
0.20
T
GERP RS
2.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.9
Varity_R
0.23
gMVP
0.28

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-39990389; API