rs1450916285

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_003718.5(CDK13):​c.20C>A​(p.Thr7Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000104 in 1,346,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T7M) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

CDK13
NM_003718.5 missense

Scores

3
2
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.82

Publications

1 publications found
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]
CDK13 Gene-Disease associations (from GenCC):
  • congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Illumina
  • syndromic intellectual disability
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.10564783).
BS2
High AC in GnomAdExome4 at 13 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDK13NM_003718.5 linkc.20C>A p.Thr7Lys missense_variant Exon 1 of 14 ENST00000181839.10 NP_003709.3 Q14004-1A0A024RA85Q9BVE2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDK13ENST00000181839.10 linkc.20C>A p.Thr7Lys missense_variant Exon 1 of 14 1 NM_003718.5 ENSP00000181839.4 Q14004-1
CDK13ENST00000340829.10 linkc.20C>A p.Thr7Lys missense_variant Exon 1 of 14 1 ENSP00000340557.5 Q14004-2

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152190
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000109
AC:
13
AN:
1194258
Hom.:
0
Cov.:
33
AF XY:
0.00000692
AC XY:
4
AN XY:
578054
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
23834
American (AMR)
AF:
0.00
AC:
0
AN:
10520
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16938
East Asian (EAS)
AF:
0.00
AC:
0
AN:
27036
South Asian (SAS)
AF:
0.00
AC:
0
AN:
50410
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
29266
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3336
European-Non Finnish (NFE)
AF:
0.0000122
AC:
12
AN:
984060
Other (OTH)
AF:
0.0000205
AC:
1
AN:
48858
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152190
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74352
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
41448
American (AMR)
AF:
0.00
AC:
0
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3468
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5190
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4836
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10614
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.0000147
AC:
1
AN:
68026
Other (OTH)
AF:
0.00
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.43
CADD
Uncertain
25
DANN
Benign
0.95
DEOGEN2
Benign
0.081
T;.
Eigen
Benign
-0.41
Eigen_PC
Benign
-0.24
FATHMM_MKL
Benign
0.29
N
LIST_S2
Benign
0.56
T;T
M_CAP
Uncertain
0.14
D
MetaRNN
Benign
0.11
T;T
MetaSVM
Benign
-1.0
T
PhyloP100
1.8
PrimateAI
Pathogenic
0.94
D
PROVEAN
Benign
-0.37
N;N
REVEL
Benign
0.031
Sift
Pathogenic
0.0
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
0.010
B;B
Vest4
0.15
MutPred
0.18
Gain of ubiquitination at T7 (P = 0.0066);Gain of ubiquitination at T7 (P = 0.0066);
MVP
0.39
MPC
2.0
ClinPred
0.74
D
GERP RS
2.8
PromoterAI
-0.035
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.16
gMVP
0.39
Mutation Taster
=91/9
polymorphism

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

Other links and lift over

dbSNP: rs1450916285; hg19: chr7-39990260; API