Variant 7-91079434-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001287135.2(CDK14):c.1108C>T(p.Arg370Cys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000014 in 1,428,348 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R370S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.000014 ( 0 hom. )

Consequence

CDK14
NM_001287135.2 missense, splice_region

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.69

Variant links:

Genes affected

CDK14 (HGNC:8883): (cyclin dependent kinase 14) Enables cyclin binding activity and cyclin-dependent protein serine/threonine kinase activity. Involved in G2/M transition of mitotic cell cycle and regulation of canonical Wnt signaling pathway. Located in cytosol; nucleoplasm; and plasma membrane. Part of cytoplasmic cyclin-dependent protein kinase holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]

CDK14 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAdExome4 at 20 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CDK14	NM_001287135.2 linkuse as main transcript	c.1108C>T	p.Arg370Cys	missense_variant, splice_region_variant	12/15	ENST00000380050.8
CDK14	NM_012395.3 linkuse as main transcript	c.1054C>T	p.Arg352Cys	missense_variant, splice_region_variant	11/14
CDK14	NM_001287136.1 linkuse as main transcript	c.970C>T	p.Arg324Cys	missense_variant, splice_region_variant	11/14
CDK14	NM_001287137.1 linkuse as main transcript	c.721C>T	p.Arg241Cys	missense_variant, splice_region_variant	10/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8 linkuse as main transcript	c.1108C>T	p.Arg370Cys	missense_variant, splice_region_variant	12/15	1	NM_001287135.2	P4	O94921-1
CDK14	ENST00000265741.7 linkuse as main transcript	c.1054C>T	p.Arg352Cys	missense_variant, splice_region_variant	11/14	1			O94921-2
CDK14	ENST00000406263.5 linkuse as main transcript	c.970C>T	p.Arg324Cys	missense_variant, splice_region_variant	11/14	1		A1	O94921-3
CDK14	ENST00000436577.3 linkuse as main transcript	c.721C>T	p.Arg241Cys	missense_variant, splice_region_variant	10/13	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000250

AC:

AN:

239908

Hom.:

AF XY:

0.0000154

AC XY:

AN XY:

129620

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000317

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000724

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000272

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000140

AC:

AN:

1428348

Hom.:

Cov.:

AF XY:

0.0000126

AC XY:

AN XY:

711488

show subpopulations

Gnomad4 AFR exome

AF:

0.0000931

Gnomad4 AMR exome

AF:

0.0000239

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000243

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000826

Gnomad4 OTH exome

AF:

0.0000844

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000312

Hom.:

Bravo

AF:

0.00000378

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 17, 2021

The c.1054C>T (p.R352C) alteration is located in exon 11 (coding exon 11) of the CDK14 gene. This alteration results from a C to T substitution at nucleotide position 1054, causing the arginine (R) at amino acid position 352 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Uncertain

0.063

BayesDel_noAF

Uncertain

0.040

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.19

T;.;.;.

Eigen

Uncertain

0.48

Eigen_PC

Uncertain

0.50

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.76

T;T;T;T

M_CAP

Benign

0.016

MetaRNN

Uncertain

0.60

D;D;D;D

MetaSVM

Benign

-0.69

MutationAssessor

Benign

1.4

L;.;.;.

MutationTaster

Benign

1.0

D;D;D;D

PrimateAI

Uncertain

0.71

PROVEAN

Uncertain

-3.1

D;D;D;D

REVEL

Uncertain

0.31

Sift

Benign

0.036

D;T;D;D

Sift4G

Benign

0.091

T;T;T;T

Polyphen

1.0

D;B;.;D

Vest4

0.64

MutPred

0.68

Loss of MoRF binding (P = 0.018);.;.;.;

MVP

0.65

MPC

0.49

ClinPred

0.90

GERP RS

4.8

Varity_R

0.31

gMVP

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over