chr17-39462829-C-G

Variant summary

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

The NM_016507.4(CDK12):ā€‹c.758C>Gā€‹(p.Ser253Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

CDK12
NM_016507.4 missense

Scores

1
6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.55
Variant links:
Genes affected
CDK12 (HGNC:24224): (cyclin dependent kinase 12) Enables RNA polymerase II CTD heptapeptide repeat kinase activity and cyclin binding activity. Involved in phosphorylation of RNA polymerase II C-terminal domain; protein autophosphorylation; and regulation of MAP kinase activity. Located in nuclear speck. Part of cyclin K-CDK12 complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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=0.22502398).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDK12NM_016507.4 linkuse as main transcriptc.758C>G p.Ser253Cys missense_variant 1/14 ENST00000447079.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDK12ENST00000447079.6 linkuse as main transcriptc.758C>G p.Ser253Cys missense_variant 1/141 NM_016507.4 P4Q9NYV4-1
CDK12ENST00000430627.6 linkuse as main transcriptc.758C>G p.Ser253Cys missense_variant 1/141 A1Q9NYV4-2
CDK12ENST00000584632.5 linkuse as main transcriptc.758C>G p.Ser253Cys missense_variant 1/135
CDK12ENST00000559663.2 linkuse as main transcriptc.758C>G p.Ser253Cys missense_variant, NMD_transcript_variant 1/215

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461884
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

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 submitterclinical testingAmbry GeneticsApr 26, 2023The c.758C>G (p.S253C) alteration is located in exon 1 (coding exon 1) of the CDK12 gene. This alteration results from a C to G substitution at nucleotide position 758, causing the serine (S) at amino acid position 253 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
0.12
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.39
CADD
Pathogenic
27
DANN
Uncertain
0.99
DEOGEN2
Benign
0.023
T;.;T
Eigen
Uncertain
0.53
Eigen_PC
Uncertain
0.49
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.77
T;T;T
M_CAP
Benign
0.049
D
MetaRNN
Benign
0.23
T;T;T
MetaSVM
Benign
-0.69
T
MutationAssessor
Benign
1.8
.;L;L
MutationTaster
Benign
0.93
D;D
PrimateAI
Uncertain
0.66
T
PROVEAN
Benign
-1.9
.;N;N
REVEL
Benign
0.11
Sift
Pathogenic
0.0
.;D;D
Sift4G
Uncertain
0.011
D;D;D
Polyphen
1.0, 1.0
.;D;D
Vest4
0.44, 0.45
MutPred
0.14
Loss of phosphorylation at S253 (P = 0.0065);Loss of phosphorylation at S253 (P = 0.0065);Loss of phosphorylation at S253 (P = 0.0065);
MVP
0.37
MPC
0.32
ClinPred
0.88
D
GERP RS
5.2
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.6
Varity_R
0.35
gMVP
0.24

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: chr17-37619082; API