rs745880233

Variant summary

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

The NM_004714.3(DYRK1B):​c.1840C>T​(p.Pro614Ser) 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. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

DYRK1B
NM_004714.3 missense

Scores

3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.24
Variant links:
Genes affected
DYRK1B (HGNC:3092): (dual specificity tyrosine phosphorylation regulated kinase 1B) This gene encodes a member of a family of nuclear-localized protein kinases. The encoded protein participates in the regulation of the cell cycle. Expression of this gene may be altered in tumor cells, and mutations in this gene were found to cause abdominal obesity-metabolic syndrome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

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=0.124304205).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DYRK1BNM_004714.3 linkc.1840C>T p.Pro614Ser missense_variant Exon 11 of 11 ENST00000323039.10 NP_004705.1 Q9Y463-1A0A024R0I0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DYRK1BENST00000323039.10 linkc.1840C>T p.Pro614Ser missense_variant Exon 11 of 11 1 NM_004714.3 ENSP00000312789.4 Q9Y463-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.075
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
20
DANN
Uncertain
0.99
DEOGEN2
Benign
0.084
T;T;.;.;.
Eigen
Benign
-0.061
Eigen_PC
Benign
0.092
FATHMM_MKL
Uncertain
0.81
D
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.12
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.81
L;L;.;.;.
PrimateAI
Uncertain
0.64
T
PROVEAN
Benign
0.25
.;N;N;.;N
REVEL
Benign
0.10
Sift
Benign
0.10
.;T;T;.;T
Sift4G
Benign
0.66
T;T;T;T;T
Polyphen
0.44
B;B;P;P;P
Vest4
0.25
MutPred
0.092
Gain of glycosylation at P614 (P = 0.0173);Gain of glycosylation at P614 (P = 0.0173);.;.;.;
MVP
0.51
MPC
0.49
ClinPred
0.38
T
GERP RS
5.0
Varity_R
0.065
gMVP
0.25

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

LitVar

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

Other links and lift over

dbSNP: rs745880233; hg19: chr19-40316405; API