19-2046223-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong

The NM_199054.3(MKNK2):​c.302G>A​(p.Cys101Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MKNK2
NM_199054.3 missense

Scores

6
9
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.95
Variant links:
Genes affected
MKNK2 (HGNC:7111): (MAPK interacting serine/threonine kinase 2) This gene encodes a member of the calcium/calmodulin-dependent protein kinases (CAMK) Ser/Thr protein kinase family, which belongs to the protein kinase superfamily. This protein contains conserved DLG (asp-leu-gly) and ENIL (glu-asn-ile-leu) motifs, and an N-terminal polybasic region which binds importin A and the translation factor scaffold protein eukaryotic initiation factor 4G (eIF4G). This protein is one of the downstream kinases activated by mitogen-activated protein (MAP) kinases. It phosphorylates the eukaryotic initiation factor 4E (eIF4E), thus playing important roles in the initiation of mRNA translation, oncogenic transformation and malignant cell proliferation. In addition to eIF4E, this protein also interacts with von Hippel-Lindau tumor suppressor (VHL), ring-box 1 (Rbx1) and Cullin2 (Cul2), which are all components of the CBC(VHL) ubiquitin ligase E3 complex. Multiple alternatively spliced transcript variants have been found, but the full-length nature and biological activity of only two variants are determined. These two variants encode distinct isoforms which differ in activity and regulation, and in subcellular localization. [provided by RefSeq, Aug 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.979

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MKNK2NM_199054.3 linkc.302G>A p.Cys101Tyr missense_variant Exon 5 of 14 ENST00000250896.9 NP_951009.1 Q9HBH9-1B3KS07
MKNK2NM_017572.4 linkc.302G>A p.Cys101Tyr missense_variant Exon 5 of 14 NP_060042.2 Q9HBH9-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MKNK2ENST00000250896.9 linkc.302G>A p.Cys101Tyr missense_variant Exon 5 of 14 5 NM_199054.3 ENSP00000250896.3 Q9HBH9-1
MKNK2ENST00000309340.11 linkc.302G>A p.Cys101Tyr missense_variant Exon 5 of 14 1 ENSP00000309485.6 Q9HBH9-2
MKNK2ENST00000586828.5 linkn.241+144G>A intron_variant Intron 3 of 11 2 ENSP00000465425.1 K7EK27
MKNK2ENST00000589509.5 linkc.*238G>A downstream_gene_variant 5 ENSP00000466147.2 K7ELN0

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1455750
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
724548
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Mar 15, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.302G>A (p.C101Y) alteration is located in exon 5 (coding exon 4) of the MKNK2 gene. This alteration results from a G to A substitution at nucleotide position 302, causing the cysteine (C) at amino acid position 101 to be replaced by a tyrosine (Y). 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
Pathogenic
1.0
BayesDel_addAF
Pathogenic
0.23
D
BayesDel_noAF
Uncertain
0.10
CADD
Pathogenic
32
DANN
Uncertain
1.0
DEOGEN2
Benign
0.33
T;.;T
Eigen
Uncertain
0.65
Eigen_PC
Uncertain
0.59
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.93
.;D;D
M_CAP
Uncertain
0.094
D
MetaRNN
Pathogenic
0.98
D;D;D
MetaSVM
Benign
-0.46
T
MutationAssessor
Benign
1.2
L;L;L
PrimateAI
Pathogenic
0.82
D
PROVEAN
Pathogenic
-8.7
.;D;D
REVEL
Uncertain
0.50
Sift
Uncertain
0.013
.;D;D
Sift4G
Uncertain
0.024
D;D;D
Polyphen
1.0
D;P;D
Vest4
0.97
MutPred
0.89
Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);
MVP
0.60
MPC
1.5
ClinPred
0.98
D
GERP RS
4.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.94
gMVP
0.86

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: chr19-2046222; API