16-30123098-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002746.3(MAPK3):c.112G>T(p.Val38Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000702 in 1,423,814 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 (★).
Frequency
Genomes: not found (cov: 28)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
MAPK3
NM_002746.3 missense
NM_002746.3 missense
Scores
3
3
13
Clinical Significance
Conservation
PhyloP100: 2.50
Genes affected
MAPK3 (HGNC:6877): (mitogen-activated protein kinase 3) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act in a signaling cascade that regulates various cellular processes such as proliferation, differentiation, and cell cycle progression in response to a variety of extracellular signals. This kinase is activated by upstream kinases, resulting in its translocation to the nucleus where it phosphorylates nuclear targets. Alternatively spliced transcript variants encoding different protein isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.27596158).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPK3 | NM_002746.3 | c.112G>T | p.Val38Leu | missense_variant | 1/9 | ENST00000263025.9 | |
MAPK3 | NM_001040056.3 | c.112G>T | p.Val38Leu | missense_variant | 1/7 | ||
MAPK3 | NM_001109891.2 | c.112G>T | p.Val38Leu | missense_variant | 1/8 | ||
MAPK3 | XR_243293.2 | n.123G>T | non_coding_transcript_exon_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPK3 | ENST00000263025.9 | c.112G>T | p.Val38Leu | missense_variant | 1/9 | 1 | NM_002746.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 28
GnomAD3 genomes
?
Cov.:
28
GnomAD4 exome AF: 7.02e-7 AC: 1AN: 1423814Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 708456
GnomAD4 exome
AF:
AC:
1
AN:
1423814
Hom.:
Cov.:
36
AF XY:
AC XY:
0
AN XY:
708456
Gnomad4 AFR exome
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Gnomad4 ASJ exome
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Gnomad4 SAS exome
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GnomAD4 genome ? Cov.: 28
GnomAD4 genome
?
Cov.:
28
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 | Dec 28, 2022 | The c.112G>T (p.V38L) alteration is located in exon 1 (coding exon 1) of the MAPK3 gene. This alteration results from a G to T substitution at nucleotide position 112, causing the valine (V) at amino acid position 38 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;.;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.;N;N
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
B;B;.;B;B
Vest4
MutPred
Gain of catalytic residue at V38 (P = 0.1576);Gain of catalytic residue at V38 (P = 0.1576);.;Gain of catalytic residue at V38 (P = 0.1576);Gain of catalytic residue at V38 (P = 0.1576);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at