chr16-30123046-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_002746.3(MAPK3):c.164T>C(p.Met55Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000545 in 1,284,972 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000023 ( 0 hom., cov: 23)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
MAPK3
NM_002746.3 missense
NM_002746.3 missense
Scores
3
4
12
Clinical Significance
Conservation
PhyloP100: 5.87
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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPK3 | NM_002746.3 | c.164T>C | p.Met55Thr | missense_variant | 1/9 | ENST00000263025.9 | |
MAPK3 | NM_001040056.3 | c.164T>C | p.Met55Thr | missense_variant | 1/7 | ||
MAPK3 | NM_001109891.2 | c.164T>C | p.Met55Thr | missense_variant | 1/8 | ||
MAPK3 | XR_243293.2 | n.175T>C | non_coding_transcript_exon_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPK3 | ENST00000263025.9 | c.164T>C | p.Met55Thr | missense_variant | 1/9 | 1 | NM_002746.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000228 AC: 2AN: 87806Hom.: 0 Cov.: 23
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GnomAD4 exome AF: 0.00000418 AC: 5AN: 1197166Hom.: 0 Cov.: 37 AF XY: 0.00000506 AC XY: 3AN XY: 593366
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GnomAD4 genome ? AF: 0.0000228 AC: 2AN: 87806Hom.: 0 Cov.: 23 AF XY: 0.0000244 AC XY: 1AN XY: 41002
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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 | Mendelics | May 04, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Benign
DEOGEN2
Benign
T;.;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;.;T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.;N;N
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Uncertain
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
B;B;.;B;B
Vest4
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at