17-19378979-C-G

Variant summary

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

The NM_002749.4(MAPK7):​c.79C>G​(p.His27Asp) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H27Y) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

MAPK7
NM_002749.4 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336
Variant links:
Genes affected
MAPK7 (HGNC:6880): (mitogen-activated protein kinase 7) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. This kinase is specifically activated by mitogen-activated protein kinase kinase 5 (MAP2K5/MEK5). It is involved in the downstream signaling processes of various receptor molecules including receptor type kinases, and G protein-coupled receptors. In response to extracelluar signals, this kinase translocates to cell nucleus, where it regulates gene expression by phosphorylating, and activating different transcription factors. Four alternatively spliced transcript variants of this gene encoding two distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

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=0.080418676).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAPK7NM_002749.4 linkc.79C>G p.His27Asp missense_variant Exon 2 of 7 ENST00000395604.8 NP_002740.2 Q13164-1A0A024QZ20

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAPK7ENST00000395604.8 linkc.79C>G p.His27Asp missense_variant Exon 2 of 7 1 NM_002749.4 ENSP00000378968.3 Q13164-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.078
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
12
DANN
Benign
0.88
DEOGEN2
Benign
0.13
T;T;T;.;T;T
Eigen
Benign
-0.92
Eigen_PC
Benign
-0.88
FATHMM_MKL
Benign
0.069
N
LIST_S2
Benign
0.67
T;.;T;T;.;T
M_CAP
Benign
0.023
T
MetaRNN
Benign
0.080
T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N;.;.;N;.
PrimateAI
Uncertain
0.62
T
PROVEAN
Benign
-0.12
N;N;.;N;N;.
REVEL
Benign
0.079
Sift
Benign
0.18
T;T;.;T;T;.
Sift4G
Benign
0.64
T;T;T;T;T;T
Polyphen
0.0
B;B;.;.;B;.
Vest4
0.18
MutPred
0.23
Gain of relative solvent accessibility (P = 0.0479);Gain of relative solvent accessibility (P = 0.0479);Gain of relative solvent accessibility (P = 0.0479);Gain of relative solvent accessibility (P = 0.0479);Gain of relative solvent accessibility (P = 0.0479);Gain of relative solvent accessibility (P = 0.0479);
MVP
0.55
MPC
0.58
ClinPred
0.030
T
GERP RS
0.88
Varity_R
0.052
gMVP
0.21

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: rs773113285; hg19: chr17-19282292; API