17-19381428-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002749.4(MAPK7):c.1219C>T(p.Pro407Ser) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MAPK7 NM_002749.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.77

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]

ACMG classification

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=0.21409386).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPK7	NM_002749.4	c.1219C>T	p.Pro407Ser	missense_variant	4/7	ENST00000395604.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPK7	ENST00000395604.8	c.1219C>T	p.Pro407Ser	missense_variant	4/7	1	NM_002749.4	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 15, 2023

The c.1219C>T (p.P407S) alteration is located in exon 4 (coding exon 3) of the MAPK7 gene. This alteration results from a C to T substitution at nucleotide position 1219, causing the proline (P) at amino acid position 407 to be replaced by a serine (S). 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	Benign	0.091
BayesDel_addAF	Benign	-0.014	T
BayesDel_noAF	Benign	-0.26
Cadd	Benign	23
Dann	Uncertain	1.0
DEOGEN2	Benign	0.25	T;.;T;T
Eigen	Benign	-0.033
Eigen_PC	Benign	0.047
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Benign	0.79	T;T;.;.
M_CAP	Benign	0.039	D
MetaRNN	Benign	0.21	T;T;T;T
MetaSVM	Benign	-0.54	T
MutationAssessor	Benign	0.77	N;.;N;N
MutationTaster	Benign	0.86	D;N;N;N
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-1.5	N;N;N;N
REVEL	Benign	0.12
Sift	Benign	0.10	T;T;T;T
Sift4G	Benign	0.070	T;T;T;T
Polyphen		0.69	P;.;P;P
Vest4		0.42
MutPred		0.15		Gain of phosphorylation at P407 (P = 0.0641);.;Gain of phosphorylation at P407 (P = 0.0641);Gain of phosphorylation at P407 (P = 0.0641);
MVP		0.78
MPC		0.42
ClinPred		0.66	D
GERP RS		3.4
Varity_R		0.087
gMVP		0.23

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: chr17-19284741;