Variant 16-30123046-A-G details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.87

Variant links:

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]

MAPK3 links:

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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
MAPK3	NM_002746.3 linkuse as main transcript	c.164T>C	p.Met55Thr	missense_variant	1/9	ENST00000263025.9
MAPK3	NM_001040056.3 linkuse as main transcript	c.164T>C	p.Met55Thr	missense_variant	1/7
MAPK3	NM_001109891.2 linkuse as main transcript	c.164T>C	p.Met55Thr	missense_variant	1/8
MAPK3	XR_243293.2 linkuse as main transcript	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 linkuse as main transcript	c.164T>C	p.Met55Thr	missense_variant	1/9	1	NM_002746.3	P1	P27361-1

Frequencies

GnomAD3 genomes

AF:

0.0000228

AC:

AN:

87806

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000446

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000418

AC:

AN:

1197166

Hom.:

Cov.:

AF XY:

0.00000506

AC XY:

AN XY:

593366

show subpopulations

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:

0.00000525

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000228

AC:

AN:

87806

Hom.:

Cov.:

AF XY:

0.0000244

AC XY:

AN XY:

41002

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000446

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000331

Hom.:

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.79

BayesDel_addAF

Benign

-0.0063

BayesDel_noAF

Benign

-0.25

Cadd

Uncertain

Dann

Benign

0.94

DEOGEN2

Benign

0.27

T;.;T;.;.

Eigen

Benign

-0.35

Eigen_PC

Benign

-0.11

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.74

T;T;T;.;T

M_CAP

Pathogenic

0.87

MetaRNN

Uncertain

0.69

D;D;D;D;D

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.1

N;N;.;N;N

MutationTaster

Benign

1.0

D;D;D;D;D;D

PrimateAI

Pathogenic

0.93

PROVEAN

Uncertain

-2.8

D;D;D;D;D

REVEL

Uncertain

0.31

Sift

Benign

0.067

T;T;T;T;T

Sift4G

Benign

0.11

T;T;T;T;T

Polyphen

0.0020

B;B;.;B;B

Vest4

0.56

MVP

0.74

MPC

0.76

ClinPred

0.91

GERP RS

3.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.61

gMVP

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over