chr16-30117158-GGA-CGG

Variant names:

• chr16-30117158-GGA-CGG
• NM_002746.3:c.901_903delTCCinsCCG
• MAPK3 p.Ser301Pro

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_002746.3(MAPK3):​c.901_903delTCCinsCCG​(p.Ser301Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: MAPK3 NM_002746.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.49
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002746.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPK3	NM_002746.3	MANE Select	c.901_903delTCCinsCCG	p.Ser301Pro	missense	N/A	NP_002737.2	L7RXH5
	MAPK3	NM_001040056.3		c.901_903delTCCinsCCG	p.Ser301Pro	missense	N/A	NP_001035145.1	P27361-3
	MAPK3	NM_001109891.2		c.776-157_776-155delTCCinsCCG		intron	N/A	NP_001103361.1	P27361-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPK3	ENST00000263025.9	TSL:1 MANE Select	c.901_903delTCCinsCCG	p.Ser301Pro	missense	N/A	ENSP00000263025.4	P27361-1
	MAPK3	ENST00000395199.7	TSL:1	c.901_903delTCCinsCCG	p.Ser301Pro	missense	N/A	ENSP00000378625.3	P27361-3
	MAPK3	ENST00000484663.5	TSL:1	c.559_561delTCCinsCCG	p.Ser187Pro	missense	N/A	ENSP00000432742.1	A1QJE5

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-30128479;