Variant rs140511 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_012324.6(MAPK8IP2):c.786dupG(p.Arg263fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)

Consequence

MAPK8IP2
NM_012324.6 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.302

Variant links:

Genes affected

MAPK8IP2 (HGNC:6883): (mitogen-activated protein kinase 8 interacting protein 2) This gene encodes a scaffold protein that is thought to be involved in the regulation of the c-Jun amino-terminal kinase signaling pathway. This protein has been shown to interact with and regulate the activity of MAPK8/JNK1 and MAP2K7/MKK7 kinases. [provided by RefSeq, Jun 2017]

MAPK8IP2 links:

MAPK8IP2 (HGNC:):

MAPK8IP2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPK8IP2	NM_012324.6 linkuse as main transcript	c.786dupG	p.Arg263fs	frameshift_variant	5/12	ENST00000329492.6	NP_036456.1	Q13387-1
MAPK8IP2	XM_011530679.3 linkuse as main transcript	c.789dupG	p.Arg264fs	frameshift_variant	5/12		XP_011528981.1
MAPK8IP2	XM_011530680.3 linkuse as main transcript	c.675dupG	p.Arg226fs	frameshift_variant	5/12		XP_011528982.1
MAPK8IP2	XM_011530681.3 linkuse as main transcript	c.654dupG	p.Arg219fs	frameshift_variant	5/12		XP_011528983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPK8IP2	ENST00000329492.6 linkuse as main transcript	c.786dupG	p.Arg263fs	frameshift_variant	5/12	1	NM_012324.6	ENSP00000330572.4		Q13387-1
MAPK8IP2	ENST00000008876.7 linkuse as main transcript	n.705dupG		non_coding_transcript_exon_variant	3/10	1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

1.00

AC:

141596

AN:

141598

Hom.:

70797

AF XY:

1.00

AC XY:

78821

AN XY:

78822

show subpopulations

Gnomad AFR exome

AF:

1.00

Gnomad AMR exome

AF:

1.00

Gnomad ASJ exome

AF:

1.00

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

1.00

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

1.00

Gnomad OTH exome

AF:

1.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Alfa

AF:

1.00

Hom.:

6675

Asia WGS

AF:

1.00

AC:

3472

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over