rs747947002

chr17-60656794-GAA-Gchr17-60656794-GAA-GAchr17-60656794-GAA-GAAA

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PP5_Moderate

The NM_003620.4(PPM1D):c.1215_1216del(p.Glu405AspfsTer28) variant causes a frameshift change. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PPM1D NM_003620.4 frameshift
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 6.30

Genes affected

PPM1D (HGNC:9277): (protein phosphatase, Mg2+/Mn2+ dependent 1D) The protein encoded by this gene is a member of the PP2C family of Ser/Thr protein phosphatases. PP2C family members are known to be negative regulators of cell stress response pathways. The expression of this gene is induced in a p53-dependent manner in response to various environmental stresses. While being induced by tumor suppressor protein TP53/p53, this phosphatase negatively regulates the activity of p38 MAP kinase, MAPK/p38, through which it reduces the phosphorylation of p53, and in turn suppresses p53-mediated transcription and apoptosis. This phosphatase thus mediates a feedback regulation of p38-p53 signaling that contributes to growth inhibition and the suppression of stress induced apoptosis. This gene is located in a chromosomal region known to be amplified in breast cancer. The amplification of this gene has been detected in both breast cancer cell line and primary breast tumors, which suggests a role of this gene in cancer development. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 38 pathogenic variants in the truncated region.
• PP5: Variant 17-60656794-GAA-G is Pathogenic according to our data. Variant chr17-60656794-GAA-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 452427.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPM1D	NM_003620.4	c.1215_1216del	p.Glu405AspfsTer28	frameshift_variant	5/6	ENST00000305921.8
PPM1D	XR_007065507.1	n.1437_1438del		non_coding_transcript_exon_variant	5/7
PPM1D	XR_934577.3	n.1437_1438del		non_coding_transcript_exon_variant	5/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPM1D	ENST00000305921.8	c.1215_1216del	p.Glu405AspfsTer28	frameshift_variant	5/6	1	NM_003620.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Oct 20, 2017

The c.1215_1216delAA variant in the PPM1D gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1215_1216delAA variant causes a frameshift starting with codon Glutamic acid 405, changes this amino acid to an Aspartic acid residue, and creates a premature Stop codon at position 28 of the new reading frame, denoted p.Glu405AspfsX28. This variant is predicted to cause loss of normal protein function through protein truncation. The c.1215_1216delAA variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.1215_1216delAA as a likely pathogenic variant -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs747947002; hg19: chr17-58734155;