10-87894101-TGTA-T

Position:

• chr10-87894101-TGTA-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1 PM2 PM4_Supporting PP5_Moderate

The ENST00000371953.8(PTEN):​c.160_162delGTA​(p.Val54del) variant causes a conservative inframe deletion, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V54V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PTEN ENST00000371953.8 conservative_inframe_deletion, splice_region
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.42

Genes affected

PTEN (HGNC:9588): (phosphatase and tensin homolog) This gene was identified as a tumor suppressor that is mutated in a large number of cancers at high frequency. The protein encoded by this gene is a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It contains a tensin like domain as well as a catalytic domain similar to that of the dual specificity protein tyrosine phosphatases. Unlike most of the protein tyrosine phosphatases, this protein preferentially dephosphorylates phosphoinositide substrates. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/PKB signaling pathway. The use of a non-canonical (CUG) upstream initiation site produces a longer isoform that initiates translation with a leucine, and is thought to be preferentially associated with the mitochondrial inner membrane. This longer isoform may help regulate energy metabolism in the mitochondria. A pseudogene of this gene is found on chromosome 9. Alternative splicing and the use of multiple translation start codons results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]

PTEN (HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PM1: In a hotspot region, there are 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 16 uncertain in ENST00000371953.8
• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in ENST00000371953.8. Strenght limited to Supporting due to length of the change: 1aa.
• PP5: Variant 10-87894101-TGTA-T is Pathogenic according to our data. Variant chr10-87894101-TGTA-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 480382.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTEN	NM_000314.8	c.160_162delGTA	p.Val54del	conservative_inframe_deletion, splice_region_variant	2/9	ENST00000371953.8	NP_000305.3
PTEN	NM_001304717.5	c.679_681delGTA	p.Val227del	conservative_inframe_deletion, splice_region_variant	3/10		NP_001291646.4
PTEN	NM_001304718.2	c.-546_-544delGTA		splice_region_variant	2/9		NP_001291647.1
PTEN	NM_001304718.2	c.-546_-544delGTA		5_prime_UTR_variant	2/9		NP_001291647.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTEN	ENST00000371953.8	c.160_162delGTA	p.Val54del	conservative_inframe_deletion, splice_region_variant	2/9	1	NM_000314.8	ENSP00000361021.3

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

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 26, 2017

The c.160_162delGTA variant (also known as p.V54del) is located in coding exon 2 of the PTEN gene. This variant results from an in-frame GTA deletion at nucleotide positions 160 to 162. This results in the deletion of a valine residue at codon 54. This alteration was reported in an individual with a personal history of endometrial as well breast cancer and she had a Cleveland Clinic score of 66 indicating Cowden syndrome (Ngeow J et al. J. Clin. Oncol., 2014 Jun;32:1818-24). Based on internal structural analysis, p.V54del is predicted to significantly disrupt the structure of the PTEN protein, which may result in a change or loss of function (Paukstelis PJ et al. Mol. Cell, 2005 Feb;17:417-28; Dunham TD et al. EMBO J., 2009 Jun;28:1792-802; Lee JO et al. Cell, 1999 Oct;99:323-34). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD) (Lek M et al. Nature, 2016 08;536:285-91). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by PROVEAN in silico analysis (Choi Y et al., Bioinformatics 2015 Aug; 31(16):2745-7). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs1554893831; hg19: chr10-89653858;