Submissions for variant NM_000314.7(PTEN):c.987_990del (p.Asn329fs) (rs587782304)

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Total submissions: 3

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PTEN Variant Curation Expert Panel	RCV000710299	SCV000840476	pathogenic	PTEN hamartoma tumor syndrome	2017-10-18	reviewed by expert panel	curation	PTEN c.987_990delTAAA (p.N329KfsX14) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the 'PTEN ACMG Specifications Summary' document (assertion method column). PVS1: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5' to c.1121 (NM_000314.4). PM2: Absent in large sequenced populations (PMID 27535533). PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID 10232405)
Ambry Genetics	RCV000169834	SCV000186140	pathogenic	Hereditary cancer-predisposing syndrome	2013-03-01	criteria provided, single submitter	clinical testing	Lines of evidence used in support of classification: Alterations resulting in premature truncation (e.g.reading frame shift, nonsense)
GeneDx	RCV000212887	SCV000222155	pathogenic	not provided	2018-02-15	criteria provided, single submitter	clinical testing	This deletion of four nucleotides in PTEN is denoted c.987_990delTAAA at the cDNA level and p.Asn329LysfsX14 (N329KfsX14) at the protein level. The normal sequence, with the bases that are deleted in brackets, is CAAA[delTAAA]GACA. The deletion causes a frameshift which changes an Asparagine to a Lysine at codon 329, and creates a premature stop codon at position 14 of the new reading frame. This variant is predicted to cause loss of normal protein function through protein truncation. PTEN c.987_990delTAAA, also reported as c.987del4, has been identified in association with Bannayan-Riley-Ruvalcaba syndrome and Cowden/Cowden-like syndrome (Marsh 1999, Ngeow 2011, Seol 2015). We consider this variant to be pathogenic.

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