Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

Variant: NM_000314.6(PTEN):c.235G>A (p.Ala79Thr)

CA000358

41682 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 0340272b-ab4c-4672-94b8-40e0525d8eda

Approved on: 2018-04-06

Published on: 2018-12-10

HGVS expressions

NM_000314.6:c.235G>A

NM_000314.6(PTEN):c.235G>A (p.Ala79Thr)

NM_000314.5:c.235G>A

NM_001304717.2:c.754G>A

NM_001304718.1:c.-516G>A

NM_000314.7:c.235G>A

NM_001304717.5:c.754G>A

NM_001304718.2:c.-516G>A

ENST00000371953.7:c.235G>A

ENST00000498703.1:n.61G>A

ENST00000610634.1:c.133G>A

NC_000010.11:g.87931071G>A

CM000672.2:g.87931071G>A

NC_000010.10:g.89690828G>A

CM000672.1:g.89690828G>A

NC_000010.9:g.89680808G>A

NG_007466.2:g.72633G>A

Likely Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"

BS2_Supporting BS1 PP2

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.235G>A (p.A79T) meets criteria to be classified as likely benign 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). BS1: Allele frequency of 0.0045 (0.45%, 9/1984 alleles) in the GME variome. (PMID 27428751) BS2_P: Meets criteria for BS2 (observed in the homozygous state in at least one healthy or PHTS-unaffected individual) but BS1 is also applied. (Internal laboratory contributor(s) SCV000222198.12) PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

BS2_Supporting

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BS1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PP2

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

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