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_000314.8(PTEN):c.402G>C (p.Met134Ile)

CA377482340

619908 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 502914e3-3945-40a1-bd9c-032f106057a8

Approved on: 2021-06-04

Published on: 2022-09-30

HGVS expressions

NM_000314.8:c.402G>C

NM_000314.8(PTEN):c.402G>C (p.Met134Ile)

NC_000010.11:g.87933161G>C

CM000672.2:g.87933161G>C

NC_000010.10:g.89692918G>C

CM000672.1:g.89692918G>C

NC_000010.9:g.89682898G>C

NG_007466.2:g.74723G>C

ENST00000686459.1:c.402G>C

ENST00000688158.1:c.*513G>C

ENST00000688308.1:c.402G>C

ENST00000688922.1:n.323G>C

ENST00000693560.1:c.921G>C

ENST00000371953.8:c.402G>C

ENST00000371953.7:c.402G>C

ENST00000498703.1:n.228G>C

ENST00000610634.1:c.300G>C

NM_000314.5:c.402G>C

NM_000314.6:c.402G>C

NM_001304717.2:c.921G>C

NM_001304718.1:c.-349G>C

NM_000314.7:c.402G>C

NM_001304717.5:c.921G>C

NM_001304718.2:c.-349G>C

Likely Pathogenic

PP2 PP1_Moderate PM2 PS4_Supporting

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.402G>C (p.Met134Ile) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM2: Absent in large sequenced populations (PMID 27535533). PP1_M: Co-segregation with disease in multiple affected family members, with 5 or 6 meioses observed. (PMID 23124040, internal laboratory contributor(s) ClinVar Organization ID: 26957) 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. PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID 23124040)

PP2

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

PP1_Moderate

Also 1 meiosis from GeneDx family = 5 total

PM2

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

PS4_Supporting

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

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