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

PS4_Supporting PP2 PP1_Moderate PM2

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)

PS4_Supporting

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

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

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.