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.521A>G (p.Tyr174Cys)

CA349032

220007 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 3905138e-990e-4b30-b0aa-96ad556248ac

Approved on: 2023-06-14

Published on: 2023-10-19

HGVS expressions

NM_000314.8:c.521A>G

NM_000314.8(PTEN):c.521A>G (p.Tyr174Cys)

NC_000010.11:g.87952146A>G

CM000672.2:g.87952146A>G

NC_000010.10:g.89711903A>G

CM000672.1:g.89711903A>G

NC_000010.9:g.89701883A>G

NG_007466.2:g.93708A>G

ENST00000686459.1:c.*107A>G

ENST00000688158.1:c.*632A>G

ENST00000688308.1:c.521A>G

ENST00000688922.1:c.442A>G

ENST00000693560.1:c.1040A>G

ENST00000371953.8:c.521A>G

ENST00000371953.7:c.521A>G

NM_000314.5:c.521A>G

NM_000314.6:c.521A>G

NM_001304717.2:c.1040A>G

NM_001304718.1:c.-71A>G

NM_000314.7:c.521A>G

NM_001304717.5:c.1040A>G

NM_001304718.2:c.-71A>G

Likely Pathogenic

PS4_Supporting PS2 PP2 PP3 PM2_Supporting

BP4

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

NM_000314.8(PTEN):c.521A>G (p.Tyr174Cys) variant meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.0.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PS2: De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. (Internal laboratory contributor(s) SCV000602123.1) PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (Internal laboratory contributor(s) SCV000602123.1). PM2_P: Absent in large sequenced populations (PMID 27535533). 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. PP3: REVEL score > 0.7 (score=0.978).

PS4_Supporting

PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (Internal laboratory contributor(s) SCV000602123.1).

PS2

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. (Internal laboratory contributor(s) SCV000602123.1)

PP2

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.

PP3

REVEL score > 0.7 (score=0.978)

PM2_Supporting

PM2_Supporting: Absent in large sequenced populations in the gnomAD cohort. (PMID 27535533).

BP4

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

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