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]

Variant: NM_000314.6(PTEN):c.520T>A (p.Tyr174Asn)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA000501

142220 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 58b7be5a-c98e-4344-9f4f-cff2dd70911d

Approved on: 2021-10-29

Published on: 2021-10-29

HGVS expressions

NM_000314.6:c.520T>A

NM_000314.6(PTEN):c.520T>A (p.Tyr174Asn)

NC_000010.11:g.87952145T>A

CM000672.2:g.87952145T>A

NC_000010.10:g.89711902T>A

CM000672.1:g.89711902T>A

NC_000010.9:g.89701882T>A

NG_007466.2:g.93707T>A

ENST00000371953.8:c.520T>A

ENST00000371953.7:c.520T>A

NM_000314.5:c.520T>A

NM_001304717.2:c.1039T>A

NM_001304718.1:c.-72T>A

NM_000314.7:c.520T>A

NM_001304717.5:c.1039T>A

NM_001304718.2:c.-72T>A

NM_000314.8:c.520T>A

NM_000314.8(PTEN):c.520T>A (p.Tyr174Asn)

Likely Pathogenic

PS3 PM2 PP2

Evidence Links 1

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.520T>A (p.Tyr174Asn) 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). PS3: Phosphatase activity <50% of wild type (PMID 10866302, PMID 29706350) PM2: 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.

PS3

Score -2.92 truncation-like range PubMed:29706350

PM2

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

Curation History

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