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.510T>A (p.Ser170Arg)

CA000492

7815 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 67ade3e6-3038-4022-903b-9caf929577ba

Approved on: 2021-10-29

Published on: 2021-10-29

HGVS expressions

NM_000314.6:c.510T>A

NM_000314.6(PTEN):c.510T>A (p.Ser170Arg)

NC_000010.11:g.87952135T>A

CM000672.2:g.87952135T>A

NC_000010.10:g.89711892T>A

CM000672.1:g.89711892T>A

NC_000010.9:g.89701872T>A

NG_007466.2:g.93697T>A

ENST00000371953.8:c.510T>A

ENST00000371953.7:c.510T>A

NM_000314.5:c.510T>A

NM_001304717.2:c.1029T>A

NM_001304718.1:c.-82T>A

NM_000314.7:c.510T>A

NM_001304717.5:c.1029T>A

NM_001304718.2:c.-82T>A

NM_000314.8:c.510T>A

NM_000314.8(PTEN):c.510T>A (p.Ser170Arg)

Pathogenic

PS4_Moderate PS3 PP2 PP1 PM2

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.510T>A (p.Ser170Arg) meets criteria to be classified as 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 17942903, PMID 10866302, PMID 9256433, PMID 21828076 PS4_M: Probands with phenotype specificity score of 2-3.5. (PMID 17526800, PMID 23335809, PMID 30528446) PM2: Absent in large sequenced populations (PMID 27535533) PP1: Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed. (PMID 17526800, PMID 9241266) 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_Moderate

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

PS3

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

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

PM2

Absent gnomAD

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