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.40dupA (p.Arg14Lysfs)

Curation History

CA254258

7834 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: d7cc25c0-43b3-408c-8e19-6aab8d40a4f1

Approved on: 2018-04-06

Published on: 2018-12-10

HGVS expressions

NM_000314.6:c.40dupA

NM_000314.6(PTEN):c.40dupA (p.Arg14Lysfs)

NC_000010.11:g.87864509dup

CM000672.2:g.87864509dup

NC_000010.10:g.89624266dup

CM000672.1:g.89624266dup

NC_000010.9:g.89614246dup

NG_007466.2:g.6071dup

NG_033079.1:g.3932dup

NM_000314.5:c.40dup

NM_000314.6:c.40dup

NM_001304717.2:c.559dup

NM_001304718.1:c.-666dup

NM_000314.7:c.40dup

NM_001304717.5:c.559dup

NM_001304718.2:c.-666dup

ENST00000371953.7:c.40dup

ENST00000462694.1:n.42dup

ENST00000487939.1:n.61dup

ENST00000610634.1:c.-63dup

ENST00000618586.1:n.9dup

Pathogenic

PM2 PM6 PS4_Supporting PVS1

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.40dupA (p.R14Kfs) 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). PVS1: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.4). PM2: Absent in large sequenced populations (PMID 27535533). PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (PMID 10777358) PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID 10777358)

PM2

Absent gnomAD

PM6

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

PVS1

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

Curation History

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