Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.407G>A (p.Cys136Tyr)

CA000451

189406 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 11de4e4a-dc77-4323-92c5-151d4868419d
Approved on: 2017-10-18
Published on: 2018-12-10

HGVS expressions

NM_000314.6:c.407G>A
NM_000314.6(PTEN):c.407G>A (p.Cys136Tyr)
NC_000010.11:g.87933166G>A
CM000672.2:g.87933166G>A
NC_000010.10:g.89692923G>A
CM000672.1:g.89692923G>A
NC_000010.9:g.89682903G>A
NG_007466.2:g.74728G>A
NM_000314.5:c.407G>A
NM_001304717.2:c.926G>A
NM_001304718.1:c.-344G>A
NM_000314.7:c.407G>A
NM_001304717.5:c.926G>A
NM_001304718.2:c.-344G>A
ENST00000371953.7:c.407G>A
ENST00000498703.1:n.233G>A
ENST00000610634.1:c.305G>A
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Pathogenic

Met criteria codes 5
PS2 PS3 PP2 PM2 PS4_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.407G>A (p.C136Y) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). 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) SCV000222113.9) PS3: Phosphatase activity <50% of wild-type OR RNA, mini-gene, or other assay shows impact on splicing. (PMID 10866302) 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. PS4_P: Probands with specificity score of 1-1.5. (PMID 9735393, internal laboratory contributor(s) SCV000222113.9)
Met criteria codes
PS2
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
PM2
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
Curation History
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