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]
Link to SEPIO compliant JSON-LD document
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.170T>G (p.Leu57Trp)

CA000131

185713 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: d0edcf69-04fa-4771-afb0-a49f8aab9ead

HGVS expressions

NM_000314.6:c.170T>G
NM_000314.6(PTEN):c.170T>G (p.Leu57Trp)
ENST00000371953.8:c.170T>G
ENST00000371953.7:c.170T>G
ENST00000610634.1:c.68T>G
NM_000314.5:c.170T>G
NM_001304717.2:c.689T>G
NM_001304718.1:c.-541-5528T>G
NM_000314.7:c.170T>G
NM_001304717.5:c.689T>G
NM_001304718.2:c.-541-5528T>G
NM_000314.8:c.170T>G
NC_000010.11:g.87925518T>G
CM000672.2:g.87925518T>G
NC_000010.10:g.89685275T>G
CM000672.1:g.89685275T>G
NC_000010.9:g.89675255T>G
NG_007466.2:g.67080T>G

Likely Pathogenic

Met criteria codes 3
PS3 PP2 PM2
Not Met criteria codes 23
PVS1 BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP1 BP4 PS2 PS4 PS1 PP4 PP1 PP3 PM3 PM1 PM4 PM5 PM6

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.170T>G (p.Leu57Trp) 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 9256433, 29706350) PM2: Absent in large sequenced populations 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.
Met criteria codes
PS3
Score -4.86, high-confidence, truncation-like PubMed:29706350
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
Absent gnomAD
Not Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
Absent gnomAD
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
Absent gnomAD
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
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
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2021-04-29
Published on: 2021-04-29
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