The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: PTEN CSPEC Genes: [ 'PTEN' ] * Message MONDOs: MONDO:0017623 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


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
UUID: d0edcf69-04fa-4771-afb0-a49f8aab9ead
Approved on: 2025-08-01
Published on: 2025-10-08

HGVS expressions

NM_000314.6:c.170T>G
NM_000314.6(PTEN):c.170T>G (p.Leu57Trp)
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
ENST00000700029.2:c.170T>G
ENST00000710265.1:c.170T>G
ENST00000472832.3:c.170T>G
ENST00000688158.2:n.905T>G
ENST00000688922.2:c.170T>G
ENST00000700021.1:c.165-5528T>G
ENST00000700022.1:c.170T>G
ENST00000700029.1:c.4T>G
ENST00000706954.1:c.170T>G
ENST00000706955.1:c.*205T>G
ENST00000686459.1:c.170T>G
ENST00000688158.1:c.*281T>G
ENST00000688308.1:c.170T>G
ENST00000688922.1:c.39T>G
ENST00000693560.1:c.689T>G
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
More

Likely Pathogenic

Met criteria codes 4
PP2 PP3 PM2_Supporting PS3_Moderate
Not Met criteria codes 22
BA1 PP4 PP1 PVS1 PM3 PM1 PM4 PM5 PM6 BS2 BS4 BS3 BS1 BP2 BP3 BP1 BP4 BP5 BP7 PS2 PS4 PS1

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.1.0

Criteria Specification Approval History
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
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL score of 0.965 in UCSC Genome Browser since no score provided in the VCI
PM2_Supporting
Absent gnomAD
PS3_Moderate
Not Met criteria codes
BA1
Absent gnomAD
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
PVS1
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
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
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
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
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
Curation History
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