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]
  • 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_000314.8(PTEN):c.1171C>T (p.Pro391Ser)

CA000118

187673 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 2353f24f-8466-46ea-838d-a36a749f6a49
Approved on: 2025-12-05
Published on: 2025-12-17

HGVS expressions

NM_000314.8:c.1171C>T
NM_000314.8(PTEN):c.1171C>T (p.Pro391Ser)
NC_000010.11:g.87965431C>T
CM000672.2:g.87965431C>T
NC_000010.10:g.89725188C>T
CM000672.1:g.89725188C>T
NC_000010.9:g.89715168C>T
NG_007466.2:g.106993C>T
ENST00000700029.2:c.1264C>T
ENST00000710265.1:c.*200C>T
ENST00000688158.2:n.1906C>T
ENST00000688922.2:c.*1001C>T
ENST00000700021.1:c.1126C>T
ENST00000700022.1:c.*510C>T
ENST00000700023.1:n.2329C>T
ENST00000700024.1:n.2563C>T
ENST00000706954.1:c.1171C>T
ENST00000706955.1:c.*1206C>T
ENST00000686459.1:c.*757C>T
ENST00000688158.1:c.*1282C>T
ENST00000688308.1:c.1171C>T
ENST00000688922.1:c.1092C>T
ENST00000693560.1:c.1690C>T
ENST00000371953.8:c.1171C>T
ENST00000371953.7:c.1171C>T
NM_000314.5:c.1171C>T
NM_000314.6:c.1171C>T
NM_001304717.2:c.1690C>T
NM_001304718.1:c.580C>T
NM_000314.7:c.1171C>T
NM_001304717.5:c.1690C>T
NM_001304718.2:c.580C>T
More

Uncertain Significance

Met criteria codes 4
PP2 PM2 BS3 BP5
Not Met criteria codes 22
PS4 PS2 PS1 PS3 PP4 PP1 PP3 PM5 PM1 PM4 PM3 PM6 BA1 BS2 BS4 BS1 PVS1 BP7 BP3 BP2 BP1 BP4

Evidence Links 0

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.1171C>T (p.Pro391Ser) PTEN c.1171C>T (p.Pro391Ser) is currently classified as a variant of uncertain significance 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). PM2: Present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (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. BS3: Missense variants with both lipid phosphatase activity AND results from a second assay appropriate to the protein domain demonstrating no statistically significant difference from wild type. (PMID 30993208, 29785012, 29706350) BS4_P: Lack of segregation in affected members of one family. (PMIDS: 28250423‚ 29706350‚ 29785012‚ 30993208‚ 32442409;internal laboratory contributor(s): SCV000218278.9,SCV000222170.9 and SCV000645550.8)
Met criteria codes
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
BS3
Phosphatase activity, stability, pAKT, and subcellular localization similar to WT
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
PS4
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
PS1
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
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
PM5
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
PM3
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
BA1
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
BS1
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
BP7
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
BP2
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
Curation History
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