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

Variant: NM_000314.6(PTEN):c.-861G>T

CA000612

7845 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: b7d1c7bd-f00c-4e8d-a6a5-e83fed03f5df
Approved on: 2021-06-04
Published on: 2022-09-30

HGVS expressions

NM_000314.6:c.-861G>T
NM_000314.6(PTEN):c.-861G>T
NC_000010.11:g.87863608G>T
CM000672.2:g.87863608G>T
NC_000010.10:g.89623365G>T
CM000672.1:g.89623365G>T
NC_000010.9:g.89613345G>T
NG_007466.2:g.5171G>T
NG_033079.1:g.4830C>A
ENST00000688308.1:c.-17+495G>T
ENST00000692337.1:n.50G>T
ENST00000693560.1:c.-342G>T
ENST00000371953.7:c.-862G>T
ENST00000610634.1:c.-964G>T
NM_000314.5:c.-861G>T
NM_001304717.2:c.-342G>T
NM_001304718.1:c.-1566G>T
NM_000314.7(PTEN):c.-861G>T

Uncertain Significance

Met criteria codes 1
PM2
Not Met criteria codes 25
PM6 PM3 PM1 PM4 PM5 BA1 BS4 BS1 BS3 BS2 PS2 PS4 PS3 PS1 BP5 BP7 BP2 BP3 BP1 BP4 PVS1 PP4 PP1 PP2 PP3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.-861G>T (NC_000010.10:g.89623365G>T) 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: Absent in large sequenced populations (PMID 27535533).
Met criteria codes
PM2
Absent in gnomAD V3
Not Met criteria codes
PM6
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
BA1
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
BS3
Reduced promoter activity (to ~50% compared to wild type) in luciferase assay and reduced (20-40%) of wild type protein expression by Western blotting. PubMed:17847000
BS2
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
PS3
Criteria not met based on review of functional data by expert panel.
Reduced promoter activity (to ~50% compared to wild type) in luciferase assay and reduced (20-40%) of wild type protein expression by Western blotting. PubMed:17847000
PS1
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
PVS1
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
PP2
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
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