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_000314.7(PTEN):c.564T>A (p.Tyr188Ter)

CA000521

7831 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 3026a8af-72dd-459e-be90-922c578fc8f6
Approved on: 2021-04-20
Published on: 2021-04-20

HGVS expressions

NM_000314.7:c.564T>A
NM_000314.7(PTEN):c.564T>A (p.Tyr188Ter)
NC_000010.11:g.87952189T>A
CM000672.2:g.87952189T>A
NC_000010.10:g.89711946T>A
CM000672.1:g.89711946T>A
NC_000010.9:g.89701926T>A
NG_007466.2:g.93751T>A
ENST00000371953.7:c.564T>A
NM_000314.5:c.564T>A
NM_000314.6:c.564T>A
NM_001304717.2:c.1083T>A
NM_001304718.1:c.-28T>A
NM_001304717.5:c.1083T>A
NM_001304718.2:c.-28T>A
NM_000314.8:c.564T>A

Likely Pathogenic

Met criteria codes 2
PM2 PVS1
Not Met criteria codes 24
PS1 PS2 PS4 PS3 PP4 PP1 PP2 PP3 PM5 PM3 PM1 PM4 PM6 BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP1 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.564T>A (p.Y188X) 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). PVS1: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.4). PM2: Absent in large sequenced populations (PMID 27535533).
Met criteria codes
PM2
Absent gnomAD
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
PS1
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
Matreyek: Low abundance class (score = -0.051127127541205); Mighell: truncation-like range (score = -2.540449404); Cannot apply this with PVS1.
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
PM5
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
PM6
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
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.