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.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: 2025-10-03
Published on: 2025-10-27

HGVS expressions

NM_000314.8:c.564T>A
NM_000314.8(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
ENST00000700029.2:c.564T>A
ENST00000710265.1:c.564T>A
ENST00000472832.3:c.564T>A
ENST00000688158.2:n.1299T>A
ENST00000688922.2:c.*394T>A
ENST00000700021.1:c.519T>A
ENST00000700022.1:c.493-5664T>A
ENST00000700023.1:n.1722T>A
ENST00000700024.1:n.1956T>A
ENST00000700025.1:n.1333T>A
ENST00000700029.1:c.398T>A
ENST00000706954.1:c.564T>A
ENST00000706955.1:c.*599T>A
ENST00000686459.1:c.*150T>A
ENST00000688158.1:c.*675T>A
ENST00000688308.1:c.564T>A
ENST00000688922.1:c.485T>A
ENST00000693560.1:c.1083T>A
ENST00000371953.8:c.564T>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_000314.7:c.564T>A
NM_001304717.5:c.1083T>A
NM_001304718.2:c.-28T>A
More

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1
Not Met criteria codes 24
BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP1 BP4 PS1 PS2 PS4 PS3 PP4 PP1 PP2 PP3 PM6 PM5 PM3 PM1 PM4

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.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 v3 (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_P: Absent in gnomad v4.
Met criteria codes
PM2_Supporting
Absent gnomAD v4.
PVS1
Variant predicted to result in nonsense mediated decay (NMD) with truncation variant upstream of NMD cutoff at c.1121 (p.D375) in biologically-relevant transcript NM_000314.8 .
Not Met criteria codes
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
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
PM6
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
Curation History
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.