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]
x This classification has been retracted/unpublished!
Link to SEPIO compliant JSON-LD document
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.761_765delAAGTA (p.Lys254Argfs)

CA000566

7830 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 3530100c-d75d-44ae-8775-47e7f7f5978c

HGVS expressions

NM_000314.6:c.761_765delAAGTA
NM_000314.6(PTEN):c.761_765delAAGTA (p.Lys254Argfs)
NC_000010.11:g.87957978_87957982del
CM000672.2:g.87957978_87957982del
NC_000010.10:g.89717735_89717739del
CM000672.1:g.89717735_89717739del
NC_000010.9:g.89707715_89707719del
NG_007466.2:g.99540_99544del
ENST00000371953.8:c.760_764del
ENST00000371953.7:c.760_764del
ENST00000472832.2:n.187_191del
NM_000314.5:c.760_764del
NM_000314.6:c.760_764del
NM_001304717.2:c.1279_1283del
NM_001304718.1:c.169_173del
NM_000314.7:c.760_764del
NM_001304717.5:c.1279_1283del
NM_001304718.2:c.169_173del
NM_000314.8:c.760_764del

Likely Pathogenic

Met criteria codes 2
PM2 PVS1
Not Met criteria codes 23
PS2 PS4 PS3 PS1 BP2 BP3 BP1 BP4 BP5 BA1 PP4 PP1 PP2 PP3 PM3 PM1 PM4 PM5 PM6 BS2 BS4 BS3 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.761_765delAAGTA (p.K254Rfs) 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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Only report is somatic.
PS3
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
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
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
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
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
Approved on: 2018-04-06
Published on: 2021-04-29
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