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]
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  • See Evidence submitted by expert panel for details.

Variant: NM_000314.7(PTEN):c.802-2del

CA10632766

301423 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 52ec80f5-412f-477c-9d53-4565fcac6821
Approved on: 2020-03-23
Published on: 2020-03-26

HGVS expressions

NM_000314.7:c.802-2del
NM_000314.7(PTEN):c.802-2del
NC_000010.11:g.87960892del
CM000672.2:g.87960892del
NC_000010.10:g.89720649del
CM000672.1:g.89720649del
NC_000010.9:g.89710629del
NG_007466.2:g.102454del
NM_000314.5:c.802-2del
NM_000314.6:c.802-2del
NM_001304717.2:c.1321-2del
NM_001304718.1:c.211-2del
NM_001304717.5:c.1321-2del
NM_001304718.2:c.211-2del
NM_000314.8:c.802-2del
ENST00000371953.7:c.802-2del
ENST00000472832.2:n.229-2del

Likely Pathogenic

Met criteria codes 2
PM2 PVS1
Not Met criteria codes 20
PS1 PS3 PS4 PS2 PP2 PP3 PP1 PM5 PM4 PM1 PM6 BA1 BS2 BS1 BS3 BS4 BP4 BP2 BP7 BP5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.802-2del (IVS7-2del) 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
Met criteria codes
PM2
Variant is absent in population databases.
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
PS3
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
PS2
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
The in silico tools of MaxEnt, NNS, and HSF all have values of -100%. No new cryptic site is predicted and there are no nearby AG's noted in UCSC.
PP1
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
PM4
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
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
BS1
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
BS4
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
BP2
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
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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