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.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: 2025-12-05
Published on: 2025-12-17

HGVS expressions

NM_000314.8:c.802-2del
NM_000314.8(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
ENST00000700029.2:c.895-2del
ENST00000710265.1:c.802-2del
ENST00000472832.3:c.802-2del
ENST00000688158.2:n.1537-2del
ENST00000688922.2:c.*632-2del
ENST00000700021.1:c.757-2del
ENST00000700022.1:c.*141-2del
ENST00000700023.1:n.1960-2del
ENST00000700024.1:n.2194-2del
ENST00000700025.1:n.1571-2del
ENST00000700026.1:n.439-2del
ENST00000700029.1:c.729-2del
ENST00000706954.1:c.802-2del
ENST00000706955.1:c.*837-2del
ENST00000686459.1:c.*388-2del
ENST00000688158.1:c.*913-2del
ENST00000688308.1:c.802-2del
ENST00000688922.1:c.723-2del
ENST00000693560.1:c.1321-2del
ENST00000371953.8:c.802-2del
ENST00000371953.7:c.802-2del
ENST00000472832.2:c.229-2del
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_000314.7:c.802-2del
NM_001304717.5:c.1321-2del
NM_001304718.2:c.211-2del
More

Pathogenic

Met criteria codes 3
PVS1_Strong PS1 PM2
Not Met criteria codes 23
PS2 PS4 PS3 PP4 PP1 PP3 PP2 PM6 PM1 PM3 PM4 PM5 BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1

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.802-2del (IVS7-2del) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant mannerusing modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.1.0). 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 gnomAD v2 and v4 PS1:Same amino acid change as a previously established pathogenic variant PTEN c.802-2A>T
Met criteria codes
PVS1_Strong
changes the A > T at the -2 position, (in-frame but truncated/altered region is critical to protein function).
PS1
PTEN c.802-2A>T (similar Splice AI predictions)
PM2
PM2_P: Absent in gnomAD (v2 and v4)
Not Met criteria codes
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
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
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. Splice AI: cannot also apply PP3 Acceptor Loss: 1.0 in-frame exon 8 skipping: r.803_1027del (p.Asp268_Lys342del) 3’NMD-escaping Acceptor Gain: 0.9 r.802_844del p.(Lys269GlnfsTer8) NMD-prone
PP2
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
PM1
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
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
BS3
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
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
BP4
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
Curation History
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