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

Variant: NM_000314.6(PTEN):c.884_900del17insG (p.Leu295Argfs)

CA645369469

428274 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: f8132715-4506-41cb-a82b-d722fa440f3d

HGVS expressions

NM_000314.6:c.884_900del17insG
NM_000314.6(PTEN):c.884_900del17insG (p.Leu295Argfs)
NC_000010.11:g.87960976_87960992delinsG
CM000672.2:g.87960976_87960992delinsG
NC_000010.10:g.89720733_89720749delinsG
CM000672.1:g.89720733_89720749delinsG
NC_000010.9:g.89710713_89710729delinsG
NG_007466.2:g.102538_102554delinsG
ENST00000686459.1:c.*470_*486delinsG
ENST00000688158.1:c.*995_*1011delinsG
ENST00000688308.1:c.884_900delinsG
ENST00000688922.1:c.805_821delinsG
ENST00000693560.1:c.1403_1419delinsG
ENST00000371953.8:c.884_900delinsG
ENST00000371953.7:c.884_900delinsG
ENST00000472832.2:c.311_327delinsG
NM_000314.5:c.884_900delinsG
NM_000314.6:c.884_900delinsG
NM_001304717.2:c.1403_1419delinsG
NM_001304718.1:c.293_309delinsG
NM_000314.7:c.884_900delinsG
NM_001304717.5:c.1403_1419delinsG
NM_001304718.2:c.293_309delinsG
NM_000314.8:c.884_900delinsG
NM_000314.8(PTEN):c.884_900delinsG (p.Leu295fs)

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_Supporting
Not Met criteria codes 23
BA1 PP4 PP1 PP2 PP3 PM6 PM3 PM1 PM4 PM5 BS4 BS3 BS1 BS2 BP7 BP2 BP3 BP1 BP4 PS2 PS4 PS3 PS1

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 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
NM_000314.8(PTEN):c.884_900delinsG (p.Leu295ArgfsTer7) variant meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.0.0). 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_000314.8). PM2_P: Absent in large sequenced populations OR present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort (PMID:27535533).
Met criteria codes
PVS1
PVS1: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.8).
PM2_Supporting
PM2_Supporting: Absent in large sequenced populations OR present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (PMID 27535533).
Not Met criteria codes
BA1
Absent in 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
PM6
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
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 in gnomAD
BS2
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
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
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-06-14
Published on: 2023-10-19
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