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
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_000314.8(PTEN):c.165-1G>A

CA000129

187590 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 8c8c1292-baf8-4fcd-abbf-e22a7793a5dd
Approved on: 2024-04-05
Published on: 2024-04-10

HGVS expressions

NM_000314.8:c.165-1G>A
NM_000314.8(PTEN):c.165-1G>A
NC_000010.11:g.87925512G>A
CM000672.2:g.87925512G>A
NC_000010.10:g.89685269G>A
CM000672.1:g.89685269G>A
NC_000010.9:g.89675249G>A
NG_007466.2:g.67074G>A
ENST00000700029.2:c.165-1G>A
ENST00000710265.1:c.165-1G>A
ENST00000472832.3:c.165-1G>A
ENST00000688158.2:n.900-1G>A
ENST00000688922.2:c.165-1G>A
ENST00000700021.1:c.165-5534G>A
ENST00000700022.1:c.165-1G>A
ENST00000706954.1:c.165-1G>A
ENST00000706955.1:c.*200-1G>A
ENST00000686459.1:c.165-1G>A
ENST00000688158.1:c.*276-1G>A
ENST00000688308.1:c.165-1G>A
ENST00000688922.1:c.34-1G>A
ENST00000693560.1:c.684-1G>A
ENST00000371953.8:c.165-1G>A
ENST00000371953.7:c.165-1G>A
ENST00000610634.1:c.63-1G>A
NM_000314.5:c.165-1G>A
NM_000314.6:c.165-1G>A
NM_001304717.2:c.684-1G>A
NM_001304718.1:c.-541-5534G>A
NM_000314.7:c.165-1G>A
NM_001304717.5:c.684-1G>A
NM_001304718.2:c.-541-5534G>A
More

Likely Pathogenic

Met criteria codes 3
PVS1_Strong PM2_Supporting PS4_Moderate
Not Met criteria codes 23
BS2 BS4 BS3 BS1 BP7 BP5 BP3 BP2 BP4 BP1 PS1 PS3 PS2 PP4 PP3 PP2 PP1 BA1 PM6 PM5 PM1 PM4 PM3

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
NM_000314.8(PTEN):c.165-1G>A 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 3.1.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PVS1_Strong: in-frame but truncated/altered region is critical to protein function. PM2_P: Absent in large sequenced populations in the gnomAD cohort. (PMID 27535533). PS4_P: Probands with phenotype specificity score of 1-1.5. (PMID: 21659347).
Met criteria codes
PVS1_Strong
PVS1_S (CDS3 acceptor site): RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (internal laboratory contributor).
PM2_Supporting
Absent in large sequenced populations in the gnomAD cohort. (PMID 27535533).
PS4_Moderate
Probands with phenotype specificity score of 2-3.5. (internal laboratory contributor)
Not Met criteria codes
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
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
BP3
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
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
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
PS2
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
PP3
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
PP1
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
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
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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