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_000314.7(PTEN):c.492+1G>T

CA377482840

427619 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 5c3ae893-8941-4e60-92cd-ad0a39dcde67
Approved on: 2024-04-10
Published on: 2024-04-10

HGVS expressions

NM_000314.7:c.492+1G>T
NM_000314.7(PTEN):c.492+1G>T
NC_000010.11:g.87933252G>T
CM000672.2:g.87933252G>T
NC_000010.10:g.89693009G>T
CM000672.1:g.89693009G>T
NC_000010.9:g.89682989G>T
NG_007466.2:g.74814G>T
ENST00000700029.2:c.492+1G>T
ENST00000710265.1:c.492+1G>T
ENST00000472832.3:c.492+1G>T
ENST00000688158.2:n.1227+1G>T
ENST00000688922.2:c.*322+1G>T
ENST00000700021.1:c.447+1G>T
ENST00000700022.1:c.492+1G>T
ENST00000700029.1:c.326+1G>T
ENST00000706954.1:c.492+1G>T
ENST00000706955.1:c.*527+1G>T
ENST00000686459.1:c.492+1G>T
ENST00000688158.1:c.*603+1G>T
ENST00000688308.1:c.492+1G>T
ENST00000688922.1:c.413+1G>T
ENST00000693560.1:c.1011+1G>T
ENST00000371953.8:c.492+1G>T
ENST00000371953.7:c.492+1G>T
ENST00000498703.1:n.319G>T
ENST00000610634.1:c.390+1G>T
NM_000314.5:c.492+1G>T
NM_000314.6:c.492+1G>T
NM_001304717.2:c.1011+1G>T
NM_001304718.1:c.-259+1G>T
NM_001304717.5:c.1011+1G>T
NM_001304718.2:c.-259+1G>T
NM_000314.8:c.492+1G>T
More

Pathogenic

Met criteria codes 4
PVS1 PM2_Supporting PM6 PS4_Supporting
Not Met criteria codes 21
PS2 PS3 PS1 BP2 BP3 BP4 BP1 BP5 BP7 BA1 PP1 PP3 PP2 PM3 PM1 PM4 PM5 BS2 BS4 BS3 BS1

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.492+1G>T (IVS5+1G>T) meets criteria to be classified as 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: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.4). PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (PMID: 28677221). PM2_P: Absent in large sequenced populations. PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (internal laboratory contributor).
Met criteria codes
PVS1
Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5' to c.1121 (NM_000314.4).
PM2_Supporting
Absent in large sequenced populations (PMID 27535533).
PM6
Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (internal laboratory contributor)
PS4_Supporting
Proband(s) with phenotype specificity score of 1-1.5. (PMID: 28677221)
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
PMID 28677221: RNA analysis shows Exon 5 skipping and results in a frameshift in the PTEN protein at valine 85 and terminates after 13 amino acids. Supports PVS1.
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
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
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
BA1
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
Noting that MaxEnt = -100%; HSF = predicts a broken donor site and creation of new donor site; NNS = -100%
PP2
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
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
Curation History
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