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_000314.7(PTEN):c.114T>G (p.Pro38=)

CA000116

184068 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: a06a1116-f26c-4129-8a43-c1ecbda9bc38
Approved on: 2024-12-06
Published on: 2024-12-16

HGVS expressions

NM_000314.7:c.114T>G
NM_000314.7(PTEN):c.114T>G (p.Pro38=)
NC_000010.11:g.87894059T>G
CM000672.2:g.87894059T>G
NC_000010.10:g.89653816T>G
CM000672.1:g.89653816T>G
NC_000010.9:g.89643796T>G
NG_007466.2:g.35621T>G
ENST00000700029.2:c.114T>G
ENST00000710265.1:c.114T>G
ENST00000472832.3:c.114T>G
ENST00000688158.2:n.899+13621T>G
ENST00000688922.2:c.114T>G
ENST00000700021.1:c.114T>G
ENST00000700022.1:c.114T>G
ENST00000706954.1:c.114T>G
ENST00000706955.1:c.*149T>G
ENST00000686459.1:c.114T>G
ENST00000688158.1:c.*275+13621T>G
ENST00000688308.1:c.114T>G
ENST00000693560.1:c.633T>G
ENST00000371953.8:c.114T>G
ENST00000371953.7:c.114T>G
ENST00000462694.1:n.116T>G
ENST00000610634.1:c.12T>G
NM_000314.5:c.114T>G
NM_000314.6:c.114T>G
NM_001304717.2:c.633T>G
NM_001304718.1:c.-592T>G
NM_001304717.5:c.633T>G
NM_001304718.2:c.-592T>G
NM_000314.8:c.114T>G
More

Likely Benign

Met criteria codes 2
BS3 BP7
Not Met criteria codes 24
BS1 BS4 BS2 BP5 BP3 BP4 BP1 BP2 PS3 PS1 PS2 PS4 PP3 PP2 PP4 PP1 PM1 PM4 PM5 PM3 PM2 PM6 PVS1 BA1

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.114T>G (p.Pro38=) meets criteria to be classified as likely benign 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). BS3: Intronic OR synonymous variant with RNA, mini-gene, or other splicing assay demonstrating no splicing impact. (internal laboratory contributor Accession: SCV000213708.7) BP7: Variant is synonymous (silent) OR intronic and at or beyond +7/-21 and no splicing impact is predicted.
Met criteria codes
BS3
BS3: Intronic OR synonymous variant with RNA, mini-gene, or other splicing assay demonstrating no splicing impact. (internal laboratory contributor Accession: SCV000213708.7)
BP7
BP7: Variant is synonymous (silent) OR intronic and at or beyond +7/-21 and no splicing impact is predicted.
Not Met criteria codes
BS1
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
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
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
Splicing impact predicted by some tools - CONFLICTING. NNsplice no impact, MES no prediction, HSF potential cryptic site predicted.
BP1
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
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
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
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
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
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
3/251,004 alleles global
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
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
Curation History
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