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.359C>A (p.Ala120Glu)

CA377482264

428222 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: e0e01473-5fd0-4b46-8e9b-df1e717121e1
Approved on: 2024-04-05
Published on: 2024-04-10

HGVS expressions

NM_000314.8:c.359C>A
NM_000314.8(PTEN):c.359C>A (p.Ala120Glu)
NC_000010.11:g.87933118C>A
CM000672.2:g.87933118C>A
NC_000010.10:g.89692875C>A
CM000672.1:g.89692875C>A
NC_000010.9:g.89682855C>A
NG_007466.2:g.74680C>A
ENST00000700029.2:c.359C>A
ENST00000710265.1:c.359C>A
ENST00000472832.3:c.359C>A
ENST00000688158.2:n.1094C>A
ENST00000688922.2:c.*189C>A
ENST00000700021.1:c.314C>A
ENST00000700022.1:c.359C>A
ENST00000700029.1:c.193C>A
ENST00000706954.1:c.359C>A
ENST00000706955.1:c.*394C>A
ENST00000686459.1:c.359C>A
ENST00000688158.1:c.*470C>A
ENST00000688308.1:c.359C>A
ENST00000688922.1:c.280C>A
ENST00000693560.1:c.878C>A
ENST00000371953.8:c.359C>A
ENST00000371953.7:c.359C>A
ENST00000498703.1:n.185C>A
ENST00000610634.1:c.257C>A
NM_000314.5:c.359C>A
NM_000314.6:c.359C>A
NM_001304717.2:c.878C>A
NM_001304718.1:c.-392C>A
NM_000314.7:c.359C>A
NM_001304717.5:c.878C>A
NM_001304718.2:c.-392C>A
More

Uncertain Significance

Met criteria codes 4
PS3_Moderate PM2_Supporting PP3 PP2
Not Met criteria codes 7
PM1 PM5 BS3 BS1 PS4 PS1 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
NM_000314.8(PTEN):c.359C>A (p.Ala120Glu) is currently classified as a variant of uncertain significance 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). PS3_M: Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -2.09 (<= -1.11) on a high throughput phosphatase assay (PMID:29706350). PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. PP3: REVEL score > 0.7 (score of this variant = 0.901). PM2_P: Absent in gnomAD.
Met criteria codes
PS3_Moderate
Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -2.09 (<= -1.11) on a high throughput phosphatase assay (PMID:29706350).
PM2_Supporting
Absent in gnomAD.
PP3
REVEL score > 0.7 (score of this variant = 0.901).
PP2
PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Not Met criteria codes
PM1
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
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
PS4
0.5 points towards PS4
PS1
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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