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
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC related information was provided by the message!
  • No CSPEC computed assertion could be determined for this classification!
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.389G>A (p.Arg130Gln)

CA000437

7829 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 844aa93c-ba66-4b09-825a-8e5e0fb0a775
Approved on: 2017-10-18
Published on: 2024-09-23

HGVS expressions

NM_000314.6:c.389G>A
NM_000314.6(PTEN):c.389G>A (p.Arg130Gln)
NC_000010.11:g.87933148G>A
CM000672.2:g.87933148G>A
NC_000010.10:g.89692905G>A
CM000672.1:g.89692905G>A
NC_000010.9:g.89682885G>A
NG_007466.2:g.74710G>A
ENST00000700029.2:c.389G>A
ENST00000710265.1:c.389G>A
ENST00000472832.3:c.389G>A
ENST00000688158.2:n.1124G>A
ENST00000688922.2:c.*219G>A
ENST00000700021.1:c.344G>A
ENST00000700022.1:c.389G>A
ENST00000700029.1:c.223G>A
ENST00000706954.1:c.389G>A
ENST00000706955.1:c.*424G>A
ENST00000686459.1:c.389G>A
ENST00000688158.1:c.*500G>A
ENST00000688308.1:c.389G>A
ENST00000688922.1:c.310G>A
ENST00000693560.1:c.908G>A
ENST00000371953.8:c.389G>A
ENST00000371953.7:c.389G>A
ENST00000498703.1:n.215G>A
ENST00000610634.1:c.287G>A
NM_000314.5:c.389G>A
NM_001304717.2:c.908G>A
NM_001304718.1:c.-362G>A
NM_000314.7:c.389G>A
NM_001304717.5:c.908G>A
NM_001304718.2:c.-362G>A
NM_000314.8:c.389G>A

Pathogenic

Met criteria codes 6
PP2 PM6_Very Strong PM1 PM2 PS4 PS3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.389G>A (p.R130Q) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM6_VS: At least four assumed de novo observations in a patient with the disease and no family history. (PMID 22595938, PMID 22327138, internal laboratory contributor(s) SCV000222111.11) PS3: Phosphatase activity <50% of wild type (PMID 10866302) PS4: Probands with phenotype specificity score of 4-15.5 (PMID 26798346, PMID 17526801, PMID 23335809, PMID 22266152) PM1: Located at a residue within a catalytic motif as defined by the ClinGen PTEN Expert Panel. PM2: Absent in large sequenced populations (PMID 27535533). 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.
Met criteria codes
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6_Very Strong
Needs to be Very Strong level, but not currently an option in the VCI.
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
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
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