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_000314.8(PTEN):c.801G>T (p.Lys267Asn)

CA377485115

536549 (ClinVar)

Gene: PTEN (HGNC:5728)
Condition: PTEN hamartoma tumor syndrome (MONDO:0017623)
Inheritance Mode: Autosomal dominant inheritance
UUID: 5c1f44d0-ab30-4090-8d98-dfaf2d2fd444
Approved on: 2025-12-05
Published on: 2025-12-17

HGVS expressions

NM_000314.8(PTEN):c.801G>T (p.Lys267Asn)
NM_000314.8:c.801G>T
NC_000010.11:g.87958019G>T
CM000672.2:g.87958019G>T
NC_000010.10:g.89717776G>T
CM000672.1:g.89717776G>T
NC_000010.9:g.89707756G>T
NG_007466.2:g.99581G>T
ENST00000700029.2:c.801G>T
ENST00000710265.1:c.801G>T
ENST00000472832.3:c.801G>T
ENST00000688158.2:n.1536G>T
ENST00000688922.2:c.*631G>T
ENST00000700021.1:c.756G>T
ENST00000700022.1:c.*140G>T
ENST00000700023.1:n.1959G>T
ENST00000700024.1:n.2193G>T
ENST00000700025.1:n.1570G>T
ENST00000700026.1:n.438G>T
ENST00000700029.1:c.635G>T
ENST00000706954.1:c.801G>T
ENST00000706955.1:c.*836G>T
ENST00000686459.1:c.*387G>T
ENST00000688158.1:c.*912G>T
ENST00000688308.1:c.801G>T
ENST00000688922.1:c.722G>T
ENST00000693560.1:c.1320G>T
ENST00000371953.8:c.801G>T
ENST00000371953.7:c.801G>T
ENST00000472832.2:c.228G>T
NM_000314.5:c.801G>T
NM_000314.6:c.801G>T
NM_001304717.2:c.1320G>T
NM_001304718.1:c.210G>T
NM_000314.7:c.801G>T
NM_001304717.5:c.1320G>T
NM_001304718.2:c.210G>T
More

Pathogenic

Met criteria codes 3
PM2 PM6_Strong PS3
Not Met criteria codes 2
PP3 PS4

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.801G>T (p.Lys267Asn) 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). PS3: RNA, mini-gene, or other assay shows impact on splicing. (internal laboratory contributor(s)) PM6_S: One proband with presumed de novo occurrence (maternity/paternity not confirmed) for a patient with highly specific phenotype. (PMID: 30528446) PM2_Supporting: Absent in large sequenced populations (PMID 27535533).
Met criteria codes
PM2
Variant absent from gnomADv4
PM6_Strong
6mo female with HC +2.9SD, with facial dysmorphism, DD/ID, vascular malformations and abnormal findings on MRI including enlarged perivascular spaces and short and thin corpus callosum.
PS3
RNA data shared by Ambry Genetics shows exon 7 skipping, r.635_801del167 (p.N212RFS*30) Allele specific expression is consistent with complete splice impact
Not Met criteria codes
PP3
REVEL score 0.62 – PP3 not met
PS4
2 patients shared by Gene DX do not quite meet weight
Curation History
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