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]

Variant: NM_000314.8(PTEN):c.634+5G>A

CA10603167

280031 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: e4a43d81-7929-4331-98f2-19cbf83ba970
Approved on: 2023-12-01
Published on: 2023-12-18

HGVS expressions

NM_000314.8:c.634+5G>A
NM_000314.8(PTEN):c.634+5G>A
NC_000010.11:g.87952264G>A
CM000672.2:g.87952264G>A
NC_000010.10:g.89712021G>A
CM000672.1:g.89712021G>A
NC_000010.9:g.89702001G>A
NG_007466.2:g.93826G>A
ENST00000686459.1:c.*220+5G>A
ENST00000688158.1:c.*745+5G>A
ENST00000688308.1:c.634+5G>A
ENST00000688922.1:c.555+5G>A
ENST00000693560.1:c.1153+5G>A
ENST00000371953.8:c.634+5G>A
ENST00000371953.7:c.634+5G>A
ENST00000472832.2:c.61+5G>A
NM_000314.5:c.634+5G>A
NM_000314.6:c.634+5G>A
NM_001304717.2:c.1153+5G>A
NM_001304718.1:c.43+5G>A
NM_000314.7:c.634+5G>A
NM_001304717.5:c.1153+5G>A
NM_001304718.2:c.43+5G>A
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Pathogenic

Met criteria codes 3
PS3 PM2_Supporting PM6_Strong
Not Met criteria codes 8
PS2 BA1 PM5 PP3 PP2 BS1 BP4 BP1

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 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
NM_000314.8(PTEN):c.634+5G>A 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 3.0.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM6_S: one proband with presumed de novo occurrence (maternity/paternity not confirmed) for a patient with highly specific phenotype (PMID:18080326). PS3: assay shows impact on splicing. (PMID:18080326). PM2_P: Absent in large sequenced populations (gnomAD).
Met criteria codes
PS3
Splicing defect causes exon 6 skipping (PMID: 18080326)
PM2_Supporting
Absent in gnomAD
PM6_Strong
One proband with presumed de novo occurrence (maternity/paternity not confirmed) for a patient with highly specific phenotype. (PMID:18080326. RNA was analyzed from peripheral lymphoblasts for patient and both parents de novo but parentage not confirmed. Proband's phenotypes meet PS4 criteria, which upgrades PM6 to PM6_S per PTEN specification)
Not Met criteria codes
PS2
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
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No REVEL data found
PP2
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
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
Curation History
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