Evidence Repository - Clinical Genome Resources

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

Variant: NM_000314.7(PTEN):c.42G>A (p.Arg14=)

CA16619040

420491 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 9cbc440e-91aa-45a2-bf57-6c217f5bdbc7

HGVS expressions

NM_000314.7:c.42G>A

NM_000314.7(PTEN):c.42G>A (p.Arg14=)

NC_000010.11:g.87864511G>A

CM000672.2:g.87864511G>A

NC_000010.10:g.89624268G>A

CM000672.1:g.89624268G>A

NC_000010.9:g.89614248G>A

NG_007466.2:g.6073G>A

NG_033079.1:g.3927C>T

ENST00000686459.1:c.42G>A

ENST00000688158.1:c.42G>A

ENST00000688308.1:c.42G>A

ENST00000693560.1:c.561G>A

ENST00000371953.8:c.42G>A

ENST00000371953.7:c.42G>A

ENST00000462694.1:n.44G>A

ENST00000487939.1:n.63G>A

ENST00000610634.1:c.-61G>A

ENST00000618586.1:n.11G>A

NM_000314.5:c.42G>A

NM_000314.6:c.42G>A

NM_001304717.2:c.561G>A

NM_001304718.1:c.-664G>A

NM_001304717.5:c.561G>A

NM_001304718.2:c.-664G>A

NM_000314.8:c.42G>A

NM_000314.8(PTEN):c.42G>A (p.Arg14=)

Uncertain Significance

PM2

BP5 BP7 BP4

Evidence Links 0

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.42G>A (p.Arg14=) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM2: Absent in large sequenced populations (PMID 27535533).

PM2

Absent in gnomAD

BP5

GDX1: Middle Eastern F child with features of BBS (obesity, night blindness, mild ID, polydactyly, heart defect) and HOMOZYGOUS PATH BBS7 variant – may be able to count towards BP5 when more co-occurrences become available. Father POSITIVE for PTEN variant, healthy, large family, no cancers/other hx concerning for PTEN.

BP7

Synonymous. PhyloP score is 5.94; nucleotide is highly conserved.

BP4

Intron 1 SDS not predicted by in silico tools

Approved on: 2021-06-04

Published on: 2022-09-30

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