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]

Variant: NM_000314.8(PTEN):c.113C>A (p.Pro38His)

CA377784500

1012092 (ClinVar)

Gene: PTEN (HGNC:5728)

Condition: PTEN hamartoma tumor syndrome (MONDO:0017623)

Inheritance Mode: Autosomal dominant inheritance

UUID: fdcde17f-877a-4da6-8a12-e65ce252cbfa

Approved on: 2026-06-16

Published on: 2026-06-26

HGVS expressions

NM_000314.8(PTEN):c.113C>A (p.Pro38His)

NM_000314.8:c.113C>A

NC_000010.11:g.87894058C>A

CM000672.2:g.87894058C>A

NC_000010.10:g.89653815C>A

CM000672.1:g.89653815C>A

NC_000010.9:g.89643795C>A

NG_007466.2:g.35620C>A

ENST00000700029.2:c.113C>A

ENST00000710265.1:c.113C>A

ENST00000472832.3:c.113C>A

ENST00000688158.2:n.899+13620C>A

ENST00000688922.2:c.113C>A

ENST00000700021.1:c.113C>A

ENST00000700022.1:c.113C>A

ENST00000706954.1:c.113C>A

ENST00000706955.1:c.*148C>A

ENST00000686459.1:c.113C>A

ENST00000688158.1:c.*275+13620C>A

ENST00000688308.1:c.113C>A

ENST00000693560.1:c.632C>A

ENST00000371953.8:c.113C>A

ENST00000371953.7:c.113C>A

ENST00000462694.1:n.115C>A

ENST00000610634.1:c.11C>A

NM_000314.5:c.113C>A

NM_000314.6:c.113C>A

NM_001304717.2:c.632C>A

NM_001304718.1:c.-593C>A

NM_000314.7:c.113C>A

NM_001304717.5:c.632C>A

NM_001304718.2:c.-593C>A

Likely Pathogenic

PS2 PS3_Moderate PM6 PM2_Supporting

PM5

Evidence Links 1

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

PTEN VCEP

PTEN c.113C>A (p.Pro38His) 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 3.2.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PS2: De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. (internal laboratory contributor SCV005079984.1) PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (internal laboratory contributor SCV005079984.1) PS3_moderate: Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = [-4.783403086] (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350). PM2_supporting: Absent in large sequenced populations in the gnomAD v4 cohort. (PMID 27535533).

PS2

De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. (internal laboratory contributor SCV005079984.1)

PS3_Moderate

Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = [-4.783403086] (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350).

Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = [-4.783403086] (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350). PubMed:29706350

PM6

Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (internal laboratory contributor SCV005079984.1)

PM2_Supporting

Absent in large sequenced populations in the gnomAD v4 cohort. (PMID 27535533).

PM5

No other missense change determined to be pathogenic or likely pathogenic (by PTEN VCEP) and with equal or lesser BLOSUM62 score has been recorded in ClinVar.

Curation History

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