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_000314.6(PTEN):c.696delA (p.Arg233Aspfs)

CA000548

7822 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: b5898872-dd1b-462b-9884-a69944868912
Approved on: 2023-06-14
Published on: 2023-10-19

HGVS expressions

NM_000314.6:c.696delA
NM_000314.6(PTEN):c.696delA (p.Arg233Aspfs)
NC_000010.11:g.87957914del
CM000672.2:g.87957914del
NC_000010.10:g.89717671del
CM000672.1:g.89717671del
NC_000010.9:g.89707651del
NG_007466.2:g.99476del
ENST00000686459.1:c.*282del
ENST00000688158.1:c.*807del
ENST00000688308.1:c.696del
ENST00000688922.1:c.617del
ENST00000693560.1:c.1215del
ENST00000371953.8:c.696del
ENST00000371953.7:c.696del
ENST00000472832.2:c.123del
NM_000314.5:c.696del
NM_000314.6:c.696del
NM_001304717.2:c.1215del
NM_001304718.1:c.105del
NM_000314.7:c.696del
NM_001304717.5:c.1215del
NM_001304718.2:c.105del
NM_000314.8:c.696del
NM_000314.8(PTEN):c.696del (p.Arg233fs)
More

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1
Not Met criteria codes 24
BS1 BS3 BS4 BS2 BP3 BP1 BP4 BP2 BP7 BP5 PS1 PS3 PS2 PS4 BA1 PP2 PP3 PP4 PP1 PM6 PM1 PM4 PM5 PM3

Evidence Links 1

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.696del (p.Arg233AspfsTer23) variant meets criteria to be classified as likely 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). PVS1: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.8). PM2_P: Absent in large sequenced populations in the gnomAD cohort (PMID:27535533).
Met criteria codes
PM2_Supporting
Absent in large sequenced populations in the gnomAD cohort (PMID:27535533).
PVS1
Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.8).
Not Met criteria codes
BS1
Absent in gnomAD
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
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
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Patient G116 (age 74) had anemia and hypoalbuminemia. Gastroscopy and colonoscopy revealed juvenile polyps throughout digestive tract. Diagnosis of JPC. Laryngeal cancer diagnosed 2 years prior (++ tobacco and etoh hx). Thyroid nodule found but unsure if treatment related (radiation therapy). Not enough clinical information to classify as PP4. PubMed:9425889
BA1
Absent in gnomAD
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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