PTEN

Final classification

Pathogenic

PTEN c.253+1G>A · p.?

PTEN

Gene

PTEN

Transcript

NM_000314.6

HGVS · transcript:coding

NM_000314.6:c.253+1G>A

Consequence

N/A

GRCh38

chr10:87931090 G>A

GRCh37

chr10:89690847 G>A

Basis Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule1 (1 Pathogenic.Very Strong + Pathogenic.Strong >=1) with applied criteria: PVS1 very strong, PS1 strong, PS3 strong, PM2 supporting; maps to Pathogenic. ▾

Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule1 (1 Pathogenic.Very Strong + Pathogenic.Strong >=1) with applied criteria: PVS1 very strong, PS1 strong, PS3 strong, PM2 supporting; maps to Pathogenic.

Classification rationale

PVS1PS1PS3PM2 Pathogenic

PTEN c.253+1G>A

c.253+1G>A is a canonical +1 splice donor variant in PTEN intron 4. Per the PTEN VCEP PVS1 decision tree, canonical GT-AG splice site disruptions at or 5' to p.D375 (c.1121) qualify for PVS1 at very strong strength.¹ Functional characterization in patient-derived lymphoblastoid cells (PMID:28677221) demonstrated that c.253+1G>A causes exon 4 skipping, resulting in a frameshift (p.Ala72Thrfs*5) with predicted NMD. PTEN protein expression was significantly decreased and P-AKT was significantly increased, satisfying PS3 at strong strength per PTEN VCEP specifications.² A different nucleotide substitution at the same position, c.253+1G>T, has been established as pathogenic with complete cosegregation with Cowden disease in family N4 (PMID:9259288). SpliceAI predicts a donor loss delta of 0.99 for c.253+1G>A, indicating impact equal to the known pathogenic variant, satisfying PS1 at strong strength.³ c.253+1G>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, satisfying PM2 at supporting strength (allele frequency <0.001% per PTEN VCEP).⁴ This variant has been reported in ClinVar as Pathogenic by 7 clinical laboratories (ClinVar Variation ID: 7820) and has been observed in somatic cancers (COSMIC, n=8).⁵ Combined classification: PVS1 (very_strong) + PS1 (strong) + PS3 (strong) + PM2 (supporting). Under the ACMG/AMP 2015 combining rules per the PTEN VCEP framework, Rule 1 is satisfied: one very strong criterion (PVS1) plus at least one strong criterion (PS1, PS3) → Pathogenic.⁶

PVS1 + PS1 + PS3 + PM2 → Pathogenic

1 vcep_pvs1_decisiontree_ptencspec ↗

2 PMID:28677221 ↗

3 PMID:9259288 ↗PMID:28677221 ↗spliceai ↗

4 gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

5 clinvar ↗

6 cspec ↗final_classification_framework

Gene diagram · NM_000314.6 · variants mapped to exon structure

PTEN NM_000314.6

Fetching transcript structure from UCSC…

Applied criteria · 4 met · select any tile

Met

Not met

Not assessed

N/A

Strength very strong supporting

Pathogenic evidence

PVS

Benign evidence

—

Rationale

Select a criterion.

Sources

Evidence used

Gaps remaining

Rule

—

Research & evidence

Population frequency · supports pathogenic

gnomAD v4.1

gnomAD v2.1

v4.1

Absent from gnomAD v4.1.

v2.1

Absent from gnomAD v2.1.

🇨🇦 CA

Absent from gnomAD-Canada v1.0.

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v2.1

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD Canada 🇨🇦

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant has been reported in ClinVar as Pathogenic (7 clinical laboratories). (ClinVarID = 7820)

ClinVar ↗

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.99). BayesDel score = 0.317417.

SpliceAI ↗

Functional No data

No calibrated functional assay or RNA evidence was identified for this variant.

OncoKB ↗

COSMIC

Somatic evidence

COSMIC

This variant has previously been reported in somatic cancers (COSMIC; COSV64289910, n = 8 times).

Hotspots

This variant does not lie in a statistically significant cancer hotspot.

COSMIC ↗

Literature · how each cited paper was used

2papers cited

Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & References.

Characterization of cryptic splicing in germline PTEN intronic variants in Cowden syndrome.

PMID 28677221 ↗ · Chen HJ et al. · 2017 Oct CLINVAR · splicing rna

Searched

c.253+1G>A253+1G>Aintron 4exon 4 skipping

Found

c.253+1G>A was characterized in a Cowden syndrome patient. RT-PCR of patient-derived lymphoblastoid cells demonstrated exon 4 skipping resulting in frameshift p.(Ala72Thrfs*5). PTEN protein expression was significantly decreased and P-AKT was significantly increased in the group of intronic variants with splicing alterations. The variant is listed in Table 1 alongside c.253+1G>T, c.253+5G>T, and c.253+5G>A, all causing exon 4 skipping.

Variant

✓ Names this variant — characterised directly

Applied to

→PS1 supports · met →PS3 supports · met →PVS1 supports · met

Why

Provides direct functional evidence for c.253+1G>A: exon 4 skipping confirmed by RNA analysis; decreased PTEN protein and increased P-AKT support damaging effect. Referenced in PVS1 and PS3 assessments.

c.253+1G>A 4 Exon 4 skipping p. (Ala72Thrfs * 5) 1

Location Table 1; Results, paragraph describing exon 4 splice mutations · Context RT-PCR from patient-derived lymphoblastoid cell lines, Western blot for PTEN/P-AKT/P-ERK1/2 protein expression · full text

Germline mutations in the PTEN/MMAC1 gene in patients with Cowden disease.

PMID 9259288 ↗ CLINVAR · functional

Searched

c.253+1G>AG to A253+1intron 4 splice

Found

Reports a splice site mutation at the same nucleotide position: c.253+1G>T (described as 'GT to TT, intron 4, splice site mutation') in family N4 with Cowden disease. The mutation was shown to completely cosegregate with CD in the family. c.253+1G>A was not identified in this paper.

Variant

◇ Residue / gene-level — variant not named

Applied to

→PS1 supports · met

Why

Establishes c.253+1G>T as a pathogenic splicing variant at the same nucleotide position, supporting PS1 application for c.253+1G>A per PTEN VCEP rule.

In family N4 the first nucleotide of intron 4 was changed from G into T causing a mutation in the nearly invariant splice site sequence GU to UU.

Location Table 1, family N4 entry; Results, splice site mutation paragraph · Context Genomic DNA sequencing from lymphocyte DNA of CD patients · full text

Sources & reference links

8Sources

CSpec VCEP

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Triaged references · 7 PMIDs not cited in assessment

16199547 ↗ Splicing in action: assessing disease causing sequence changes. CLINVAR

20600018 ↗ Frequent gastrointestinal polyps and colorectal adenocarcinomas in a prospective series of PTEN mutation carriers. CLINVAR

30311380 ↗ Gene-specific criteria for PTEN variant curation: Recommendations from the ClinGen PTEN Expert Panel. CLINVAR

9467011 ↗ Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation. CLINVAR

9740666 ↗ Mapping an endometrial cancer tumor suppressor gene at 10q25 and development of a bacterial clone contig for the consensus deletion interval. CLINVAR

17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR

28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR