PTEN c.974T>C, p.Leu325Pro

NM_000314.4:c.974T>C

COSM86052

Classification Summary

Likely Pathogenic

The PTEN L325P variant is classified as Likely Pathogenic based on two Moderate criteria (PS3_moderate from PTEN-specific functional data and PM5) and two Supporting criteria (PM2 and PP3) in accordance with VCEP PTEN guidelines.

Population Frequency

0.0 in 100,000

Rare

ClinVar Classification

Likely Pathogenic

2 publications

REVEL Score

0.922

Likely Pathogenic

COSMIC Recurrence

1 occurrences

No Criteria Applied

Classification Evidence

Very Strong (PVS)

None applied

Strong (PS/BS)

None applied

Moderate (PM/BA)

PS3 PM5

Supporting (PP/BP)

PM2 PP3

ClinVar COSMIC OncoKB JAX-CKB SpliceAI

Created: 2025-05-21T11:40:25.972348

Detailed Information

Genetic Information Clinical Evidence Functional Studies Computational Evidence VCEP Guidelines

Genetic Information

Gene & Transcript Details

Gene

PTEN

Transcript

                                        
                                            NM_000314.8
                                        
                                                    MANE Select

Total Exons

Strand

Forward (+)

Reference Sequence

                                        NC_000010.10
                                    

Alternative Transcripts

ID	Status	Details
NM_000314.7	RefSeq Select	9 exons \| Forward
NM_000314.5	Alternative	9 exons \| Forward
NM_000314.4	Alternative	9 exons \| Forward
NM_000314.3	Alternative	9 exons \| Forward
NM_000314.6	Alternative	9 exons \| Forward

Variant Details

HGVS Notation

NM_000314.4:c.974T>C

Protein Change

L325P

Location

Exon 8 (Exon 8 of 9)

5' Exon Structure (9 total) 3'

Functional Consequence

Loss of Function

Related Variants

ClinVar reports other pathogenic variants at position 325: L325R

Alternate Identifiers

                                    COSM86052
                                

Variant interpretation based on transcript NM_000314.8

Clinical Evidence

Population Frequency

Global Frequency

0.0 in 100,000

Extremely Rare

Global: 0.0%

0.0005%

0.001%

0.01%

0.05%

1%+

ACMG Criteria Applied

PM2

This variant is not present in gnomAD (PM2 criteria applies).

ClinVar 2025-05-21T11:39:07.067727

Classification

2 publications

Likely Pathogenic

Based on 3 submitter reviews in ClinVar

Submitter Breakdown

2 LP

1 VUS

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Publications

2 publications

Show publication details

PMID: 29706350

The c.974T>C (p.L325P) alteration is located in exon 8 (coding exon 8) of the PTEN gene. This alteration results from a T to C substitution at nucleotide position 974, causing the leucine (L) at amino acid position 325 to be replaced by a proline (P). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant was reported in an individual who met clinical criteria for PTEN hamartoma tumor syndrome (Mighell, 2020). This amino acid position is highly conserved in available vertebrate species. In a massively parallel functional assay, this variant demonstrates deficient phosphatase activity (Mighell, 2018). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic.

PMID: 35931053

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 325 of the PTEN protein (p.Leu325Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer (PMID: 35931053). ClinVar contains an entry for this variant (Variation ID: 428231). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PTEN protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Publication Summary:

- **29706350**: This study reports that the c.974T>C (p.L325P) alteration in the PTEN gene is likely pathogenic. The variant was not found in population databases and was observed in an individual meeting clinical criteria for PTEN hamartoma tumor syndrome. Functional assays showed deficient phosphatase activity, and in silico analysis predicted a deleterious effect. - **32442409**: This citation is associated with the classification of the PTEN variant as likely pathogenic, based on clinical testing and functional studies indicating a damaging effect on protein function. - **35931053**: This publication discusses the PTEN variant observed in individuals with breast cancer. Advanced modeling suggests the variant is not expected to disrupt PTEN protein function, leading to its classification as a Variant of Uncertain Significance.

Clinical Statement

This variant has been reported in ClinVar as Likely pathogenic (2 clinical laboratories) and as Uncertain significance (1 clinical laboratories).

COSMIC

COSMIC ID

COSM86052

Recurrence

1 occurrences

PM1 Criteria

Not Applied

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Functional Domain

Cancer Hotspots

Hotspot Status

Not a hotspot

Domain Summary

This variant is not located in a mutational hotspot or critical domain (0 mutations).

Related Variants in This Domain

ClinVar reports other pathogenic variants at position 325: L325R

PM5 criterion applied: Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Functional Studies

Functional Impact

OncoKB JAX-CKB

Summary

The PTEN L325P variant has not been functionally characterized.

Computational Evidence

Pathogenicity Predictions

REVEL Score

0.922

Likely Benign 0.0

Uncertain (Low) 0.2

Uncertain (Med) 0.5

Likely Pathogenic 0.75

REVEL scores ≥ 0.75 are considered strong evidence of pathogenicity (PP3)

Predictor Consensus

Mixed/VUS

PP3 Applied

Yes

Additional Predictors

Pathogenic:

mutationtaster: D metasvm: D metalr: D primateai: D

Benign:

CADD: 5.70

Neutral: Show all

SpliceAI Scores Window: ±500bp

Effect Type	Score	Position
- Acceptor Loss	0.0	120 bp
- Donor Loss	0.01	-152 bp
+ Acceptor Gain	0.01	-129 bp
+ Donor Gain	0.0	52 bp

High impact (≥0.5)

Medium impact (0.2-0.49)

Low impact (<0.2)

VCEP Guidelines

Applied ACMG/AMP Criteria VCEP Guidelines

PVS1

PVS1 (Not Applied) Strength Modified

According to VCEP guidelines: PVS1 requires a null variant predicted to undergo NMD or loss of function per PTEN PVS1 decision tree. The evidence for this variant shows it is a missense change (L325P), not predicted to truncate or affect splicing. Therefore, PVS1 is not applied because the variant is a missense substitution, not a loss-of-function alteration.

PS1

PS1 (Not Applied) Strength Modified

According to VCEP guidelines: PS1 requires the same amino acid change as an established pathogenic variant regardless of nucleotide change. The evidence for this variant shows no other variant results in the same L325P substitution. Therefore, PS1 is not applied.

PS2

PS2 (Not Applied) Strength Modified

According to VCEP guidelines: PS2 requires de novo occurrence with confirmed parental identity. No de novo data are available for this variant. Therefore, PS2 is not applied.

PS3

PS3 (Moderate) Strength Modified

According to PTEN Pre-processing guidelines: the rule/finding for PS3_Moderate is "Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Phosphatase activity ≤ -1.11 per Mighell et al. 2018, PMID: 29706350; pre-processing score -4.4888 < -1.11." The evidence for this variant shows a functional score of -4.4888, meeting the threshold. Therefore, PS3 is applied at Moderate strength because the PTEN-specific functional assay indicates a damaging effect.

PS4

PS4 (Not Applied) Strength Modified

According to VCEP guidelines: PS4 requires an increased prevalence of the variant in affected individuals or a proband specificity score ≥4. No case data or specificity scores are available. Therefore, PS4 is not applied.

PM1

PM1 (Not Applied) Strength Modified

According to VCEP guidelines: PM1 applies when a variant is located in a mutational hotspot or critical domain (residues 90–94, 123–130, 166–168). The evidence for this variant shows position 325 is outside these regions. Therefore, PM1 is not applied.

PM2

PM2 (Supporting) Strength Modified

According to VCEP guidelines: PM2 Supporting requires absence in population databases at <0.00001 allele frequency. The evidence for this variant shows it is absent from gnomAD. Therefore, PM2 is applied at Supporting strength.

PM3

PM3 (Not Applied) Strength Modified

According to VCEP guidelines: PM3 applies to variants observed in trans with a pathogenic PTEN variant. No trans-phase data are available. Therefore, PM3 is not applied.

PM4

PM4 (Not Applied) Strength Modified

According to standard ACMG guidelines: PM4 applies to in-frame insertions/deletions altering protein length. The evidence for this variant shows it is a missense substitution. Therefore, PM4 is not applied.

PM5

PM5 (Moderate)

According to VCEP guidelines: PM5 Moderate requires a novel missense change at a residue where a different missense change determined to be pathogenic has been seen, with BLOSUM62 score requirement. The evidence for this variant shows a previously established pathogenic missense at codon 325. Therefore, PM5 is applied at Moderate strength.

PM6

PM6 (Not Applied) Strength Modified

According to VCEP guidelines: PM6 applies to presumed de novo variants without confirmed parentage. No de novo or parental data are available. Therefore, PM6 is not applied.

PP1

PP1 (Not Applied) Strength Modified

According to VCEP guidelines: PP1 requires co-segregation with disease in multiple affected family members. No segregation data are available. Therefore, PP1 is not applied.

PP2

PP2 (Not Applied) Strength Modified

According to standard ACMG guidelines: PP2 applies to missense variants in genes with low benign variation and common missense disease mechanism. PTEN has multiple benign missense variants reported and no specific constraint data here. Therefore, PP2 is not applied.

PP3

PP3 (Supporting)

According to VCEP guidelines: PP3 Supporting requires REVEL score >0.7 for missense variants. The evidence for this variant shows a REVEL score of 0.92. Therefore, PP3 is applied at Supporting strength.

PP4

PP4 (Not Applied) Strength Modified

According to VCEP guidelines: PP4 applies when patient phenotype is highly specific for PTEN-related disease. No phenotype information is provided. Therefore, PP4 is not applied.

PP5

PP5 (Not Applied) Strength Modified

According to standard ACMG guidelines: PP5 applies when a reputable source reports variant as pathogenic but evidence is unavailable. Although ClinVar lists this variant as Likely pathogenic by two labs, VCEP guidelines discourage PP5 use. Therefore, PP5 is not applied.

BA1

BA1 (Not Applied) Strength Modified

According to VCEP guidelines: BA1 Stand-alone requires allele frequency >0.056%. The evidence for this variant shows it is absent from population databases. Therefore, BA1 is not applied.

BS1

BS1 (Not Applied) Strength Modified

According to VCEP guidelines: BS1 Strong requires allele frequency between 0.0043% and 0.056%. The evidence for this variant shows it is absent from population databases. Therefore, BS1 is not applied.

BS2

BS2 (Not Applied) Strength Modified

According to VCEP guidelines: BS2 applies when variant is homozygous in healthy individuals. No such observations exist. Therefore, BS2 is not applied.

BS3

BS3 (Not Applied) Strength Modified

According to VCEP guidelines: BS3 applies when functional studies show no damaging effect. The PTEN functional score indicates damaging effect. Therefore, BS3 is not applied.

BS4

BS4 (Not Applied) Strength Modified

According to VCEP guidelines: BS4 applies to lack of segregation in multiple affected family members. No segregation data are available. Therefore, BS4 is not applied.

BP1

BP1 (Not Applied) Strength Modified

According to standard ACMG guidelines: BP1 applies to missense in genes where only truncating variants cause disease. PTEN disease mechanism includes missense. Therefore, BP1 is not applied.

BP2

BP2 (Not Applied) Strength Modified

According to VCEP guidelines: BP2 applies when observed in trans or cis with other pathogenic variants. No such data. Therefore, BP2 is not applied.

BP3

BP3 (Not Applied) Strength Modified

According to standard ACMG guidelines: BP3 applies to in-frame indels in repetitive regions. The variant is missense. Therefore, BP3 is not applied.

BP4

BP4 (Not Applied) Strength Modified

According to VCEP guidelines: BP4 Supporting requires REVEL <0.5. The evidence for this variant shows REVEL 0.92. Therefore, BP4 is not applied.

BP5

BP5 (Not Applied) Strength Modified

According to VCEP guidelines: BP5 applies when variant found in case with an alternate molecular basis. No such evidence. Therefore, BP5 is not applied.

BP6

BP6 (Not Applied) Strength Modified

According to standard ACMG guidelines: BP6 applies when a reputable source reports variant as benign. No such reports exist. Therefore, BP6 is not applied.

BP7

BP7 (Not Applied) Strength Modified

According to VCEP guidelines: BP7 applies to synonymous or intronic variants with no splicing impact. The variant is missense. Therefore, BP7 is not applied.

LYFE SCIENCES

PTEN c.974T>C, p.Leu325Pro

Classification Summary

Genetic Information

Clinical Evidence

Functional Studies

Computational Evidence

VCEP Guidelines