PTENc.210-2A>GLikely pathogenic

Print report

Variant interpretation report

PTEN c.210-2A>G, p.?

NM_000314.8:c.210-2A>G NP_000305.3:p.? View identifiers

Classification

Likely pathogenic

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is likely pathogenic. Select a step to read what it means.

Likely pathogenic.A likely pathogenic classification under the recorded framework.

In plain language

Gene-level background from the recorded interpretation.

About PTEN

No gene-level summary was recorded for this case.

Key facts

Evidence used: 1 very strong (pathogenic) · 1 supporting (pathogenic)
Expert rules: ClinGen PTEN VCEP v3.2.0
Other laboratories (ClinVar): 2 Likely pathogenic · 1 Pathogenic
Pipeline record: 9 Jun 2026

Evidence considered

View criteria

Applied evidence criteria

PVS1 (very strong): NM_000314.8:c.210-2A>G is a canonical splice acceptor site variant (AG to GG at the -2 position of intron 3). Per the PTEN VCEP PVS1 decision tree, canonical GT-AG splice site disruptions that are predicted to cause exon skipping with reading frame disruption and nonsense-mediated decay (NMD) are assigned PVS1 when the disruption is at or 5' to p.D375 (c.1121) in the biologically-relevant transcript NM_000314.8. This variant is at c.210 (intron 3 acceptor), well 5' of the c.1121 threshold; exon 4 skipping is predicted to cause a frameshift (p.Ala72Thrfs*5) with premature termination and NMD. Related variants at the same splice junction (c.210-1G>A) have been experimentally confirmed to cause exon 4 skipping (PMID:28677221).
PM2 (supporting): The variant is absent from gnomAD v2.1 and v4.1 (allele frequency = 0.0000). Per the PTEN VCEP, PM2_Supporting applies when the variant is present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. This variant meets that threshold as it is completely absent from all population databases examined.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.

01The reasoning

How it was classified

The recorded framework is ClinGen PTEN VCEP v3.2.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 2 Benign evidence criteria: 0

Pathogenic criteria applied · 2

PVS1Very strong

PVS1 · very strong

NM_000314.8:c.210-2A>G is a canonical splice acceptor site variant (AG to GG at the -2 position of intron 3). Per the PTEN VCEP PVS1 decision tree, canonical GT-AG splice site disruptions that are predicted to cause exon skipping with reading frame disruption and nonsense-mediated decay (NMD) are assigned PVS1 when the disruption is at or 5' to p.D375 (c.1121) in the biologically-relevant transcript NM_000314.8. This variant is at c.210 (intron 3 acceptor), well 5' of the c.1121 threshold; exon 4 skipping is predicted to cause a frameshift (p.Ala72Thrfs*5) with premature termination and NMD. Related variants at the same splice junction (c.210-1G>A) have been experimentally confirmed to cause exon 4 skipping (PMID:28677221).

PM2Supporting

PM2 · supporting

The variant is absent from gnomAD v2.1 and v4.1 (allele frequency = 0.0000). Per the PTEN VCEP, PM2_Supporting applies when the variant is present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. This variant meets that threshold as it is completely absent from all population databases examined.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Likely pathogenic

Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule20 (1 Pathogenic.Very Strong + 1 Pathogenic.Supporting) with applied criteria: PVS1 very strong, PM2 supporting; maps to Likely Pathogenic.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1

gnomAD v2.1

Population frequency

Not recorded

gnomAD v4.1 allele counts were not recorded for this variant.

gnomAD v2.1

Absent from gnomAD v2.1.

Applied · PM2 →

gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗

SpliceAI score

0.000 maximum delta

Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗

ClinVar submissions

3 reported laboratory submissions

2 Likely pathogenic · 1 Pathogenic.

Context only ClinVar ↗

No screenshot for this evidence

Functional evidence

Not recorded

No standalone functional evidence summary is recorded in evidence_summary.functional.

No listed criterion applied OncoKB ↗

Somatic evidence

4 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV64302273, n = 4 times).

Context only COSMIC ↗

For specialists

Technical detail

ACMG/AMP criteria under ClinGen PTEN VCEP v3.2.0, with the data and sources behind each one.

26 criteria with recorded statuses: 2 met · 4 not met · 12 not assessed · 8 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic

PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM5 PM6 PP1 PP2 PP3 PP4 PP5 PS5

Benign

BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP4 BP5 BP6 BP7

Met Not met Not assessed Not applicable

NM_000314.8:c.210-2A>G is a canonical splice acceptor site variant (AG>GG at the -2 position of intron 3) in PTEN, a gene where loss of function is an established mechanism for PTEN hamartoma tumor syndrome (PHTS).

Per the ClinGen PTEN VCEP v3.2.0 PVS1 decision tree, this variant qualifies for PVS1 (Very Strong): it disrupts a canonical GT-AG splice site at a position 5' to p.D375 (c.1121), is predicted to cause exon 4 skipping with frameshift (p.Ala72Thrfs*5) and nonsense-mediated decay, and affects a biologically-relevant transcript (NM_000314.8). The closely related variant c.210-1G>A at the same splice junction has been experimentally confirmed to cause exon 4 skipping (PMID:28677221).

The variant is absent from gnomAD v2.1 and v4.1, meeting the PTEN VCEP threshold for PM2_Supporting (allele frequency <0.001%).

No direct functional evidence (RNA assay, minigene, or splicing study) was identified for c.210-2A>G specifically. The Mighell et al. 2018 phosphatase activity assay (mmc2.xlsx) only covers missense variants and is not applicable to this splice variant.

SpliceAI predicts a max delta score of 0.00, which is anomalous for a canonical splice acceptor variant and may represent a lookup artifact. SpliceAI predictions should be independently verified before relying on computational splicing evidence for this variant.

ClinVar reports this variant as Likely pathogenic (2 clinical laboratories) and Pathogenic (1 clinical laboratory) under ClinVar ID 576440, with review status 'criteria provided, single submitter.' However, BP6 is not for use per PTEN VCEP, and ClinVar classifications alone are not used as independent evidence.

This variant has been observed in somatic cancers (COSMIC COSV64302273, n=4), supporting its potential role in tumorigenesis, though somatic occurrence alone is not an ACMG/AMP criterion for germline classification.

A systematic review of the five available full-text publications (PMIDs: 16199547, 28677221, 29758562, 9467011, 21194675) confirmed that none mention the exact variant NM_000314.8:c.210-2A>G. The most relevant paper (PMID:28677221) studied 34 PTEN intronic variants including c.210-1G>A at the same splice junction, but c.210-2A>G was not among the variants analyzed.

Combined evidence: PVS1 (Very Strong) + PM2_Supporting. Under the PTEN VCEP combination rules v3.2.0, this specific combination (1 Very Strong + 1 Supporting without an intermediate Moderate criterion) does not match any defined pathogenic or likely pathogenic rule. Under the generic ACMG/AMP 2015 framework (PMID:25741868), 1 Very Strong + 1 Supporting likewise does not reach the threshold for Likely Pathogenic (requires >=2 Supporting or >=1 Moderate). Using a Bayesian point system (PVS1=8, PM2=1, total=9), this falls within the Likely Pathogenic range (6-9 points). A final classification should be determined by the interpreting clinical laboratory considering the strength of the PVS1 call and the anomalous SpliceAI result.

Met · 2

PVS1 Very strongNM_000314.8:c.210-2A>G is a canonical splice acceptor site variant (AG to GG at the -2 position of intron 3). Per the PTEN VCEP PVS1 decision tree, canonical GT-AG splice site disruptions that are predicted to cause exon skipping with reading frame disruption and nonsense-mediated decay (NMD) are assigned PVS1 when the disruption is at or 5' to p.D375 (c.1121) in the biologically-relevant transcript NM_000314.8. This variant is at c.210 (intron 3 acceptor), well 5' of the c.1121 threshold; exon 4 skipping is predicted to cause a frameshift (p.Ala72Thrfs*5) with premature termination and NMD. Related variants at the same splice junction (c.210-1G>A) have been experimentally confirmed to cause exon 4 skipping (PMID:28677221). Details ▾Hide ▴

Evidence considered

Canonical splice acceptor site (AG>GG) at intron 3 -2 position
PTEN VCEP PVS1 decision tree: disruption at or 5' to p.D375 (c.1121)
predicted NMD
c.210-1G>A at the same splice junction experimentally shown to cause exon 4 skipping and frameshift p.(Ala72Thrfs*5) (PMID:28677221)
PTEN loss of function is an established disease mechanism per ClinGen PTEN VCEP v3.2.0

Still missing

No direct RNA/minigene assay for c.210-2A>G specifically
functional consequence inferred from closely related variant c.210-1G>A

Sources

cspec ↗pvs1_gene_contextpvs1_variant_assessmentvcep_pvs1_decisiontree_ptenPMID:28677221 ↗28677221

PM2 SupportingThe variant is absent from gnomAD v2.1 and v4.1 (allele frequency = 0.0000). Per the PTEN VCEP, PM2_Supporting applies when the variant is present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. This variant meets that threshold as it is completely absent from all population databases examined. Details ▾Hide ▴

Evidence considered

Absent from gnomAD v2.1 (0 alleles)
Absent from gnomAD v4.1 (0 alleles)
Allele frequency below PTEN VCEP PM2_Supporting threshold of <0.001%

Sources

gnomad_v2 ↗gnomad_v4 ↗

Not met · 4 · evaluated, threshold not reached

PS1 PS1 requires the same nucleotide position as a known pathogenic splicing variant. The known pathogenic variant c.210-1G>A is at position c.210-1, while the variant under assessment is at position c.210-2. These are different nucleotide positions; therefore PS1 does not apply. Details ▾Hide ▴

Evidence considered

c.210-1G>A is a known pathogenic variant at the adjacent nucleotide position
not the same position

Sources

28677221

PP3 The PTEN VCEP specifies PP3_Supporting for splicing variants requires concordance of SpliceAI and VarSeak predictions of splicing impact (SpliceAI scores 0.5-1, VarSeak Class 4-5). SpliceAI returns a max delta score of 0.00 for this variant, which is below the pathogenic threshold. Additionally, per ClinGen SVI PVS1 guidance (PMC6185798), PP3 should not be stacked with PVS1 for the same splice-effect prediction evidence, as PVS1 already accounts for the predicted splice disruption. No VarSeak data is available. Details ▾Hide ▴

Evidence considered

SpliceAI max delta score = 0.00 (below pathogenic threshold of 0.5)
PVS1 already accounts for predicted splice impact
PP3 should not be double-counted
VarSeak data not available

Still missing

SpliceAI delta of 0.00 is anomalous for a canonical -2 splice acceptor variant
may represent a lookup artifact
VarSeak assessment not performed

Sources

spliceai ↗pvs1_variant_assessment

BA1 BA1 under the PTEN VCEP requires a gnomAD filtering allele frequency >0.00056 (0.056%). The variant is absent from both gnomAD v2.1 and v4.1 (allele frequency = 0.0000), which is far below the BA1 threshold. Details ▾Hide ▴

Evidence considered

Variant absent from gnomAD
AF = 0.0000
threshold for BA1 is >0.056%

Sources

gnomad_v2 ↗gnomad_v4 ↗

BS1 BS1 under the PTEN VCEP requires a gnomAD filtering allele frequency of 0.000043 (0.0043%) to 0.00056 (0.056%) for BS1_Strong, or 0.0000043 (0.00043%) to 0.000043 (0.0043%) for BS1_Supporting. The variant is absent from both gnomAD v2.1 and v4.1, so it does not meet either threshold. Details ▾Hide ▴

Evidence considered

Variant absent from gnomAD
AF = 0.0000
below BS1_Supporting threshold of 0.00043%

Sources

gnomad_v2 ↗gnomad_v4 ↗

Not assessed · 12 · no assessment recorded

PS2 No confirmed de novo observations (with both maternity and paternity confirmed) have been identified for NM_000314.8:c.210-2A>G in any reviewed publication or database. Details ▾Hide ▴

Still missing

No de novo reports available

PS3 The PTEN VCEP specifies PS3_Strong for RNA/minigene assays demonstrating splicing impact, and PS3_Moderate for phosphatase activity <= -1.11 per Mighell et al. 2018 (mmc2.xlsx). No RNA or minigene splicing assay data were found for c.210-2A>G. The Mighell et al. phosphatase assay (mmc2.xlsx) is limited to missense variants and does not include this splice variant. The closely related variant c.210-1G>A was shown to cause exon 4 skipping in PMID:28677221, but that is a different variant and cannot be directly applied as PS3 evidence for c.210-2A>G. Details ▾Hide ▴

Evidence considered

c.210-1G>A experimentally causes exon 4 skipping (PMID:28677221)
but this is a different variant

Still missing

No direct functional assay (RNA/minigene) for c.210-2A>G
mmc2.xlsx phosphatase assay is missense-only
not applicable to splice variants

Sources

PMID:28677221 ↗28677221

PS4 PS4 under the PTEN VCEP requires proband specificity scoring or case-control data. No proband counts with phenotype specificity scoring were available for c.210-2A>G. PMID:28677221 studied 34 PTEN intronic variants in 61 CS patients but c.210-2A>G was not among them. PMID:21194675 (Tan et al. 2011) is a large cohort study of 3042 probands for PTEN mutation testing but does not specifically report c.210-2A>G. Details ▾Hide ▴

Evidence considered

None of the reviewed publications specifically report proband counts for c.210-2A>G

Still missing

No proband specificity scoring data for this variant
Large PTEN cohort studies do not enumerate this specific variant

Sources

PMID:28677221 ↗PMID:21194675 ↗2867722121194675

PM6 No presumed or confirmed de novo observations have been identified for NM_000314.8:c.210-2A>G in any reviewed publication, ClinVar submission, or database. The variant is absent from the large CS patient cohort study of Chen et al. 2017 (PMID:28677221) which examined 34 PTEN intronic variants from 61 patients. Details ▾Hide ▴

Still missing

No de novo reports for this specific variant

Sources

PMID:28677221 ↗28677221

PP1 No co-segregation data (meiosis counts across affected family members) was identified for NM_000314.8:c.210-2A>G. The PTEN VCEP requires at least 3-4 meioses for PP1_Supporting, 5-6 for PP1_Moderate, and >=7 across at least 2 families for PP1_Strong. Details ▾Hide ▴

Still missing

No family segregation data available

BS2 No observations of NM_000314.8:c.210-2A>G in the homozygous state in a healthy or PHTS-unaffected individual were identified. The variant is entirely absent from gnomAD, so no homozygous observations are available. Details ▾Hide ▴

Evidence considered

No homozygous observations in gnomAD

Still missing

No homozygous genotype data available

Sources

gnomad_v2 ↗gnomad_v4 ↗

BS3 BS3 under the PTEN VCEP requires RNA/minigene/splicing assay demonstrating no splicing impact (BS3_Strong) or functional studies showing no damaging effect (BS3_Supporting via phosphatase activity >0 per Mighell et al. 2018). No splicing assay data exist for c.210-2A>G. The Mighell phosphatase assay (mmc2.xlsx) is limited to missense variants and does not apply to splice variants. Details ▾Hide ▴

Evidence considered

No functional assay data for this specific variant
mmc2.xlsx Mighell assay is missense-only

Still missing

No RNA/minigene splicing assay for c.210-2A>G

BS4 No segregation data demonstrating lack of segregation in affected family members was identified for NM_000314.8:c.210-2A>G. Details ▾Hide ▴

Still missing

No segregation data available

BP2 No observations of NM_000314.8:c.210-2A>G in trans with a pathogenic or likely pathogenic PTEN variant, nor in cis/unknown phase with different pathogenic/likely pathogenic PTEN variants, were identified in any reviewed source. Details ▾Hide ▴

Still missing

No phase data available

BP4 BP4 under the PTEN VCEP requires concordance of SpliceAI (scores 0-0.2) and VarSeak (Class 1-2) predicting no splicing impact. The VCEP explicitly cautions against applying BP4 to variants within the canonical splice site region. c.210-2A>G is at the -2 position of the canonical splice acceptor and falls within this cautioned region. While SpliceAI returns a max delta of 0.00 (nominally within the 0-0.2 range), this value is anomalous for a canonical -2 splice site disruption and may represent a lookup artifact. VarSeak data is not available. Given the VCEP caution and the anomalous SpliceAI result, BP4 cannot be reliably assessed. Details ▾Hide ▴

Evidence considered

SpliceAI max delta = 0.00 (anomalous for canonical -2 splice site)
VCEP cautions against BP4 for variants in the canonical splice site region
VarSeak data not available

Still missing

SpliceAI result likely artifact
needs manual verification
VarSeak assessment not performed

Sources

spliceai ↗

BP5 No cases were identified where NM_000314.8:c.210-2A>G was found in a patient with an alternate molecular basis for disease. The PTEN VCEP requires at least two such cases for BP5 to apply. Details ▾Hide ▴

Still missing

No alternate molecular basis cases identified

PS5 PS5 is not included in the PTEN VCEP criteria set (ClinGen PTEN Expert Panel Specifications v3.2.0). The criterion is not defined for this gene/framework. Details ▾Hide ▴

Evidence considered

PS5 is absent from the PTEN VCEP v3.2.0 criteria specification

Not applicable · 8· recorded as not applicable Show reasons ▾Hide reasons ▴

PM1 N/APM1 under the PTEN VCEP is defined for residues within catalytic motifs (WPD loop 90-94, P-loop 123-130, TI-loop 166-168; NP_000305.3). NM_000314.8:c.210-2A>G is an intronic splice site variant in intron 3 and does not alter a residue within any of the defined catalytic motifs. The variant causes exon 4 skipping which removes protein sequence, but the variant itself is not located in a catalytic motif residue. Details ▾Hide ▴

Evidence considered

Variant is intronic (intron 3
c.210-2)
not in catalytic motif residues 90-94
123-130
or 166-168

Sources

cspec ↗

PM5 N/APM5 requires a missense change at an amino acid residue where a different pathogenic missense change has been observed. NM_000314.8:c.210-2A>G is a canonical splice site variant in intron 3, not a missense variant. The pm5_candidates analysis confirms this variant class is not missense-like and is ineligible for classic same-residue PM5 evaluation. Details ▾Hide ▴

Evidence considered

Variant class is splice site
not missense
No protein residue context available (NP_000305.3:p.?)

Sources

pm5_candidates

PP2 N/APP2 applies to missense variants in genes with a low rate of benign missense variation where missense variants are a common disease mechanism. NM_000314.8:c.210-2A>G is a canonical splice site variant, not a missense variant. Details ▾Hide ▴

Evidence considered

Variant is a splice site variant
not a missense variant

Sources

cspec ↗

PP4 VCEPPP4 is designated as Not Applicable by the ClinGen PTEN VCEP v3.2.0. Phenotype specificity has been incorporated into the PS4 rule specifications. Details ▾Hide ▴

Evidence considered

PTEN VCEP v3.2.0: PP4 is Not Applicable

Sources

cspec ↗

PP5 VCEPPP5 is designated as Not Applicable for this VCEP by the ClinGen Sequence Variant Interpretation VCEP Review Committee. This criterion is not for use in PTEN variant interpretation. Details ▾Hide ▴

Evidence considered

PTEN VCEP v3.2.0: PP5 is Not Applicable for this VCEP

Sources

cspec ↗

BP1 VCEPBP1 is designated as Not Applicable by the PTEN VCEP v3.2.0. This rule is not applicable to PTEN according to the ClinGen PTEN Expert Panel. Details ▾Hide ▴

Evidence considered

PTEN VCEP v3.2.0: BP1 is Not Applicable

Sources

cspec ↗

BP6 VCEPBP6 is designated as Not Applicable for this VCEP by the ClinGen Sequence Variant Interpretation VCEP Review Committee. This criterion is not for use in PTEN variant interpretation. Details ▾Hide ▴

Evidence considered

PTEN VCEP v3.2.0: BP6 is Not Applicable for this VCEP

Sources

cspec ↗

BP7 N/ABP7 under the PTEN VCEP applies to synonymous or intronic variants at or beyond +7/-21 for which splicing prediction algorithms predict no impact. NM_000314.8:c.210-2A>G is at the -2 position of intron 3, which is well within the critical splice site region (not at or beyond -21). This variant affects a canonical AG splice acceptor dinucleotide and therefore BP7 does not apply. Details ▾Hide ▴

Evidence considered

Variant is at c.210-2 (within -21 boundary
not at or beyond -21)
Disrupts the canonical AG splice acceptor dinucleotide

Sources

cspec ↗

Identifiers

Gene: PTEN
Transcript: NM_000314.8
Coding (HGVS c.): NM_000314.8:c.210-2A>G
Protein (HGVS p.): NP_000305.3:p.?
GRCh38: chr10:87931044 A>G
GRCh37: chr10:89690801 A>G
COSMIC: COSV64302273

Gene diagram

Every interpreted variant in PTEN, mapped onto the exon structure of NM_000314.8. Select a row to find it on the plot.

PTENNM_000314.8

Fetching transcript structure from UCSC…

Exons

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Transcript span

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Strand

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Variants mapped

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Source

UCSC ncbiRefSeqCurated

All variants in PTEN — Select a row to find it on the plot; use the link to open its page.

	Protein	Location	Classification	Link

gnomAD v4.1 Allele count data not recorded

gnomAD v2.1 Allele count data not recorded

gnomAD-Canada v1.0 0 / 0 alleles AF 0 · 0 homozygotes · FAF 0

By genetic ancestry

gnomAD-Canada

AF 0 · 0 / 0 alleles · 0 hom

Statements

gnomAD v4.1

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

Pangolin splice lossmagnitude shown

-0.850

Pangolin splice gain

0.170

Other predictors

REVEL: Not available
BayesDel: 0.224

How the predictions were used

Evidence considered

SpliceAI max delta score = 0.00 (below pathogenic threshold of 0.5)
PVS1 already accounts for predicted splice impact
PP3 should not be double-counted
VarSeak data not available

Still missing

SpliceAI delta of 0.00 is anomalous for a canonical -2 splice acceptor variant
may represent a lookup artifact
VarSeak assessment not performed

Sources

spliceai ↗pvs1_variant_assessment

Evidence considered

SpliceAI max delta = 0.00 (anomalous for canonical -2 splice site)
VCEP cautions against BP4 for variants in the canonical splice site region
VarSeak data not available

Still missing

SpliceAI result likely artifact
needs manual verification
VarSeak assessment not performed

Sources

spliceai ↗

Evidence considered

Variant is at c.210-2 (within -21 boundary
not at or beyond -21)
Disrupts the canonical AG splice acceptor dinucleotide

Sources

cspec ↗

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.224139.

6 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

Splicing in action: assessing disease causing sequence changes.

No paper-specific finding is recorded.

PMID 16199547 ↗
Characterization of cryptic splicing in germline PTEN intronic variants in Cowden syndrome.

No paper-specific finding is recorded.

PMID 28677221 ↗
Clinical relevance of systematic phenotyping and exome sequencing in patients with short stature.

No paper-specific finding is recorded.

PMID 29758562 ↗
Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation.

No paper-specific finding is recorded.

PMID 9467011 ↗
A clinical scoring system for selection of patients for PTEN mutation testing is proposed on the basis of a prospective study of 3042 probands.

No paper-specific finding is recorded.

PMID 21194675 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

No paper-specific finding is recorded.

PMID 28492532 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

gnomAD v4.1 Captured gnomAD v4.1 source record Open source ↗

gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗

SpliceAI Lookup Recorded maximum delta 0.000 Open source ↗

ClinVar 2 Likely pathogenic · 1 Pathogenic Open source ↗

COSMIC Captured COSMIC source record Open source ↗

ClinGen CSpec Captured ClinGen CSpec source record Open source ↗

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

ClinVar

This variant has been reported in ClinVar as Likely pathogenic (2 clinical laboratories) and as Pathogenic (1 clinical laboratory). (ClinVarID = 576440)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.224139.

Somatic

This variant has previously been reported in somatic cancers (COSMIC; COSV64302273, n = 4 times).