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PIK3CAc.331_336delUncertain significance
Print report
Variant interpretation report

PIK3CA c.331_336del, p.(Lys111_Ile112del)

NM_006218.4:c.331_336del NP_006209.2:p.(Lys111_Ile112del) In frame indel unknown · exon 2 View identifiers
Classification
Uncertain significance

Variant description:

No variant summary was recorded for this case.

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

Uncertain.The recorded classification is uncertain significance.

In plain language

Gene-level background from the recorded interpretation.

About PIK3CA

PIK3CA encodes the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K), an enzyme that converts the membrane lipid PIP2 into PIP3, thereby activating signaling cascades such as the AKT-mTOR pathway that promote cell survival, proliferation, growth, and motility. It is among the most commonly mutated genes in cancer, and aberrant activation of PI3K signaling is a driving event in tumor development, with the gene implicated in cancers including cervical cancer. Because this pathway is central to tumor growth, it is a major target of cancer therapies, although drug-induced pathway activation can also contribute to treatment resistance.

NCBI Gene ↗ OncoKB ↗
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 PIK3CA VCEP v1.1. 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
PS4Supporting
PS4 · supporting

Met at supporting: two COSMIC occurrences contribute 0.5 points, which falls within the VCEP PS4 supporting range of 0.5–1.25 points after PM2 is satisfied.

PM2Supporting
PM2 · supporting

Met at supporting strength: the variant is absent from gnomAD v2.1, v4.1, and non-cancer subsets, with 0 observed people versus the VCEP maximum of 1.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Uncertain significance

VUS: PS4 (supporting) plus PM2 (supporting) provide two supporting criteria, insufficient for a pathogenic, likely pathogenic, benign, or likely benign ACMG combination.

02The sources

Evidence at a glance

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

SpliceAI score
0.110 maximum delta

Recorded SpliceAI maximum delta score: 0.110. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗
ClinVar submissions
Not recorded

A ClinVar laboratory submission summary was not recorded.

Context only ClinVar ↗
Functional evidence
Statement recorded

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
2 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV55941739, n = 2 times).

Cancer Hotspots

This variant lies in a statistically significant hotspot.

Context only
COSMIC ↗Cancer Hotspots ↗
For specialists

Technical detail

ACMG/AMP criteria under ClinGen PIK3CA VCEP v1.1, with the data and sources behind each one.

28 criteria with recorded statuses: 2 met · 3 not met · 5 not assessed · 18 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM3PM4PM5PM6PP1PP2PP3PP4PP5
Benign
BA1BS1BS2BS3BS4BP1BP2BP3BP4BP5BP6BP7
Met Not met Not assessed Not applicable

Population evidence supports PM2 at supporting strength because the variant was absent from the available gnomAD datasets.

BA1, BS1, and BS2 are not met because no population observations or homozygotes were reported and the VCEP frequency and homozygote thresholds were not reached.

Met · 2

PS4 SupportingMet at supporting: two COSMIC occurrences contribute 0.5 points, which falls within the VCEP PS4 supporting range of 0.5–1.25 points after PM2 is satisfied. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP specification requires PM2 before PS4 and assigns tumor-sample occurrences 0.25 points each in Table 2A. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, satisfying the prerequisite described by the specification. COSMIC reports this exact variant as COSV55941739 with n = 2 somatic occurrences, yielding 2 x 0.25 = 0.5 points. The exact VCEP rule states: "PS4_Supporting = 0.5 – 1.25 points." Explicit range check: 0.5 <= 0.5 <= 1.25? yes. Therefore PS4 is met at supporting strength. Human review remains appropriate because the available COSMIC result does not expose sample-level details confirming that both occurrences are separately countable under the VCEP's tumor-occurrence instructions.

Rule
ClinGen Brain Malformations VCEP PS4: phenotype points are assigned from Table 2A only after PM2; PS4 supporting is 0.5–1.25 points, with tumor-sample presence scored at 0.25 points per occurrence.
Evidence considered
  • The ClinGen Brain Malformations VCEP specification states that PS4 phenotype criteria require PM2 and that tumor-sample presence contributes 0.25 points per occurrence in Table 2A.
  • The same specification states: "PS4_Supporting = 0.5 – 1.25 points." The explicit range check is 0.5 <= 0.5 <= 1.25? yes.
  • The case evidence reports the exact variant as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada.
  • The case evidence reports COSMIC COSV55941739 for this exact variant with n = 2 somatic occurrences; applying the VCEP tumor-occurrence value gives 2 x 0.25 = 0.5 points.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
  • COSMIC sample-level details are unavailable, so the separate-primary or separate-individual status of both reported occurrences cannot be independently confirmed.
Sources
cspec ↗gnomad_v2 ↗gnomad_v4 ↗PMID:29533785 ↗
PM2 SupportingMet at supporting strength: the variant is absent from gnomAD v2.1, v4.1, and non-cancer subsets, with 0 observed people versus the VCEP maximum of 1. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP applies PM2 at supporting strength when the variant is absent or rare in an ethnically matched population sample, with a maximum of one person. The variant was absent from gnomAD v2.1, gnomAD v4.1, and the available non-cancer subsets, so the observed count is 0 and satisfies the VCEP one-person maximum. The VCEP file contained no exact variant-specific entry under c.331_336del, p.Lys111_Ile112del, or p.K111_I112del.

Rule
PM2 is met at supporting strength when absent or rare in the relevant population sample, with no more than 1 observed person, under the ClinGen Brain Malformations VCEP specification.
Evidence considered
  • The ClinGen Brain Malformations VCEP specifies PM2 at supporting strength for an absent or rare variant in an ethnically matched population sample, with a one-person maximum.
  • The variant was reported absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer; the observed count is 0.
  • The VCEP text was searched for c.331_336del, p.Lys111_Ile112del, and p.K111_I112del, with no variant-specific entry found.
Still missing
  • No c.331_336del, p.Lys111_Ile112del, or p.K111_I112del entry was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PIK3CA/fulltext/clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.
Sources
cspec ↗gnomad_v2 ↗gnomad_v4 ↗

Not met · 3 · evaluated, threshold not reached

BA1 Not met: the variant is absent from gnomAD v2.1 and v4.1, giving observed allele frequency 0 versus the VCEP BA1 threshold of >0.0926%. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP specifies BA1 when allele frequency is greater than 0.0926%. The variant was absent from gnomAD v2.1 and gnomAD v4.1, so its observed allele frequency is 0 and does not meet the threshold. The VCEP file contained no exact variant-specific entry under c.331_336del, p.Lys111_Ile112del, or p.K111_I112del.

Rule
BA1 is met only when allele frequency is >0.0926% under the ClinGen Brain Malformations VCEP specification.
Evidence considered
  • The ClinGen Brain Malformations VCEP specifies BA1 at allele frequency >0.0926%.
  • The variant was reported absent from gnomAD v2.1 and gnomAD v4.1; therefore the observed allele frequency is 0%.
  • The VCEP text was searched for c.331_336del, p.Lys111_Ile112del, and p.K111_I112del, with no variant-specific entry found.
Still missing
  • No c.331_336del, p.Lys111_Ile112del, or p.K111_I112del entry was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PIK3CA/fulltext/clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.
Sources
cspec ↗gnomad_v2 ↗gnomad_v4 ↗
BS1 Not met: the variant is absent from gnomAD v2.1 and v4.1, giving observed allele frequency 0 versus the VCEP BS1 threshold of >0.0185%. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP specifies BS1 when allele frequency is greater than 0.0185%. The variant was absent from gnomAD v2.1 and gnomAD v4.1, so its observed allele frequency is 0 and does not meet the threshold. The VCEP file contained no exact variant-specific entry under c.331_336del, p.Lys111_Ile112del, or p.K111_I112del.

Rule
BS1 is met only when allele frequency is >0.0185% under the ClinGen Brain Malformations VCEP specification.
Evidence considered
  • The ClinGen Brain Malformations VCEP specifies BS1 at allele frequency >0.0185%.
  • The variant was reported absent from gnomAD v2.1 and gnomAD v4.1; therefore the observed allele frequency is 0%.
  • The VCEP text was searched for c.331_336del, p.Lys111_Ile112del, and p.K111_I112del, with no variant-specific entry found.
Still missing
  • No c.331_336del, p.Lys111_Ile112del, or p.K111_I112del entry was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PIK3CA/fulltext/clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.
Sources
cspec ↗gnomad_v2 ↗gnomad_v4 ↗
BS2 Not met: gnomAD v2.1 and v4.1 report 0 variant observations, below the VCEP requirement of at least 3 homozygotes or qualifying family heterozygotes. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP requires at least 3 homozygous gnomAD occurrences or at least 3 heterozygous occurrences in well-phenotyped family members for BS2. The variant was absent from gnomAD v2.1 and gnomAD v4.1, providing 0 reported homozygotes; no qualifying family observations were provided. The VCEP file contained no exact variant-specific entry under c.331_336del, p.Lys111_Ile112del, or p.K111_I112del.

Rule
BS2 is met at strong strength only with >=3 homozygotes in gnomAD or >=3 heterozygotes in well-phenotyped family members under the ClinGen Brain Malformations VCEP specification.
Evidence considered
  • The ClinGen Brain Malformations VCEP requires at least 3 homozygotes in gnomAD or at least 3 heterozygotes in well-phenotyped family members for BS2.
  • The variant was reported absent from gnomAD v2.1 and gnomAD v4.1, corresponding to 0 reported homozygous occurrences; no qualifying family observations were supplied.
  • The VCEP text was searched for c.331_336del, p.Lys111_Ile112del, and p.K111_I112del, with no variant-specific entry found.
Still missing
  • No c.331_336del, p.Lys111_Ile112del, or p.K111_I112del entry was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/PIK3CA/fulltext/clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.
Sources
cspec ↗gnomad_v2 ↗gnomad_v4 ↗

Not assessed · 5 · no assessment recorded

PS2 Not assessed: no documented proband allele fraction, parental maternity/paternity testing, or affected-versus-other-tissue comparison satisfies the VCEP PS2 criteria. Details ▾Hide ▴
Reasoning

The Brain Malformations VCEP requires PS2_Strong only when the variant is detected in affected tissue, absent from parental samples with confirmed maternity and paternity, and present at a lower or absent fraction in another tissue; PS2_Moderate requires the parental criterion or the affected-tissue criterion when parents are unavailable. The available case evidence documents no proband allele fraction, parental testing, maternity or paternity confirmation, affected-tissue result, alternate-tissue comparison, or family-history assessment. Therefore PS2 cannot be assigned from the available evidence. The exact variant was not found in the governing VCEP full-text file after searching c.331_336del, p.Lys111_Ile112del, and p.K111_I112del.

Rule
PS2_Strong requires Criteria 1 and 2; PS2_Moderate requires Criteria 1 or, if parents are unavailable, Criteria 2. Criteria 1 requires detectable variant in the proband and absence from parental samples with confirmed maternity and paternity. Criteria 2 requires detectable variant in affected tissue and absence or lower fraction in another tissue.
Evidence considered
  • The governing VCEP specifies PS2_Strong only when both parental absence with confirmed maternity and paternity and affected-tissue mosaic/tissue-distribution criteria are fulfilled.
  • The governing VCEP specifies PS2_Moderate when the parental criterion is fulfilled, or when parents are unavailable but the affected-tissue criterion is fulfilled.
  • The case materials contain no usable proband, parental, tissue-distribution, or family-history data for this variant.
Still missing
  • No proband allele fraction or assay-confirmation details are documented.
  • No parental samples, confirmed maternity, or confirmed paternity are documented.
  • No affected-tissue and alternate-tissue variant fractions are documented.
  • No family-history assessment is documented.
  • No exact variant entry was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt when searched as c.331_336del, p.Lys111_Ile112del, and p.K111_I112del.
Sources
cspec ↗
PS3 Not assessed: no validated assay result for the exact p.K111_I112del variant was identified, and the available paper tested only the distinct nearby K111delK variant. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP requires PS3 functional evidence to follow SVI recommendations with validated assay quality metrics and minimum controls: WT positive control, an empty-vector or blank-transfection negative control, and technical replicates documented at least in triplicate for phosphorylation, DEPTOR-binding, or cell-survivability assays; cell-proliferation evidence additionally requires biological replicates for animal studies and multiple measurements in triplicate. The exact variant NM_006218.4:c.331_336del (NP_006209.2:p.(Lys111_Ile112del)/p.(K111_I112del)) was not found in the governing VCEP full-text file under any of the three requested notations. The only fetched functional paper, PMID:29533785, explicitly reports a different nearby variant, PIK3CA K111delK, and its extraction states that the case variant was not mentioned; therefore it cannot establish a damaging effect for this variant. No validated variant-specific functional assay result is available to assess PS3 at any strength.

Rule
Follow SVI recommendations with Brain Malformation VCEP quality metrics and minimum validation controls; variant-specific functional evidence is required for PS3.
Evidence considered
  • The governing VCEP specifies PS3 using SVI recommendations and requires validated assay quality metrics and minimum controls; evidence above supporting requires positive and negative validation controls, with 8-34 variants for moderate and 35 or more variants for strong evidence.
  • The governing VCEP supplementary assay requirements specify WT as a basic positive control, empty vector or blank transfection as a basic negative control, and documented technical replicates in at least triplicate for phosphorylation, DEPTOR-binding, and cell-survivability assays.
  • Searches of clingen_brainmalform_acmg_specifications_v1_1.pdf.txt found no occurrence of c.331_336del, p.Lys111_Ile112del, or p.K111_I112del.
  • PMID:29533785 was reviewed through its extracted finding; it states that PIK3CA K111delK, a distinct nearby variant, had the strongest activating mutation score, while the exact K111_I112del variant was not mentioned.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.
  • A variant-specific functional assay with required controls and replicate documentation was not identified.
  • PMID:29533785 reports other PIK3CA variants, not the exact case variant.
Sources
cspec ↗PMID:29533785 ↗
BS3 Not assessed: no validated benign functional result for the exact p.K111_I112del variant was identified; PMID:29533785 tested a different nearby variant. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP requires BS3 functional evidence to follow SVI recommendations with validated assay quality metrics and minimum controls. No assay showing absence of a damaging effect for NM_006218.4:c.331_336del (NP_006209.2:p.(Lys111_Ile112del)/p.(K111_I112del)) was identified. The exact variant was absent from the governing VCEP full-text file under all three requested notations, and PMID:29533785 concerns other PIK3CA variants, including the distinct K111delK variant, rather than this deletion. Consequently, the available evidence cannot establish benign functional impact or support BS3 at any strength.

Rule
Follow SVI recommendations with Brain Malformation VCEP quality metrics and minimum validation controls; variant-specific functional evidence showing no damaging effect is required for BS3.
Evidence considered
  • The governing VCEP defines BS3 as well-established in vitro or in vivo functional evidence showing no damaging effect and requires SVI/Brain Malformation Group quality metrics and minimum validation controls.
  • Searches of clingen_brainmalform_acmg_specifications_v1_1.pdf.txt found no occurrence of c.331_336del, p.Lys111_Ile112del, or p.K111_I112del.
  • PMID:29533785 was reviewed through its extracted finding; the exact case variant was not mentioned, so its functional results for other PIK3CA variants cannot establish benign impact for p.K111_I112del.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.
  • A variant-specific assay demonstrating no damaging effect, with required controls and replicate documentation, was not identified.
  • PMID:29533785 reports other PIK3CA variants, not the exact case variant.
Sources
cspec ↗PMID:29533785 ↗
BP2 Not assessed: no cis/trans observation with a known pathogenic PIK3CA variant or phase result is available for this variant. Details ▾Hide ▴
Reasoning

The governing VCEP permits BP2 at Supporting strength when the variant is observed in cis or trans with a known pathogenic variant in the same gene. The case materials provide no affected-proband observation, paired pathogenic PIK3CA variant, or phase result establishing cis or trans for NM_006218.4:c.331_336del (p.Lys111_Ile112del). BP2 is therefore not assessed. The exact variant was not found under c.331_336del, p.Lys111_Ile112del, or p.K111_I112del in the governing VCEP full-text file.

Rule
Observed in cis or trans with a known pathogenic variant in the same gene.
Evidence considered
  • The ClinGen Brain Malformations VCEP specification allows BP2 when a variant is observed in cis or trans with a known pathogenic variant in the same gene.
  • The reviewed case evidence contains no report of this variant with a second pathogenic PIK3CA variant and no parental, offspring, or other molecular phase result establishing cis or trans status.
Still missing
  • No case-level phase data, affected-proband record, or paired pathogenic PIK3CA variant is available to evaluate cis or trans status.
  • The governing file clingen_brainmalform_acmg_specifications_v1_1.pdf was searched for c.331_336del, p.Lys111_Ile112del, and p.K111_I112del; no variant-specific entry was found, which does not establish absence of evidence.
Sources
cspec ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
BP5 Not assessed: two COSMIC cancer occurrences are reported, but no alternate molecular basis in a different gene is documented for those cases. Details ▾Hide ▴
Reasoning

The governing VCEP leaves BP5 applicable as originally described: a variant found in a case with an alternate molecular basis for disease, specifically an alternate pathogenic finding in a different gene. The available evidence reports this variant in two somatic cancer occurrences but provides no case-level phenotype, alternate-gene diagnosis, or alternate molecular basis. Therefore BP5 cannot be assigned or excluded from the available evidence.

Rule
ClinGen Brain Malformations VCEP BP5: supporting evidence requires the variant to be observed in a case with an alternate molecular basis for disease in a different gene.
Evidence considered
  • The ClinGen Brain Malformations VCEP defines BP5 as a variant found in a case with an alternate molecular basis for disease and specifies an alternate molecular basis in a different gene.
  • The available COSMIC evidence reports two somatic occurrences of the exact variant but does not provide an alternate gene or case-level molecular diagnosis.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
  • Case-level clinical records and an alternate pathogenic molecular finding in a different gene are unavailable.
Sources
cspec ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
Not applicable · 18· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 VCEPPVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_006218.4:c.331_336del in PIK3CA is an in-frame insertion/deletion of undetermined repeat-region status predicted to produce NP_006209.2:p.(Lys111_Ile112del). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies. Details ▾Hide ▴
VCEP rule
deterministic_prefilter: requires_null_variant_class
Evidence considered
  • Deterministic consequence classification: in_frame_indel_unknown (prefetch.json normalized protein consequence)
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
PS1 N/APS1 (Richards et al. 2015, PMID:25741868) requires the same amino acid change as a previously established pathogenic variant, evaluated regardless of the underlying nucleotide change. NM_006218.4:c.331_336del in PIK3CA is an in-frame insertion/deletion of undetermined repeat-region status predicted to produce NP_006209.2:p.(Lys111_Ile112del). As a result, no altered amino acid exists at this position to compare against any previously established pathogenic missense variant, so PS1's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies. Details ▾Hide ▴
Rule
deterministic_prefilter: requires_missense
Evidence considered
  • Deterministic consequence classification: in_frame_indel_unknown (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules
PM1 N/APM1 (Richards et al. 2015, PMID:25741868) applies to a missense variant located in a mutational hot spot and/or a critical, well-established functional domain without benign variation. NM_006218.4:c.331_336del in PIK3CA is an in-frame insertion/deletion of undetermined repeat-region status predicted to produce NP_006209.2:p.(Lys111_Ile112del). As a result, no altered residue exists to evaluate for mutational hot-spot or critical-domain membership, so PM1's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies. Details ▾Hide ▴
Rule
deterministic_prefilter: requires_missense
Evidence considered
  • Deterministic consequence classification: in_frame_indel_unknown (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules
PM3 VCEPNot applicable: the VCEP excludes PM3 because PIK3CA brain-malformation disease-causing variants are heterozygous, not recessive in-trans observations. Details ▾Hide ▴
Reasoning

The ClinGen Brain Malformations VCEP specification marks PM3 not applicable because PIK3CA brain-malformation disease-causing variants are heterozygous, so the recessive in-trans requirement does not apply. The exact variant was not found under c.331_336del, p.Lys111_Ile112del, or p.K111_I112del in the governing VCEP full-text file. No PM3 evidence is therefore assigned.

VCEP rule
Not applicable since disease-causing variants are heterozygous.
Evidence considered
  • The ClinGen Brain Malformations VCEP specification states that PM3 is not applicable because disease-causing variants in these disorders are heterozygous.
  • The same specification defines PM3 as a recessive criterion requiring detection in trans with a pathogenic variant and parental or offspring phase testing.
Still missing
  • The governing file clingen_brainmalform_acmg_specifications_v1_1.pdf was searched for c.331_336del, p.Lys111_Ile112del, and p.K111_I112del; no variant-specific entry was found, which does not establish absence of evidence.
Sources
cspec ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
PM4 VCEPNot applicable: the PIK3CA VCEP excludes PM4 despite this 6-nucleotide in-frame deletion producing p.(Lys111_Ile112del). Details ▾Hide ▴
Reasoning

The variant is an in-frame 6-nucleotide deletion on the relevant PIK3CA transcript NM_006218.4, predicted as NP_006209.2:p.(Lys111_Ile112del) in exon 2. The governing ClinGen Brain Malformations VCEP specification designates PM4 not applicable for PIK3CA: although rare in-frame indels causing overgrowth have been reported, most insertion/deletions are associated with loss-of-function and PM4 is not used for this gain-of-function disease mechanism. Therefore the generic PM4 protein-length-change rule is superseded by the VCEP specification.

VCEP rule
VCEP PM4: Not Applicable for this VCEP; reported in-frame deletion/insertions are exceptionally rare, most insertion/deletions are associated with a LoF mechanism, and PM4 will not be used for these genes.
Evidence considered
  • NM_006218.4:c.331_336del is a 6-nucleotide in-frame deletion predicted to produce NP_006209.2:p.(Lys111_Ile112del) in exon 2.
  • The ClinGen Brain Malformations VCEP specification states that PM4 is not applicable for PIK3CA because most insertion/deletions are associated with a loss-of-function mechanism and PM4 will not be used even when an in-frame indel might have a gain-of-function effect.
Sources
cspec ↗
PM5 N/APM5 (Richards et al. 2015, PMID:25741868) requires a novel missense change at an amino acid residue where a different missense change has previously been determined to be pathogenic. NM_006218.4:c.331_336del in PIK3CA is an in-frame insertion/deletion of undetermined repeat-region status predicted to produce NP_006209.2:p.(Lys111_Ile112del). As a result, no missense change exists at this residue to compare against a different pathogenic missense change at the same position, so PM5's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies. Details ▾Hide ▴
Rule
deterministic_prefilter: requires_missense
Evidence considered
  • Deterministic consequence classification: in_frame_indel_unknown (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules
PM6 VCEPNot applicable: the VCEP explicitly directs that PM6 is addressed through PS2 and will not be used independently. Details ▾Hide ▴
Reasoning

The governing Brain Malformations VCEP explicitly states that PM6 is addressed according to PS2 and will not be used. PM6 is therefore not applicable independently, regardless of whether de novo status is suspected or parental confirmation is incomplete. The exact variant was not found in the governing VCEP full-text file after searching c.331_336del, p.Lys111_Ile112del, and p.K111_I112del.

VCEP rule
PM6 is addressed according to PS2 and will not be used.
Evidence considered
  • The VCEP marks PM6 as not applicable and states that this point is addressed according to PS2 and will not be used.
Still missing
  • No independent PM6 assessment is permitted under the governing VCEP.
  • No exact variant entry was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt when searched as c.331_336del, p.Lys111_Ile112del, and p.K111_I112del.
Sources
cspec ↗
PP1 VCEPNot applicable: the VCEP excludes PP1 because these PIK3CA disease-causing variants are typically germline mosaic, de novo, or mosaic. Details ▾Hide ▴
Reasoning

The governing Brain Malformations VCEP marks PP1 as not applicable because disease-causing PIK3CA variants in this disease context are germline mosaic, de novo, or mosaic. Accordingly, segregation among multiple affected family members is not used for PP1 in this framework. The exact variant was not found in the governing VCEP full-text file after searching c.331_336del, p.Lys111_Ile112del, and p.K111_I112del.

VCEP rule
PP1 is not applicable since disease-causing variants are germline mosaic, de novo, or mosaic.
Evidence considered
  • The VCEP marks PP1 as not applicable because the relevant disease-causing variants are germline mosaic, de novo, or mosaic.
Still missing
  • No independent PP1 segregation assessment is permitted under the governing VCEP.
  • No exact variant entry was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt when searched as c.331_336del, p.Lys111_Ile112del, and p.K111_I112del.
Sources
cspec ↗
PP2 N/APP2 (Richards et al. 2015, PMID:25741868) applies to a missense variant in a gene with a low rate of benign missense variation, where missense variants are a common mechanism of disease. NM_006218.4:c.331_336del in PIK3CA is an in-frame insertion/deletion of undetermined repeat-region status predicted to produce NP_006209.2:p.(Lys111_Ile112del). As a result, the gene's missense-constraint properties are irrelevant because no missense change is present to evaluate, so PP2's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies. Details ▾Hide ▴
Rule
deterministic_prefilter: requires_missense
Evidence considered
  • Deterministic consequence classification: in_frame_indel_unknown (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules
PP3 VCEPNot applicable: the in-frame p.(Lys111_Ile112del) deletion is a protein-length-changing variant outside the VCEP's PP3 scope. Details ▾Hide ▴
Reasoning

PP3 is not applicable. The variant is an in-frame deletion, NM_006218.4:c.331_336del, producing p.(Lys111_Ile112del), and therefore is a protein-length-changing variant outside the permitted PP3 missense or splice-region/intronic scope. The governing Brain Malformations VCEP specification independently states that PP3 is not applicable for these PIK3CA gain-of-function variants because traditional computational pathogenicity predictors focus on loss-of-function mechanisms. REVEL and SpliceAI were not used to assign PP3.

VCEP rule
ClinGen Brain Malformations VCEP PP3: not applicable for these PIK3CA gain-of-function variants; computational pathogenicity prediction algorithms are not applicable under the specification.
Evidence considered
  • The governing ClinGen Brain Malformations VCEP specification states that PP3 is not applicable for these PIK3CA gain-of-function variants because traditional mutation pathogenicity prediction algorithms focus on loss-of-function mechanisms.
  • Case normalization identifies NM_006218.4:c.331_336del as NP_006209.2:p.(Lys111_Ile112del), an in-frame deletion with protein-length change; consequently no REVEL or SpliceAI score was used for PP3.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
Sources
cspec ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
PP4 VCEPNot applicable: the VCEP states that phenotype specificity is accounted for under PS4 rather than assigned separately as PP4. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP explicitly states that PP4 is not applicable because phenotype specificity is accounted for under PS4. No independent PP4 assignment is made.

VCEP rule
ClinGen Brain Malformations VCEP PP4: not applicable because phenotype specificity is accounted for under PS4.
Evidence considered
  • The ClinGen Brain Malformations VCEP specification states: "Not applicable since this criterion is accounted for under PS4."
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
Sources
cspec ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
PP5 VCEPNot applicable: the VCEP prohibits PP5, and ClinVar has no exact-variant expert-panel pathogenic or likely-pathogenic classification. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP marks PP5 not applicable and states that the criterion is not for use. Independently, ClinVar contains no exact-variant record or expert-panel classification for NM_006218.4:c.331_336del, so the required exact-variant ClinVar expert-panel trigger is absent.

VCEP rule
ClinGen Brain Malformations VCEP PP5: not applicable; PP5 is not for use. The additional exact-variant ClinVar expert-panel rule is also not triggered because no such classification exists.
Evidence considered
  • The ClinGen Brain Malformations VCEP states that PP5 is not for use and marks it not applicable.
  • ClinVar exact-variant searches found no variation ID, classification, review status, submission, or expert-panel assertion for NM_006218.4:c.331_336del and its equivalent protein notations.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
Sources
cspec ↗clinvar ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
BS4 VCEPNot applicable: the VCEP excludes BS4 for these de novo, germline-mosaic, or post-zygotic PIK3CA disease mechanisms. Details ▾Hide ▴
Reasoning

The governing Brain Malformations VCEP marks BS4 as not applicable because the relevant PIK3CA variants are de novo, germline mosaic, or post-zygotic mutations. Lack of segregation in affected family members is therefore not used for BS4 in this framework. The exact variant was not found in the governing VCEP full-text file after searching c.331_336del, p.Lys111_Ile112del, and p.K111_I112del.

VCEP rule
BS4 is not applicable as these are de novo, germline mosaic, or post-zygotic mutations.
Evidence considered
  • The VCEP marks BS4 as not applicable because these variants are de novo, germline mosaic, or post-zygotic mutations.
Still missing
  • No independent BS4 non-segregation assessment is permitted under the governing VCEP.
  • No exact variant entry was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt when searched as c.331_336del, p.Lys111_Ile112del, and p.K111_I112del.
Sources
cspec ↗
BP1 VCEPBP1 (Richards et al. 2015, PMID:25741868) applies to a missense variant in a gene for which primarily truncating variants are known to cause disease. NM_006218.4:c.331_336del in PIK3CA is an in-frame insertion/deletion of undetermined repeat-region status predicted to produce NP_006209.2:p.(Lys111_Ile112del). As a result, the gene's truncating-variant mechanism is irrelevant because no missense change is present to evaluate, so BP1's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies. Details ▾Hide ▴
VCEP rule
deterministic_prefilter: requires_missense
Evidence considered
  • Deterministic consequence classification: in_frame_indel_unknown (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules
BP3 VCEPNot applicable: the PIK3CA VCEP states its exon regions lack repetitive regions without known function, excluding BP3 for this in-frame deletion. Details ▾Hide ▴
Reasoning

The variant is an in-frame deletion predicted to remove Lys111_Ile112 from PIK3CA on the relevant NM_006218.4 transcript. BP3 would require an in-frame deletion or insertion in a repetitive region without a known function, but the governing ClinGen Brain Malformations VCEP specification explicitly designates BP3 not applicable for PIK3CA because its exon regions do not contain repetitive regions without a known function. The generic BP3 definition therefore cannot be applied.

VCEP rule
VCEP BP3: Not Applicable for this VCEP; the exon regions do not have repetitive regions without a known function.
Evidence considered
  • NM_006218.4:c.331_336del is an in-frame deletion predicted to produce NP_006209.2:p.(Lys111_Ile112del).
  • The ClinGen Brain Malformations VCEP specification states that BP3 is not applicable because the specified genes do not have exon regions containing repetitive regions without a known function.
Sources
cspec ↗
BP4 N/ANot applicable: the in-frame p.(Lys111_Ile112del) deletion is outside BP4's specified synonymous, intronic, splice-region, and UTR scope. Details ▾Hide ▴
Reasoning

BP4 is not applicable. The variant is an in-frame deletion, NM_006218.4:c.331_336del, producing p.(Lys111_Ile112del), so it is a protein-length-changing variant rather than a synonymous, intronic, splice-region, or UTR variant within the governing VCEP's BP4 scope. Although SpliceAI reports a max delta score of 0.11, the score was not evaluated because the variant consequence is outside BP4 scope; it cannot be used to assign BP4 to this in-frame deletion.

Rule
ClinGen Brain Malformations VCEP BP4: applicable only to synonymous, intronic positions excluding canonical splice sites, and non-coding UTR variants when two of three splice-prediction tools predict no splice change.
Evidence considered
  • The governing ClinGen Brain Malformations VCEP specification limits BP4 to synonymous, intronic positions excluding canonical splice sites, and non-coding UTR variants when two of three splice-prediction tools show no impact.
  • The case bundle reports SpliceAI max delta 0.11, but this score was not used because BP4 is upstream not_applicable for this protein-length-changing in-frame deletion.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
Sources
cspec ↗spliceai ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
BP6 VCEPNot applicable: the VCEP prohibits BP6, and ClinVar has no exact-variant expert-panel benign or likely-benign classification. Details ▾Hide ▴
Reasoning

The governing ClinGen Brain Malformations VCEP marks BP6 not applicable and states that the criterion is not for use. Independently, ClinVar contains no exact-variant record or expert-panel benign or likely-benign classification for NM_006218.4:c.331_336del, so the required exact-variant ClinVar expert-panel trigger is absent.

VCEP rule
ClinGen Brain Malformations VCEP BP6: not applicable; BP6 is not for use. The additional exact-variant ClinVar expert-panel rule is also not triggered because no such classification exists.
Evidence considered
  • The ClinGen Brain Malformations VCEP states that BP6 is not for use and marks it not applicable.
  • ClinVar exact-variant searches found no variation ID, classification, review status, submission, or expert-panel assertion for NM_006218.4:c.331_336del and its equivalent protein notations.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
Sources
cspec ↗clinvar ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
BP7 N/ABP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_006218.4:c.331_336del in PIK3CA is an in-frame insertion/deletion of undetermined repeat-region status predicted to produce NP_006209.2:p.(Lys111_Ile112del). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies. Details ▾Hide ▴
Rule
deterministic_prefilter: requires_synonymous
Evidence considered
  • Deterministic consequence classification: in_frame_indel_unknown (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules

Identifiers

Gene
PIK3CA
Transcript
NM_006218.4
Coding (HGVS c.)
NM_006218.4:c.331_336del
Protein (HGVS p.)
NP_006209.2:p.(Lys111_Ile112del)
GRCh38
chr3:179199155 AAAGATC>A
GRCh37
chr3:178916943 AAAGATC>A
Location and type
Exon 2 · in frame indel unknown
COSMIC
COSV55941739

Gene diagram

Every interpreted variant in PIK3CA, mapped onto the exon structure of NM_006218.4. Select a row to find it on the plot.

PIK3CANM_006218.4
Fetching transcript structure from UCSC…
gnomAD v4.1 Allele count data not recorded
gnomAD v2.1 Allele count data not recorded
gnomAD-Canada v1.0 Allele count data not recorded

Statements

gnomAD v4.1

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -28 bp
0.004
SpliceAI acceptor gainat -114 bp
0.002
SpliceAI donor lossat +22 bp
0.021
SpliceAI donor gainat -120 bp
0.110
Pangolin splice lossmagnitude shown
-0.052
Pangolin splice gain
0.012

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

PP3 VCEPNot applicable: the in-frame p.(Lys111_Ile112del) deletion is a protein-length-changing variant outside the VCEP's PP3 scope. Details ▾Hide ▴
Reasoning

PP3 is not applicable. The variant is an in-frame deletion, NM_006218.4:c.331_336del, producing p.(Lys111_Ile112del), and therefore is a protein-length-changing variant outside the permitted PP3 missense or splice-region/intronic scope. The governing Brain Malformations VCEP specification independently states that PP3 is not applicable for these PIK3CA gain-of-function variants because traditional computational pathogenicity predictors focus on loss-of-function mechanisms. REVEL and SpliceAI were not used to assign PP3.

VCEP rule
ClinGen Brain Malformations VCEP PP3: not applicable for these PIK3CA gain-of-function variants; computational pathogenicity prediction algorithms are not applicable under the specification.
Evidence considered
  • The governing ClinGen Brain Malformations VCEP specification states that PP3 is not applicable for these PIK3CA gain-of-function variants because traditional mutation pathogenicity prediction algorithms focus on loss-of-function mechanisms.
  • Case normalization identifies NM_006218.4:c.331_336del as NP_006209.2:p.(Lys111_Ile112del), an in-frame deletion with protein-length change; consequently no REVEL or SpliceAI score was used for PP3.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
Sources
cspec ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
BP4 N/ANot applicable: the in-frame p.(Lys111_Ile112del) deletion is outside BP4's specified synonymous, intronic, splice-region, and UTR scope. Details ▾Hide ▴
Reasoning

BP4 is not applicable. The variant is an in-frame deletion, NM_006218.4:c.331_336del, producing p.(Lys111_Ile112del), so it is a protein-length-changing variant rather than a synonymous, intronic, splice-region, or UTR variant within the governing VCEP's BP4 scope. Although SpliceAI reports a max delta score of 0.11, the score was not evaluated because the variant consequence is outside BP4 scope; it cannot be used to assign BP4 to this in-frame deletion.

Rule
ClinGen Brain Malformations VCEP BP4: applicable only to synonymous, intronic positions excluding canonical splice sites, and non-coding UTR variants when two of three splice-prediction tools predict no splice change.
Evidence considered
  • The governing ClinGen Brain Malformations VCEP specification limits BP4 to synonymous, intronic positions excluding canonical splice sites, and non-coding UTR variants when two of three splice-prediction tools show no impact.
  • The case bundle reports SpliceAI max delta 0.11, but this score was not used because BP4 is upstream not_applicable for this protein-length-changing in-frame deletion.
Still missing
  • No entry for c.331_336del, p.Lys111_Ile112del, or p.K111_I112del was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this search result is not evidence that the variant is absent from the specification.
Sources
cspec ↗spliceai ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
BP7 N/ABP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_006218.4:c.331_336del in PIK3CA is an in-frame insertion/deletion of undetermined repeat-region status predicted to produce NP_006209.2:p.(Lys111_Ile112del). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false; framework_mode=unstructured_ruleset); the generic ACMG/AMP 2015 fallback applies. Details ▾Hide ▴
Rule
deterministic_prefilter: requires_synonymous
Evidence considered
  • Deterministic consequence classification: in_frame_indel_unknown (prefetch.json normalized protein consequence)
Sources
generic_acmg_combination_rules

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.11).

1 paper record 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

  • Systematic Functional Annotation of Somatic Mutations in Cancer.
    The paper does not explicitly mention the exact PIK3CA variant c.331_336del, NP_006209.2:p.(K111_I112del). It reports functional screening of other PIK3CA variants in Ba/F3 and MCF10A cell models, including the distinct nearby variant K111delK, and provides no proband, parental, segregation, or de novo evidence for the variant under review.
    Does not name this variant
    PMID 29533785 ↗
    Quoted passage
    PIK3CAK111delK had the strongest activating mutation score in both the pooled and individual in vitro formats.

    Results, Development of a Versatile Functional Genomic Platform; paragraph describing parallel pooled and individual screens of 29 PIK3CA mutants

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 0.110 Open source ↗
ClinVar Captured ClinVar source record Open source ↗
COSMIC Captured COSMIC source record Open source ↗
Cancer hotspots Captured Cancer Hotspots source record Open source ↗
OncoKB Captured OncoKB 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.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant is absent from ClinVar.

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.11).

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.

Somatic

This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55941739, n = 2 times).

Cancer Hotspots

This variant lies in a statistically significant hotspot.