CDK4 c.803G>A, p.(Gly268Glu)

Reasoning

PM2 is met at supporting strength under the generic ACMG/AMP framework. The exact CDK4 NM_000075.3:c.803G>A (p.Gly268Glu) variant is reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. The case bundle does not provide ancestry-stratified counts, coverage, or disease-specific maximum credible allele-frequency calculations, so the conclusion is limited to the generic absence-based PM2 assessment.

Rule

Generic ACMG/AMP PM2: absent from controls in population databases; apply at supporting strength here because no CDK4-specific VCEP specification was retrieved.

Evidence considered

• The exact variant is absent from gnomAD v2.1.
• The exact variant is absent from gnomAD v4.1.
• The exact variant is absent from gnomAD-Canada v1.0.
• Generic ACMG/AMP PM2 supports rare-variant evidence when a variant is absent from population databases; no disease-specific VCEP rule was available for CDK4 in this case.

Still missing

• Population sample sizes, coverage metrics, and ancestry-stratified frequencies are not included in the retrieved records.
• A disease-specific maximum credible allele-frequency calculation incorporating prevalence and penetrance is unavailable.

Sources

Reasoning

PM1 requires the variant to fall in a mutational hotspot or well-established functional domain without benign variation. Codon 268 (NP_000066.1:p.Gly268Glu) lies in the C-terminal portion of the CDK4 kinase domain but is not flagged as a statistically significant hotspot: the CancerHotspots.org lookup for 'CDK4 G268' returned no result, COSMIC has no somatic reports at this position, and OncoKB provides no variant-specific reviewed functional evidence (classification 'Unknown Oncogenic Effect', not_reviewed=true), only generic gene-level context. No CDK4 CSPEC/VCEP domain framework is available in this bundle to define a critical functional domain boundary. CDK4's well-characterized germline disease mechanism in familial melanoma is a gain-of-function loss of p16INK4a binding concentrated at a distinct residue (Arg24) rather than at codon 268, further arguing against a hotspot/critical-domain classification here.

Evidence considered

• CancerHotspots.org search for 'CDK4 G268' returned search_status=no_result, found=false (evidence.json hotspots block).
• COSMIC search for 'CDK4 c.803G>A' returned search_status=no_result, found=false (evidence.json cosmic block).
• OncoKB lookup for CDK4/G268E: classification 'Unknown Oncogenic Effect', is_variant_specific=false, not_reviewed=true; only generic gene-level narrative about CDK4 kinase alterations in sarcomas/gliomas is provided, no domain-criticality statement for residue 268.

Still missing

• No CDK4-specific VCEP/CSPEC PM1 domain or hotspot framework is available to formally define critical functional regions for this gene.

Sources

Reasoning

No governing VCEP CSPEC or gene-specific PP3/BP4 lookup was found for CDK4 (cspec.found=false, vcep_materials empty, framework_mode=generic_acmg), so generic ACMG computational-evidence rules apply. NM_000075.3:c.803G>A is a missense substitution (NP_000066.1:p.(Gly268Glu)); consequence_class=missense, canonical_splice_consensus=false, so the splice-impact path is not the governing mechanism here. REVEL score = 0.469 (source: revel), which falls in the indeterminate zone between the ClinGen SVI-calibrated benign-supporting cutoff (<=0.290) and pathogenic-supporting cutoff (>=0.644) established in the REVEL calibration publication (PMID:36413997), so it does not reach the threshold needed to apply PP3. BayesDel score (0.160283) was also computed but has no verified published calibration threshold available to this pipeline and is therefore treated as not_available for PP3/BP4 per standing policy, regardless of the numeric value. SpliceAI (source: spliceai) shows max delta score 0.083 (DS_AG 0.083, DS_DG 0.057, others 0.0), far below any splice-impact threshold, confirming there is no plausible in-silico splicing mechanism for this exonic missense change that would provide an alternate PP3 basis.

Rule

generic_acmg_PP3_missense_and_splice_insilico

Evidence considered

• REVEL score 0.469 for NM_000075.3:c.803G>A (source_registry: revel) falls in the indeterminate zone per ClinGen SVI-calibrated REVEL thresholds (PMID:36413997): pathogenic-supporting >=0.644, benign-supporting <=0.290.
• SpliceAI (source_registry: spliceai) predicts no significant splice impact, max delta score 0.083 (DS_AG 0.083, DS_DG 0.057, DS_AL/DS_DL 0.0), well below any recognized splice-disruption threshold, so no alternate splicing-based PP3 evidence applies to this missense variant.
• BayesDel score 0.160283 was computed (source_registry: bayesdel) but is treated as not_available for PP3/BP4 because no verified published calibration threshold/PMID exists for it in this pipeline.
• No CDK4-specific VCEP CSPEC or PP3/BP4 lookup spreadsheet was found (case_summary.json cspec.found=false; vcep_materials.json summaries={} and files_found=[]), so no VCEP pre-assigned code exists to apply directly.

Still missing

• REVEL score is in the calibrated indeterminate zone (0.290-0.644), too weak to support pathogenic in-silico evidence.
• BayesDel score exists but has no pipeline-verified published calibration threshold, so it cannot be used to support PP3.
• No gene-specific VCEP PP3/BP4 lookup table is available for CDK4 to override the generic assessment.

Sources

Reasoning

PP5 is not met. The exact-variant ClinVar record has no expert-panel submission; it contains two single-submitter laboratory classifications of uncertain significance. Ordinary laboratory submissions and non-expert assertions cannot trigger PP5.

Evidence considered

• ClinVar variation 3575005 exactly matches NM_000075.3:c.803G>A / p.Gly268Glu, but the submission audit reports zero expert-panel submissions and two single-submitter uncertain-significance classifications.
• No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification is present.

Sources

Reasoning

BA1 is not met. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, providing no evidence of an allele frequency above the stand-alone benign threshold of 5% under the generic ACMG/AMP framework.

Rule

Generic ACMG/AMP BA1: allele frequency greater than 5% supports stand-alone benign evidence; absence from population databases does not meet BA1.

Evidence considered

• gnomAD v2.1 reports the exact variant as absent.
• gnomAD v4.1 reports the exact variant as absent.
• gnomAD-Canada v1.0 reports the exact variant as absent.
• The generic ACMG/AMP framework treats BA1 as a stand-alone benign criterion when the allele frequency is greater than 5%; no such frequency is present here.

Sources

Reasoning

Same computational evidence base as PP3 assessed under generic ACMG rules (no CDK4 VCEP CSPEC/lookup available). REVEL = 0.469 (source: revel) sits in the indeterminate zone of the ClinGen SVI-calibrated REVEL scale (PMID:36413997: benign-supporting <=0.290, pathogenic-supporting >=0.644), so it is not low enough to support BP4 via the missense path. SpliceAI (source: spliceai) predicts no splice impact (max delta 0.083), but this variant is missense with no canonical splice-consensus involvement, so the negative splice score does not independently substitute for a positive missense benign-in-silico call at this locus and is only corroborative that no alternate splicing mechanism exists. BayesDel (0.160283) remains not_available for PP3/BP4 due to lack of a verified published threshold in this pipeline.

Rule

generic_acmg_BP4_missense_and_splice_insilico

Evidence considered

• REVEL score 0.469 (source_registry: revel) falls between the calibrated benign-supporting (<=0.290) and pathogenic-supporting (>=0.644) REVEL thresholds from PMID:36413997, so it does not meet BP4.
• SpliceAI (source_registry: spliceai) max delta score 0.083 indicates no predicted splicing disruption, consistent with (but not sufficient alone to trigger) a benign computational call, since the variant's primary mechanism under evaluation is missense protein change, not splicing.
• BayesDel score 0.160283 (source_registry: bayesdel) is treated as not_available for BP4 because no verified published calibration threshold/PMID exists for it in this pipeline.
• No CDK4-specific VCEP CSPEC or PP3/BP4 lookup spreadsheet was found (case_summary.json cspec.found=false; vcep_materials.json empty), so no VCEP pre-assigned code exists to apply directly.

Still missing

• REVEL score is in the indeterminate zone, not low enough to meet the calibrated benign-supporting cutoff for BP4.
• BayesDel score exists but lacks a pipeline-verified published calibration threshold and cannot be used to support BP4.
• No gene-specific VCEP PP3/BP4 lookup table is available for CDK4 to override the generic assessment.

Sources

Reasoning

BP6 is not met. The exact-variant ClinVar record has no expert-panel submission and no Benign or Likely benign expert-panel classification. The available laboratory submissions are uncertain significance, and ordinary laboratory or aggregate ClinVar labels cannot trigger BP6.

Evidence considered

• ClinVar variation 3575005 exactly matches NM_000075.3:c.803G>A / p.Gly268Glu, but the submission audit reports zero expert-panel submissions and two single-submitter uncertain-significance classifications.
• No exact-variant ClinVar expert-panel Benign or Likely benign classification is present.

Sources

Reasoning

PS1 requires an established pathogenic variant that produces the identical amino-acid change (p.Gly268Glu) via a different nucleotide substitution. No CDK4 CSPEC/VCEP is available for this gene (cspec.found=false), and the pm5_candidates artifact explicitly reports eligible_for_classic_pm5_search=false with 0 same-residue candidates harvested, instructing that PM5/PS1-style comparator conclusions should not be drawn from that artifact alone. No other source in the case bundle (ClinVar record, OncoKB, COSMIC, hotspots) provides a same-amino-acid-change comparator variant.

Evidence considered

• pm5_candidates.json records reference_aa=G, position=268, observed_alt_aa=E, but candidate_summary shows total_candidates_seen=0 and same_residue_candidates=0, with an explicit recommendation not to apply PM5-type conclusions from this artifact alone.
• case_summary.json cspec.found=false confirms no CDK4-specific VCEP specification is available to define PS1 semantics for this gene.

Still missing

• No same-amino-acid-change (p.Gly268Glu) comparator variant with established pathogenic classification was identified or searched for in this bundle.
• Classic PM5/PS1 same-residue candidate harvesting was explicitly skipped by the upstream pm5_candidates step (pm5_mode=unknown, eligible_for_classic_pm5_search=false).

Sources

Reasoning

No proband-level de novo evidence or parental testing results are provided in the case-evidence bundle. PS2 cannot be assessed without confirmed absence of the variant in both biological parents and appropriate maternity/paternity confirmation.

Rule

Generic ACMG/AMP PS2: confirmed de novo occurrence in a patient with the disease and no evidence of parental mosaicism; parental origin should be established with appropriate testing.

Evidence considered

• The consolidated case-evidence bundle contains no proband pedigree, parental testing, de novo statement, or maternity/paternity confirmation for NM_000075.3:c.803G>A (CDK4 p.Gly268Glu).
• No publication in the case bundle provides variant-specific de novo or parental-testing evidence.

Still missing

• Proband pedigree and phenotype context
• Variant testing results for both biological parents
• Maternity/paternity confirmation and testing methodology

Reasoning

No ClinGen VCEP/CSPEC exists for CDK4 in this case (cspec.found=false), so no gene-specific functional evidence specification is available. No validated functional/biochemical assay data (e.g. kinase activity, in vitro binding, cell proliferation rescue) for NM_000075.3:c.803G>A (p.Gly268Glu) was identified anywhere in the case bundle. OncoKB was queried and explicitly reported no variant-specific reviewed functional evidence, only gene-level context. The literature set returned by ClinVar/PubMed for this variant (PMID:25741868 = ACMG/AMP 2015 methods guideline; PMID:26389258 and PMID:26389333 = PDQ health-professional overview articles with no abstract content retrievable) contains no experimental assay results and none were flagged as functional-theme papers with actual data.

Still missing

• No validated in vitro/in vivo functional assay (e.g. CDK4 kinase activity, Rb phosphorylation, cell cycle rescue) reported for this specific variant in the reviewed sources.
• No CDK4-specific VCEP/CSPEC PS3 assay-validation framework was available to calibrate assay strength.
• OncoKB gene-level page did not surface variant-specific functional data.

Reasoning

No case-control enrichment dataset, affected-case series, or validated excess of the exact variant in affected individuals versus controls was provided. The available ClinVar record contains two single-submitter laboratory assertions and does not provide usable case-count evidence.

Evidence considered

• The exact variant is present in ClinVar variation 3575005, but the record contains only two clinical-laboratory submissions classified as uncertain significance and no case-control counts or affected-case enrichment analysis.
• The triaged literature sources were not available as full text for this group and no source in the bundle documented exact-variant case-control enrichment.

Still missing

• A case-control study or adequately documented affected-case series for NM_000075.3:c.803G>A (NP_000066.1:p.Gly268Glu) is unavailable.

Sources

Reasoning

No applicable CDK4-specific VCEP/CSPEC framework was retrieved, so the generic ACMG/AMP framework was used. The case bundle contains no affected-proband observations, pathogenic/likely pathogenic second-allele information, phase determination, or inheritance data demonstrating this variant in trans with a pathogenic variant for a recessive disorder.

Rule

Generic ACMG/AMP 2015 PM3: pathogenic or likely pathogenic variants observed in trans with the variant under evaluation, with strength dependent on the quality and number of observations; phase and inheritance must be established.

Evidence considered

• The case bundle identifies CDK4:c.803G>A (p.Gly268Glu) but provides no family-level or proband-level allelic data relevant to PM3.
• The generic ACMG/AMP framework was consulted because no CDK4-specific VCEP/CSPEC framework was available; absence of phase and affected-proband evidence prevents assessment of PM3.

Still missing

• Affected-proband genotype and phenotype details are unavailable.
• No pathogenic or likely pathogenic variant in the same individual is documented.
• No validated cis/trans phase information is documented.
• No applicable inheritance model supporting PM3 is documented.

Sources

Reasoning

PM5 requires a different missense change at the same residue (Gly268) previously established as pathogenic. The dedicated pm5_candidates.json artifact confirms residue position 268 (reference_aa=G) but reports total_candidates_seen=0 and same_residue_candidates=0, with pm5_mode=unknown and eligible_for_classic_pm5_search=false; the artifact's own recommendation instructs not to apply PM5 from it alone. No other same-residue comparator variant data (e.g., other CDK4 codon-268 substitutions with pathogenic ClinVar classifications) is present anywhere in the case bundle.

Evidence considered

• pm5_candidates.json: candidate_summary.same_residue_candidates=0, candidate_summary.total_candidates_seen=0, recommendation.level='not_applicable', explicitly stating classic same-residue PM5 semantics could not be confirmed safely and candidate harvesting was skipped.

Still missing

• No same-residue (codon 268) alternate amino-acid-change comparator variants were identified or systematically searched for; the upstream PM5 candidate harvesting step was explicitly skipped for this variant.

Sources

Reasoning

No variant-specific report or clinical record in the case-evidence bundle describes a presumed de novo occurrence without parental testing. PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: presumed de novo occurrence in a patient with the disease when parental testing is unavailable or incomplete; this is weaker than confirmed de novo evidence.

Evidence considered

• The consolidated case-evidence bundle provides no variant-specific de novo assertion, family history, or parental testing limitation for NM_000075.3:c.803G>A (CDK4 p.Gly268Glu).
• The available ClinVar record reports uncertainty and does not provide usable de novo evidence for this criterion.

Still missing

• Variant-specific clinical case description
• Proband phenotype and disease ascertainment
• Evidence that the variant was presumed de novo despite unavailable or incomplete parental testing

Reasoning

No affected relatives, variant genotypes, phenotype assessments, or informative meioses are documented. Co-segregation cannot be evaluated, and no strength can be assigned.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease; strength depends on the amount and informativeness of segregation evidence.

Evidence considered

• The consolidated case-evidence bundle contains no family segregation data, affected-relative testing, phenotype concordance assessment, or meiosis count for NM_000075.3:c.803G>A (CDK4 p.Gly268Glu).
• No relevant variant-specific segregation publication was available in the case bundle.

Still missing

• Pedigree with affected and unaffected relatives
• Variant testing results for relatives
• Phenotype consistency and diagnostic ascertainment in relatives
• Number of informative meioses

Reasoning

PP2 requires that the gene has a low rate of benign missense variation and that missense variants are a common/recognized mechanism of disease for that gene. No CDK4-specific VCEP/CSPEC is available in this bundle to confirm formal PP2 gene-level eligibility, and no curated missense-constraint metric (e.g., ExAC/gnomAD missense Z-score, ClinGen gene curation) is present in the case evidence. CDK4's familial-melanoma disease mechanism is generally understood in the literature to be a narrow, site-specific gain-of-function effect rather than broadly distributed missense intolerance, which would argue against a standard PP2 gene profile, but no citable source within this case's evidence bundle substantiates that gene-level determination for this specific criterion.

Evidence considered

• case_summary.json cspec.found=false and vcep_materials.json note='no cspec url available' confirm no CDK4-specific PP2 gene-eligibility guidance exists in this case bundle.

Still missing

• No CDK4-specific VCEP/CSPEC PP2 gene-eligibility statement is available in this bundle.
• No missense-constraint or benign-missense-rate metric for CDK4 is present in the case evidence to formally assess PP2 applicability.

Reasoning

The case bundle does not provide a sufficiently specific, well-established phenotype or a documented phenotype match for the patient carrying this exact variant. Gene-level association with familial melanoma is not sufficient to apply PP4 without case phenotype evidence.

Still missing

• Patient phenotype and a disease-specific phenotype match are not documented in the available case-evidence bundle.

Reasoning

BS1 cannot be assessed from the available population evidence. The variant is absent from the available population datasets, but no disease-specific maximum credible allele frequency, prevalence, penetrance, inheritance model, or observed allele count/frequency is provided to establish the BS1 threshold of a frequency greater than expected for the disorder.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder; apply only with a disease-specific expected-frequency threshold and interpretable population frequency evidence.

Evidence considered

• The exact variant is reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• Absence does not demonstrate the BS1 condition of an allele frequency greater than expected for the disease; a disease-specific expected-frequency threshold and auditable population counts are missing.

Still missing

• Disease-specific maximum credible allele frequency or equivalent expected-frequency threshold is unavailable.
• Population allele counts, coverage, and ancestry-stratified frequencies are unavailable in the case evidence bundle.
• CDK4-associated disease prevalence, penetrance, and inheritance parameters relevant to this variant are not established in the available evidence.

Sources

Reasoning

BS2 cannot be assessed. The available population records report absence of the variant but provide no observations in healthy adults, no homozygotes, and no compound heterozygotes. Absence from population databases is not evidence that the variant was observed in unaffected individuals.

Rule

Generic ACMG/AMP BS2: the variant is observed in a healthy adult individual for a fully penetrant dominant disorder, or in a healthy adult homozygote/compound heterozygote for a recessive disorder; absence from databases does not satisfy BS2.

Evidence considered

• gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 each report the exact variant as absent.
• Because no unaffected carriers or homozygous/compound-heterozygous individuals are reported, the evidence does not establish BS2.

Still missing

• No verified healthy-adult observations are available.
• No homozygote or compound-heterozygote observations are available.
• No ascertainment, phenotype, age, or penetrance information is available for any population carriers.

Sources

Reasoning

As with PS3, no ClinGen VCEP/CSPEC exists for CDK4 in this case (cspec.found=false) and no functional assay data of any kind (showing normal/wild-type-like activity) was identified for NM_000075.3:c.803G>A (p.Gly268Glu) in the case bundle. OncoKB found no variant-specific reviewed functional evidence, and the retrieved literature (PMID:25741868 ACMG guideline; PMID:26389258, PMID:26389333 PDQ overviews) contains no experimental assay results relevant to benign functional impact.

Still missing

• No functional assay showing normal/wild-type activity has been reported for this variant in the reviewed sources.
• No CDK4-specific VCEP/CSPEC BS3 assay-validation framework was available.

Reasoning

No affected relatives or family genotyping results are available to demonstrate that the variant does not segregate with disease. BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; requires informative affected relatives and reliable genotype and phenotype data.

Evidence considered

• The consolidated case-evidence bundle contains no documented affected relatives who lack the variant and no other variant-specific non-segregation evidence for NM_000075.3:c.803G>A (CDK4 p.Gly268Glu).
• Absence of family data is insufficient to apply BS4 and is not evidence of non-segregation.

Still missing

• Pedigree identifying affected relatives
• Genotypes of affected relatives
• Reliable phenotype and age-of-onset data for tested relatives
• Assessment of informative non-segregation

Reasoning

BP1 requires that missense variation is NOT a common disease mechanism for the gene (i.e., loss-of-function/truncating variants predominate). No CDK4-specific VCEP/CSPEC or curated gene-mechanism statement is present in this bundle to formally evaluate whether missense variants are an atypical/benign-leaning mechanism for CDK4, so this criterion cannot be reliably assessed from the available evidence.

Evidence considered

• case_summary.json cspec.found=false and vcep_materials.json note='no cspec url available' confirm no CDK4-specific gene-mechanism guidance exists in this case bundle to assess BP1.

Still missing

• No CDK4-specific VCEP/CSPEC or curated gene-mechanism data addressing whether missense is an unusual disease mechanism (required to assess BP1 applicability) is available in this bundle.

Reasoning

No applicable CDK4-specific VCEP/CSPEC framework was retrieved, so the generic ACMG/AMP framework was used. The case bundle contains no documentation that this variant was observed in cis with a pathogenic/likely pathogenic variant, nor sufficient phase or inheritance information to evaluate BP2.

Rule

Generic ACMG/AMP 2015 BP2: the variant is observed in trans/cis with a pathogenic variant for a fully penetrant recessive disorder or in cis with a pathogenic variant for a dominant disorder, as applicable; phase and disease context must be established.

Evidence considered

• The case bundle contains no affected-proband, family, phase, or linked-variant observations that could establish occurrence of this variant in cis with a pathogenic/likely pathogenic variant.
• The generic ACMG/AMP framework was consulted because no CDK4-specific VCEP/CSPEC framework was available; the available evidence is insufficient to assess BP2.

Still missing

• No second pathogenic or likely pathogenic variant is documented in the relevant individual(s).
• No validated cis-phase determination is documented.
• No inheritance or family segregation data are available for BP2 assessment.

Sources

Reasoning

No evidence was provided that the exact variant is established as pathogenic for a different molecular or phenotypic disease mechanism while being evaluated for the current condition. The available ClinVar assertions are uncertain significance and cannot establish BP5.

Evidence considered

• ClinVar variation 3575005 reports the exact variant as uncertain significance in two single-submitter laboratory records and provides no established alternate-disease pathogenic classification.

Still missing

• A documented alternate-disease pathogenic association for the exact variant is unavailable.

Sources