CDK4 c.736C>T, p.(Arg246Cys)

Reasoning

PM2 is not met because the variant is present in population databases. It is observed at AF 9.91304e-06 (16/1,614,036 alleles) in gnomAD v4.1 and AF 2.78567e-05 (7/251,286 alleles) in gnomAD v2.1. Both datasets report zero homozygotes, but presence of the variant, even at a very low frequency, precludes a strict absent-from-controls PM2 call under the generic ACMG/AMP rule.

Rule

Generic ACMG/AMP PM2: variant is absent from or extremely rare in population databases appropriate for the disorder; a strict absence-based application is not satisfied when the variant is observed.

Evidence considered

• gnomAD v4.1 directly reports the variant in 16/1,614,036 alleles with AF 9.91304e-06 and 0 homozygotes.
• gnomAD v2.1 directly reports the variant in 7/251,286 alleles with AF 2.78567e-05 and 0 homozygotes.
• The generic ACMG/AMP PM2 rule concerns absence or extreme rarity in population databases; this variant is not absent, so strict PM2 is not met.

Sources

Reasoning

CDK4 c.736C>T (p.(Arg246Cys)) is a missense variant. No CDK4 VCEP/CSPEC computational-evidence rule or gene-specific lookup was available, so the generic missense-only REVEL path applies. REVEL is 0.386, within the 0.250-0.750 gray zone and below the >0.750 PP3 threshold; PP3 is not met. SpliceAI was not used because splice prediction is not evidence for the substituted amino acid in this missense variant.

Rule

Generic ACMG/AMP fallback: missense variants are assessed with REVEL only; REVEL >0.750 supports PP3, REVEL <0.250 supports BP4, and scores from 0.250 through 0.750 meet neither criterion.

Evidence considered

• The case normalization identifies NM_000075.4:c.736C>T as the missense substitution NP_000066.1:p.(Arg246Cys). No governing CDK4 VCEP/CSPEC material or gene-specific PP3/BP4 lookup is present in the consolidated case evidence.
• REVEL score is 0.386. Under the supplied generic missense calibration, PP3 requires REVEL >0.750; this score is in the gray zone. The REVEL calibration publication is Pejaver et al., 'Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria' (PMID:36413997).
• PMID:26252490 was reviewed because it explicitly includes R246C, but its SIFT, PolyPhen-2, and I-Mutant results are not used: the applicable generic rule specifies REVEL only for a missense variant.

Sources

Reasoning

The exact ClinVar record has no expert-panel submission and no Pathogenic/Likely pathogenic expert-panel classification.

Rule

Apply PP5 only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• The exact ClinVar record for c.736C>T/p.Arg246Cys has three single-submitter Uncertain significance submissions and zero expert-panel submissions; ordinary laboratory assertions and aggregate labels were not used.

Still missing

• An exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion would be required.

Sources

Reasoning

No applicable CDK4 VCEP or gene-specific framework was available, so generic ACMG/AMP criteria were used. NM_000075.4:c.736C>T (NP_000066.1:p.Arg246Cys) is rare in gnomAD: AF 9.91304e-06 (16/1,614,036 alleles) in gnomAD v4.1 and AF 2.78567e-05 (7/251,286 alleles) in gnomAD v2.1, with zero homozygotes. These frequencies are far below the generic BA1 threshold of 5%; BA1 is not met.

Rule

Generic ACMG/AMP BA1: allele frequency >5% in population databases supports a benign stand-alone criterion.

Evidence considered

• gnomAD v4.1 reports 16/1,614,036 alleles, AF 9.91304e-06, and 0 homozygotes.
• gnomAD v2.1 reports 7/251,286 alleles, AF 2.78567e-05, and 0 homozygotes.
• The generic ACMG/AMP BA1 threshold is 5% (Richards et al., 2015, PMID:25741868); both observed frequencies are orders of magnitude below it.

Sources

Reasoning

No applicable CDK4 VCEP or gene-specific population-frequency threshold was available, so generic ACMG/AMP reasoning was used. The variant is observed only at very low frequency in gnomAD v4.1 (AF 9.91304e-06; maximum reported population AF 3.33322e-05) and gnomAD v2.1 (AF 2.78567e-05; maximum reported population AF 3.11915e-04 in a small Remaining individuals subgroup). These data do not show a frequency higher than expected for a rare, high-penetrance hereditary melanoma susceptibility allele and do not support BS1.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder; apply a disease- and gene-appropriate threshold when available.

Evidence considered

• gnomAD v4.1 reports overall AF 9.91304e-06, maximum listed population AF 3.33322e-05 in Admixed American individuals, and grpmax FAF 6.15e-06.
• gnomAD v2.1 reports overall AF 2.78567e-05, maximum listed subgroup AF 3.11915e-04 in 1/3,206 alleles from the Remaining individuals XY subgroup, and grpmax FAF 9.58e-06.
• PMID:25394175 describes CDK4 mutations in approximately 2–3% of families with at least three melanoma cases, but does not provide a variant-specific population-frequency threshold or data for c.736C>T; it supplies disease-context only and cannot establish BS1 by itself.
• Because the observed frequencies are extremely low rather than elevated, the available population data do not meet BS1; absence of a formal CDK4-specific maximum credible AF limits confidence in the threshold comparison.

Still missing

• No CDK4-specific maximum credible population allele frequency incorporating disease prevalence and penetrance was available.
• The highest subgroup frequencies are based on very small allele counts and should not be treated as stable ancestry-specific estimates.

Sources

Reasoning

CDK4 c.736C>T (p.(Arg246Cys)) is a missense variant and is assessed on the generic REVEL-only missense path. REVEL is 0.386, which is above the <0.250 BP4 threshold and within the gray zone; BP4 is not met. The SpliceAI score is not used for BP4 because it does not assess the protein-level impact of this missense substitution.

Rule

Generic ACMG/AMP fallback: missense variants are assessed with REVEL only; REVEL >0.750 supports PP3, REVEL <0.250 supports BP4, and scores from 0.250 through 0.750 meet neither criterion.

Evidence considered

• The case normalization identifies NM_000075.4:c.736C>T as the missense substitution NP_000066.1:p.(Arg246Cys). No governing CDK4 VCEP/CSPEC material or gene-specific PP3/BP4 lookup is present in the consolidated case evidence.
• REVEL score is 0.386. Under the supplied generic missense calibration, BP4 requires REVEL <0.250; this score is in the gray zone. The REVEL calibration publication is Pejaver et al., 'Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria' (PMID:36413997).

Sources

Reasoning

The exact ClinVar record has no expert-panel submission and no Benign/Likely benign expert-panel classification.

Rule

Apply BP6 only for an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• The exact ClinVar record for c.736C>T/p.Arg246Cys has three single-submitter Uncertain significance submissions and zero expert-panel submissions; ordinary laboratory assertions and aggregate labels were not used.

Still missing

• An exact-variant ClinVar expert-panel Benign or Likely benign assertion would be required.

Sources

Reasoning

The variant is CDK4 c.736C>T (p.Arg246Cys), but the case bundle provides no established pathogenic or likely pathogenic variant with the same amino-acid change. ClinVar reports this exact variant as uncertain significance, which cannot serve as an independent pathogenic comparator. Therefore PS1 cannot be applied.

Rule

Generic ACMG/AMP PS1 requires the same amino-acid change as an established pathogenic variant; no such independent comparator is documented here.

Evidence considered

• The normalized variant is NM_000075.4:c.736C>T / NP_000066.1:p.(Arg246Cys).
• ClinVar variation 141602 contains three single-submitter uncertain-significance submissions and no expert-panel classification; an uncertain-significance classification cannot establish the pathogenic comparator required for PS1.

Still missing

• A documented pathogenic or likely pathogenic comparator with the identical p.Arg246Cys amino-acid change is not available in the case evidence.

Sources

Reasoning

No proband-level parental testing, validated de novo observation, maternity/paternity confirmation, or mosaicism assessment is provided for CDK4 NM_000075.4:c.736C>T (p.Arg246Cys). The criterion cannot be assessed.

Rule

Generic ACMG/AMP PS2: a confirmed de novo variant in a patient with the disease and no family history, with confirmed maternity and paternity; strength may depend on confirmation and phenotype context.

Evidence considered

• The consolidated case-evidence bundle contains no proband-level parental testing or confirmed de novo report for NM_000075.4:c.736C>T (p.Arg246Cys).
• No applicable CDK4 VCEP/CSPEC framework was retrieved; the case is marked generic ACMG fallback.

Still missing

• Documented proband phenotype and indication
• Parental genotype results for the exact variant
• Confirmed maternity and paternity
• Assessment for parental or proband mosaicism

Reasoning

No validated experimental functional assay was identified for CDK4 NM_000075.4:c.736C>T (p.Arg246Cys). PMID:26252490 reports in-silico predictions, docking, and molecular-dynamics analyses only; these do not establish a validated disease-relevant functional assay with appropriate controls. OncoKB likewise reports no variant-specific reviewed functional evidence.

Rule

Generic ACMG/AMP PS3 requires well-established functional studies showing a damaging effect, with appropriate controls and assay validation; computational modeling alone is insufficient.

Evidence considered

• PMID:26252490 explicitly evaluates R246C using SIFT, PolyPhen-2, I-Mutant 3.0, docking, and molecular-dynamics simulations, but the paper provides no experimental functional assay or assay-control data for the variant.
• The paper's reported computational findings include altered predicted docking and CDK4-Cyclin D1 molecular-dynamics properties; these are insufficient to apply PS3 without validated experimental calibration.
• OncoKB reports no variant-specific reviewed functional evidence for CDK4 R246C.

Still missing

• No validated biochemical, cellular, or other disease-relevant functional assay for p.Arg246Cys was identified.
• No assay controls, replicate data, quantitative effect size, or validated pathogenic reference controls were reported for this variant.
• The available computational structural analyses cannot substitute for PS3 functional evidence.

Sources

Reasoning

No case-control or other statistically valid enrichment data for CDK4 c.736C>T (p.Arg246Cys) were identified.

Rule

Generic ACMG/AMP PS4 requires a statistically significant increase in variant prevalence among affected individuals compared with controls.

Evidence considered

• PMID:26252490 mentions p.R246C only in computational prediction, docking, and molecular-dynamics analyses; it reports no clinical cohort, affected-case count, control count, or enrichment statistic.
• PMID:25394175 describes CDK4 mutations at the gene level in hereditary-melanoma families but does not report c.736C>T/p.Arg246Cys or a variant-specific case-control comparison.

Still missing

• A variant-specific, phenotype-defined case series or case-control study with control data and an enrichment analysis is needed.

Sources

Reasoning

No applicable CDK4-specific VCEP or gene framework was available. The authoritative vcep_materials.json domain_tables object is empty, and the hotspot source reports no statistically significant hotspot for CDK4 R246. The bundle does not provide a criterion-ready, variant-specific demonstration that Arg246 lies in a critical functional domain or mutational hotspot meeting PM1 requirements, so PM1 cannot be applied.

Rule

Generic ACMG/AMP PM1 requires a well-established critical functional domain or mutational hotspot, with appropriate disease-relevant evidence; no criterion-ready domain or hotspot evidence is available in this case.

Evidence considered

• vcep_materials.json reports no applicable framework and an empty domain_tables object for CDK4; therefore there is no authoritative gene-specific domain entry to check for residue 246.
• The Cancer Hotspots result for CDK4 R246 is no result and states that the variant does not lie in a statistically significant hotspot.
• OncoKB supplies only non-variant-specific gene context that CDK4 is an intracellular kinase and does not identify reviewed functional evidence for p.Arg246Cys; this is insufficient by itself for PM1.

Still missing

• No CDK4-specific approved domain table or other authoritative critical-domain assessment is available.
• No statistically significant hotspot evidence is available for residue Arg246.

Reasoning

The case concerns p.Arg246Cys, but the evidence bundle contains no confirmed pathogenic or likely pathogenic missense variant at CDK4 residue 246. The PM5 candidate artifact reports zero same-residue candidates and explicitly indicates that automatic candidate harvesting was not eligible. PM5 cannot be applied.

Rule

Generic ACMG/AMP PM5 requires a pathogenic missense variant at the same amino-acid residue but with a different amino-acid substitution; no such comparator is documented here.

Evidence considered

• The PM5 candidate summary reports zero same-residue candidates, zero expert-panel or non-expert-majority pathogenic/likely pathogenic candidates, and a recommendation not to apply PM5 from that artifact alone.
• The exact p.Arg246Cys variant is classified as uncertain significance in ClinVar, so it cannot be used as a pathogenic same-residue comparator.

Still missing

• A pathogenic or likely pathogenic alternate missense change at CDK4 residue Arg246 is not documented.

Sources

Reasoning

No reported suspected de novo occurrence without adequate confirmation is available for this variant. There is no case-level parental testing or clinical report establishing a likely de novo event.

Rule

Generic ACMG/AMP PM6: assumed de novo, without confirmation of maternity and paternity, in a patient with the disease and no family history.

Evidence considered

• The bundle provides ClinVar submissions and general literature citations but no case-level suspected de novo observation for NM_000075.4:c.736C>T (p.Arg246Cys).
• The extracted papers reviewed in the bundle do not report segregation, parental testing, or a de novo occurrence for this exact variant.

Still missing

• A clinical case report or laboratory record describing the variant in a proband
• Parental testing or other evidence supporting suspected de novo origin
• Phenotype and family-history details

Reasoning

No affected relatives carrying the exact variant, informative meioses, pedigree, or quantitative segregation analysis is provided. Phenotype consistency and familial transmission therefore cannot be evaluated.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members in a gene known to cause the disease; strength may be increased according to the number and informativeness of meioses.

Evidence considered

• The consolidated bundle contains no family pedigree, relative-level genotypes, meiosis count, or segregation result for NM_000075.4:c.736C>T (p.Arg246Cys).
• The extracted PMID:26252490 paper is computational and provides no clinical, familial, or segregation data for the variant; the other extracted papers do not report this exact variant.

Still missing

• Pedigree with affected and unaffected relatives
• Genotypes for informative relatives
• Number of informative meioses and co-segregating individuals
• Clinical phenotype consistency and age-dependent penetrance assessment

Sources

Reasoning

The bundle does not establish that CDK4 is a gene in which missense variation is a well-established disease mechanism and in which benign missense variation is uncommon under a criterion-specific framework. The available literature identifies CDK4 in hereditary melanoma but does not provide the required gene-wide missense mechanism and benign-missense context for PP2. PP2 cannot be applied.

Rule

Generic ACMG/AMP PP2 requires a gene where missense variation is a common disease mechanism and benign missense variation is uncommon; those gene-level prerequisites are not established in this case.

Evidence considered

• The case has no applicable CDK4-specific VCEP framework and falls back to generic ACMG/AMP.
• The available CDK4 literature extraction is variant-specific computational modeling or broad hereditary-melanoma background and does not establish the gene-wide PP2 prerequisites.

Still missing

• No applicable CDK4-specific framework or validated gene-level missense-enrichment/benign-missense assessment is available.

Sources

Reasoning

No phenotype for the tested individual is supplied, and the reviewed evidence does not link this exact variant to a highly specific CDK4-associated phenotype.

Rule

Generic ACMG/AMP PP4 requires a patient's phenotype or family history to be highly specific for a disease with a single genetic etiology.

Evidence considered

• PMID:25394175 identifies CDK4 as a hereditary-melanoma-associated gene, but its full-text extraction found no mention of c.736C>T/p.Arg246Cys and describes no variant-specific phenotype.

Still missing

• Detailed proband phenotype, personal and family cancer history, and assessment of whether the presentation is highly specific for a CDK4-associated hereditary melanoma syndrome are needed.

Sources

Reasoning

gnomAD shows zero homozygotes among 1,614,036 alleles in v4.1 and 251,286 alleles in v2.1, so there is no homozygote-based benign evidence. However, CDK4 hereditary melanoma is an autosomal-dominant cancer-predisposition context, and BS2 requires observation in healthy adults (or homozygotes when relevant), not merely an allele count in a reference database. The bundle contains no individual-level age, phenotype, ascertainment, or unaffected-carrier information sufficient to establish BS2.

Rule

Generic ACMG/AMP BS2: observation in healthy adults for a fully penetrant dominant disorder, or in healthy homozygotes for a recessive disorder, supports benign evidence; phenotype and relevant inheritance context must be established.

Evidence considered

• gnomAD v4.1 reports 0 homozygotes for 16 observed variant alleles.
• gnomAD v2.1 reports 0 homozygotes for 7 observed variant alleles.
• PMID:25394175 provides hereditary melanoma disease context for CDK4 but does not report healthy carriers or this exact variant.
• The population bundle does not establish that any observed heterozygotes were healthy adults with adequate age and phenotype information; therefore BS2 cannot be applied.

Still missing

• No phenotype- and age-annotated healthy adult carrier data were provided.
• No applicable CDK4-specific BS2 specification was available.

Sources

Reasoning

No validated experimental functional assay was identified demonstrating that CDK4 p.Arg246Cys preserves normal protein function. The available paper is computational only and therefore cannot establish benign functional evidence or support BS3.

Rule

Generic ACMG/AMP BS3 requires well-established functional studies showing no damaging effect on protein function or a relevant biological assay; computational modeling alone is insufficient.

Evidence considered

• PMID:26252490 contains only computational predictions, docking, and molecular-dynamics analyses and does not demonstrate preserved CDK4 function experimentally.
• The available computational analyses do not provide validated evidence for a benign or functionally normal effect.
• OncoKB reports no variant-specific reviewed functional evidence for CDK4 R246C.

Still missing

• No validated benign functional assay for p.Arg246Cys was identified.
• No normal-function control comparison, assay validation, replicate data, or benign reference controls were reported for this variant.
• Absence of reported functional evidence is not evidence of a normal functional effect.

Sources

Reasoning

No unaffected relatives known to be at risk have been tested and shown to carry the exact variant, and no informative non-segregation analysis is available. BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family, or observation of the variant in unaffected members of a family, when the phenotype is expected to be highly penetrant and the relatives are informative.

Evidence considered

• The case-evidence bundle contains no tested unaffected relatives or documented non-segregation of NM_000075.4:c.736C>T (p.Arg246Cys).
• No source in the bundle supplies family-level data sufficient to establish benign non-segregation evidence.

Still missing

• At-risk unaffected relatives with reliable phenotype evaluation
• Exact-variant genotypes for those relatives
• Pedigree structure and informative meioses
• Consideration of age-dependent penetrance and phenocopies

Reasoning

The bundle does not establish a CDK4 disease mechanism dominated by truncating or other loss-of-function variants with missense variation generally benign. The available evidence is insufficient to satisfy the gene-level prerequisite for BP1, so BP1 cannot be applied.

Rule

Generic ACMG/AMP BP1 requires a gene in which truncating variants are a known disease mechanism and missense variants are generally benign; those prerequisites are not established here.

Evidence considered

• No CDK4-specific VCEP framework is available in the case bundle.
• The bundle does not provide a validated gene-wide assessment supporting the BP1 pattern of predominantly truncating disease mechanism and generally benign missense variation.

Still missing

• No applicable CDK4-specific framework or validated gene-level evidence showing a truncating/LoF-dominant mechanism with generally benign missense variation is available.

Reasoning

No CDK4-specific VCEP framework was retrieved, so the generic ACMG/AMP definition applies. BP2 requires an informative allelic observation, such as the variant being in trans with a pathogenic variant for a fully penetrant recessive disorder or in cis with a pathogenic variant. The case bundle contains no family genotypes, affected-proband genotype, or phase-resolved pathogenic partner-variant data. BP2 cannot be applied or excluded from the available evidence.

Rule

Apply BP2 only when an informative pathogenic partner variant and phase are established under the relevant inheritance model; absence of phase-resolved data is insufficient.

Evidence considered

• The case bundle states that no CDK4 CSPEC/VCEP specification was found and that generic ACMG/AMP 2015 rules are the fallback.
• The available evidence contains no affected-proband allelic observations, pathogenic in-trans or in-cis partner variant, segregation data, or phase information for NM_000075.4:c.736C>T (p.Arg246Cys).

Still missing

• Family or proband testing with identified pathogenic partner variant(s).
• Phase determination establishing cis or trans configuration.
• Confirmation that the observed allelic configuration matches the applicable inheritance model.

Sources

Reasoning

No proband phenotype, molecular diagnosis, or evidence of an alternative molecular cause is provided.

Rule

Generic ACMG/AMP BP5 requires the variant to be found in a case with an alternative molecular basis for disease.

Still missing

• A documented alternate molecular diagnosis that fully explains the proband's phenotype is needed.