Variant classification summary

NM_000075.4:c.71G>T

CDK4 · NP_000066.1:p.(Arg24Leu) · NM_000075.4

GRCh37: chr12:58145430 C>A · GRCh38: chr12:57751647 C>A

Gene: CDK4 Transcript: NM_000075.4

Final call

Likely Pathogenic

PS3 supporting PM1 moderate PM2 supporting PM5 moderate BP4 supporting benign

Variant details

Gene

CDK4

Transcript

NM_000075.4

Protein

NP_000066.1:p.(Arg24Leu)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

The CDK4 c.71G>T (p.Arg24Leu) missense variant is located at codon 24 within the protein kinase domain, a statistically significant mutational hotspot per cancerhotspots.org where established pathogenic gain-of-function missense variants (p.Arg24Cys, p.Arg24His) cause familial melanoma (PM1, moderate).

2

This is a novel missense change (p.Arg24Leu) at the same amino acid residue where different missense changes have been determined to be pathogenic — p.Arg24Cys and p.Arg24His are well-established pathogenic CDK4 variants associated with familial melanoma susceptibility (PM5, moderate).

3

The variant is absent from gnomAD-Canada v1.0; gnomAD v2.1 and v4.1 data were unavailable at the time of assessment. Absence from available population databases supports rarity below the 0.1% PM2 threshold (PM2, supporting).

4

OncoKB, a curated somatic cancer knowledgebase, classifies this specific variant as Likely Oncogenic with a Likely Gain-of-function biological effect, providing a secondary citation for a deleterious functional impact at this well-characterized residue (PS3, supporting).

5

Multiple in silico predictors yield benign scores: REVEL 0.242 (benign), BayesDel -0.0848 (benign), and SpliceAI max delta 0.00 (no splice impact). While these results favor a benign interpretation (BP4, supporting benign), they do not outweigh the pathogenic evidence from the hotspot location, same-residue pathogenic comparator variants, population absence, and curated functional annotation.

6

Applying the generic ACMG/AMP 2015 combination rules (PMID:25741868): 2 moderate criteria (PM1, PM5) plus 2 supporting criteria (PM2, PS3) meet the threshold for Likely Pathogenic. One supporting benign criterion (BP4) is present but is insufficient to offset the pathogenic evidence.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	This is a missense variant (c.71G>T, p.Arg24Leu) and does not fall into the null variant buckets (nonsense, frameshift, or canonical ±1,2 splice consensus) required for PVS1 application under the ClinGen SVI PVS1 framework (PMC6185798). The pvs1_variant_assessment confirms variant_bucket='other' and apply_generic_pvs1_framework=false.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	PS1 requires the same amino acid change as a previously established pathogenic variant. This variant results in p.Arg24Leu (R24L), whereas the established pathogenic CDK4 variants at this residue are p.Arg24Cys (R24C) and p.Arg24His (R24H) — different amino acid substitutions. PS1 is not satisfied.	oncokb
PS2	Not met	No de novo data are available for this variant. No reports of de novo occurrence were identified in ClinVar, the literature, or any other evidence source in the case.
PS3	Met	OncoKB, a curated knowledgebase, classifies this specific variant (CDK4 R24L) as Likely Oncogenic with a Likely Gain-of-function biological effect. The primary functional literature is not available in the case folder; this represents a secondary citation supporting a deleterious functional effect. The R24 residue is in the CDK4 kinase domain and is critical for p16(INK4A) binding; gain-of-function missense mutations at this position are established in melanomagenesis.	oncokb
PS4	Not met	No case-control data demonstrating statistically significant enrichment of this variant in affected individuals versus controls are available. COSMIC reports 16 somatic occurrences, but germline case-control statistics are absent.
PS5	N/A	PS5 is not a criterion in the standard ACMG/AMP 2015 framework (Richards et al. 2015, PMID:25741868) used for this assessment.	generic_acmg_combination_rules
PM1	Met	This variant is located at residue R24 within the CDK4 protein kinase domain, a statistically significant mutational hotspot per cancerhotspots.org. The R24 residue lies in a critical functional domain involved in p16(INK4A) binding and cell cycle regulation. Multiple pathogenic missense variants (R24C, R24H) are established at this residue in familial melanoma, confirming the critical nature of this domain.	oncokb
PM2	Met	This variant is absent from gnomAD-Canada v1.0. gnomAD v2.1 and v4.1 data were unavailable due to query timeout. Absence from available population databases supports rarity at a level below the PM2 threshold (<0.1%).	gnomad_canada
PM5	Met	This variant is a novel missense change (p.Arg24Leu) at the same amino acid residue where different pathogenic missense changes are established: p.Arg24Cys (c.70C>T) and p.Arg24His (c.71G>A) are well-characterized pathogenic CDK4 variants associated with familial melanoma. Under generic ACMG/AMP PM5, a novel missense change at a residue where a different pathogenic missense change has been seen qualifies. Automated PM5 candidate harvesting returned no results due to query limitations; manual review confirms the R24 residue is a known pathogenic locus.	pm5_candidates oncokb
PM6	Not met	No de novo data are available for this variant. PM6 requires a de novo observation with confirmed maternity and paternity.
PP1	Not met	No co-segregation data are available for this variant. PP1 requires co-segregation with disease in multiple affected family members.
PP2	Not assessed	Constraint metrics for CDK4 (z-score, HCI prior) are not available in this case. The HCI prior lookup returned gene_not_supported. Without statistical evidence of low benign missense variation or a high missense z-score, PP2 cannot be assessed.
PP3	Not met	Multiple in silico tools predict a benign impact: REVEL score 0.242 (below 0.5 threshold, predicted benign), BayesDel score -0.0848 (negative, predicted benign), and SpliceAI max delta score 0.00 (no predicted splice impact). These results do not support a damaging effect; rather they support a benign interpretation (see BP4).	revel bayesdel spliceai
PP4	Not met	No phenotype specificity data are available. PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology.
PP5	N/A	PP5 is not a criterion in the standard ACMG/AMP 2015 framework (Richards et al. 2015, PMID:25741868) used for this assessment.	generic_acmg_combination_rules
BA1	Not met	This variant is not observed at an allele frequency >1% in any population database. It is absent from gnomAD-Canada; gnomAD v2.1 and v4.1 data were unavailable.	gnomad_canada
BS1	Not met	This variant is not observed at an allele frequency >0.3% in any available population database. It is absent from gnomAD-Canada; gnomAD v2.1 and v4.1 data were unavailable. The variant does not meet the BS1 threshold.	gnomad_canada
BS2	Not met	No data are available regarding observation of this variant in healthy adult individuals. BS2 requires observation in a healthy adult for a fully penetrant disorder expected to have occurred by that age.
BS3	Not met	No well-established functional studies demonstrate a neutral or benign effect for this variant. OncoKB classifies this variant as Likely Oncogenic with Likely Gain-of-function, indicating a deleterious rather than benign functional effect. BS3 requires evidence of no damaging effect in a well-established functional assay.	oncokb
BS4	Not met	No segregation data are available. BS4 requires lack of segregation with disease in affected family members.
BP1	N/A	BP1 applies to missense variants in genes where truncating variants are the primary pathogenic mechanism. In CDK4, the primary germline pathogenic mechanism is gain-of-function via missense mutations (e.g., R24C, R24H) rather than loss-of-function via truncating variants. Missense is the established disease mechanism, so BP1 is not applicable.	oncokb
BP2	Not met	No data are available regarding observation of this variant in trans with a known pathogenic CDK4 variant. BP2 requires observation in trans for a fully penetrant dominant disorder.
BP3	N/A	This is a missense substitution, not an in-frame deletion or insertion in a repetitive region.
BP4	Met	Multiple in silico tools consistently predict a benign impact: REVEL score 0.242 (below 0.5 threshold, predicted benign), BayesDel score -0.0848 (negative, predicted benign), and SpliceAI max delta score 0.00 (no predicted splicing impact). No in silico predictor suggests a damaging effect.	revel bayesdel spliceai
BP5	Not met	No alternate molecular cause of disease has been identified in this case. BP5 requires observation in a case where an alternate molecular basis for disease has been found.
BP6	Not met	No reputable source reports this variant as benign. ClinVar has no entry for this variant, and no other database or publication classifies it as benign.	clinvar
BP7	N/A	This is a missense variant resulting in p.Arg24Leu, not a synonymous variant. BP7 applies only to synonymous variants with no predicted splice impact.

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