Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
CDK4
Final classification
Likely Pathogenic
CDK4 c.71G>T · p.Arg24Leu
CDK4

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).

Gene
CDK4
Transcript
NM_000075.4
HGVS · transcript:coding
NM_000075.4:c.71G>T
Consequence
N/A
GRCh38
chr12:57751647 C>A
GRCh37
chr12:58145430 C>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 supporting, PM1 moderate, PM2 supporting, PM5 moderate, BP4 supporting benign; combination = 2 moderate + 2 supporting + 1 supporting benign, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 supporting, PM1 moderate, PM2 supporting, PM5 moderate, BP4 supporting benign; combination = 2 moderate + 2 supporting + 1 supporting benign, which maps to Likely Pathogenic.
Classification rationale
PS3PM1PM2PM5 BP4 Likely Pathogenic
CDK4 c.71G>T

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).1 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).2 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).3 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).4 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.5 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.6

PS3 + PM1 + PM2 + PM5 + BP4 Likely Pathogenic
2 pm5_candidatesoncokb ↗
5 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
Gene diagram · NM_000075.4 · variants mapped to exon structure
CDK4 NM_000075.4
Fetching transcript structure from UCSC…
Applied criteria · 5 applied · 16 assessed
Applied · 5
Strength Supporting Moderate Strong Very strong
PS3 supporting review Pathogenic
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 curated classification: Likely OncogenicLikely Gain-of-function (secondary citationprimary literature not in case folder).
PM1 moderate Pathogenic
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.
Statistically significant hotspot at cancerhotspots.orgresidue R24 in critical CDK4 kinase domainestablished pathogenic missense variants at this residue.
PM2 supporting review Pathogenic
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%).
Absent from gnomAD-Canada v1.0 (AC=0). gnomAD v2.1/v4.1 unavailable (timeout).
PM5 moderate review Pathogenic
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.
Different missense change (R24L) at same codon as established pathogenic R24C and R24H variants. Automated PM5 harvest returned 0 candidatesmanually identified.
BP4 supporting Benign
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: 0.242 (benign)BayesDel: -0.0848 (benign)SpliceAI max delta: 0.00 (no splice effect). All in silico tools predict benign.
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change as a previously established pathogenic variant.
PS2 No de novo data are available for this variant.
PS4 No case-control data demonstrating statistically significant enrichment of this variant in affected individuals versus controls are available.
PM6 No de novo data are available for this variant.
PP1 No co-segregation data are available for this variant.
PP2 Constraint metrics for CDK4 (z-score, HCI prior) are not available in this case.
PP3 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).
PP4 No phenotype specificity data are available.
Benign
BA1 This variant is not observed at an allele frequency >1% in any population database.
BS1 This variant is not observed at an allele frequency >0.3% in any available population database.
BS2 No data are available regarding observation of this variant in healthy adult individuals.
BS3 No well-established functional studies demonstrate a neutral or benign effect for this variant.
BS4 No segregation data are available.
BP2 No data are available regarding observation of this variant in trans with a known pathogenic CDK4 variant.
BP5 No alternate molecular cause of disease has been identified in this case.
BP6 No reputable source reports this variant as benign.
N/A · 5 PVS1 · PP5 · BP1 · BP3 · BP7
Research & evidence
Population frequency · supports pathogenic
v4.1
This variant is absent from gnomAD v4.1.
v2.1
This variant is absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.242. BayesDel score = -0.0848312.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56983700, n = 16 times).
Hotspots
This variant lies in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots