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CDK4
Final classification
VUS
CDK4 c.322C>T · p.Pro108Ser
CDK4

NM_000075.3:c.322C>T (p.Pro108Ser) is a missense variant in CDK4, a gene in which activating missense variants are associated with autosomal dominant familial melanoma.

Gene
CDK4
Transcript
NM_000075.3
HGVS · transcript:coding
NM_000075.3:c.322C>T
Consequence
N/A
GRCh38
chr12:57751239 G>A
GRCh37
chr12:58145022 G>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: PM2 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CDK4 c.322C>T

NM_000075.3:c.322C>T (p.Pro108Ser) is a missense variant in CDK4, a gene in which activating missense variants are associated with autosomal dominant familial melanoma. This variant is absent from all large population databases including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, supporting moderate evidence for pathogenicity (PM2).1 Multiple lines of computational evidence suggest a benign effect: REVEL score is 0.251 (below the pathogenic threshold), BayesDel score is -0.25851 (negative, predicting benign), and SpliceAI predicts no splicing impact (max delta = 0.01). This supports BP4 (supporting benign).2 No functional studies, case-control data, segregation data, or clinical phenotype information are available for this variant. The variant is absent from ClinVar and has not been reported in the somatic or germline literature.3 The variant is a missense substitution at a residue (Pro108) that is not a recognized mutational hotspot and has no comparator pathogenic variants at the same position. Overall, the only applicable criterion is PM2 (moderate) for absence from population databases, and BP4 (supporting benign) for concordant benign computational predictions. With one moderate pathogenic criterion and one supporting benign criterion, the evidence is insufficient to classify this variant as pathogenic or likely pathogenic, and insufficient evidence exists to classify it as benign. This variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_000075.3 · variants mapped to exon structure
CDK4 NM_000075.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
This variant is absent from all large population databases including gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), with a combined allele count of zero across all populations. Under generic ACMG/AMP rules, an allele frequency below 0.1% in population databases supports moderate evidence for pathogenicity.
Absent from gnomAD v2.1 (AC=0AF=0).Absent from gnomAD v4.1 (AC=0
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.251 (below the 0.5 pathogenic threshold and within the indeterminate-to-benign range), BayesDel score is -0.25851 (negative, indicating a benign prediction), and SpliceAI predicts no splicing impact (max delta = 0.01). Three independent computational predictors are concordant in suggesting a benign effect.
REVEL score 0.251 (below pathogenic thresholdconsistent with benign).BayesDel score -0.25851 (negative
Assessed · not applied
Pathogenic
PS1 A different pathogenic missense change at the same amino acid residue (Pro108) has not been reported in ClinVar or the literature.
PS2 No de novo occurrence with confirmed paternity and maternity has been reported for this variant in the literature or available case data.
PS3 No well-established in vitro or in vivo functional studies have been identified for NM_000075.3:c.322C>T (p.Pro108Ser) or a systematically characterized range that includes this position.
PS4 No case-control studies or cohort analyses demonstrate enrichment of this variant in affected individuals compared to controls.
PM1 This variant (p.Pro108Ser) does not lie within a statistically significant mutational hotspot as assessed by cancerhotspots.org, and no literature was identified characterizing residue Pro108 as part of a critical functional domain with established pathogenic missense variation.
PM5 No different pathogenic missense variant has been reported at the same amino acid residue (Pro108) in CDK4.
PM6 No de novo observation (without confirmation of paternity) has been reported for this variant in the literature or available case data.
PP1 No co-segregation data with disease in multiple affected family members is available for this variant.
PP2 PP2 requires a gene with a low rate of benign missense variation (typically Z-score > 3.09) where missense variants are a common disease mechanism.
PP3 Multiple in silico predictors do not support a deleterious effect.
PP4 No phenotypic data or clinical history is available for the individual carrying this variant to assess phenotype specificity for a CDK4-associated disorder.
PP5 This variant is absent from ClinVar entirely; no reputable source has classified it as pathogenic.
Benign
BA1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 No data are available regarding the observation of this variant in healthy adult controls with full penetrance expected at an early age.
BS3 No well-established in vitro or in vivo functional studies demonstrate no damaging effect for this variant.
BS4 No segregation data are available to demonstrate lack of co-segregation with disease in affected family members.
BP1 BP1 applies when a missense variant is found in a gene for which primarily truncating variants cause disease.
BP2 No data are available regarding observation of this variant in trans with a pathogenic variant in a recessive disorder, or in cis with a pathogenic variant in a dominant disorder.
BP5 No data are available demonstrating that this variant is found in a case with an alternate molecular basis for disease.
BP6 This variant is absent from ClinVar entirely; no reputable source has classified it as benign.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 = 0.01). REVEL score = 0.251. BayesDel score = -0.25851.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. CDK4, an intracellular kinase, is altered by amplification or mutation in various cancer types including soft tissue sarcomas and gliomas.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots