Starting
Initialising…
0%
CCND1
Final classification
VUS
CCND1 c.838G>T · p.Glu280Ter
CCND1

NM_053056.3:c.838G>T (NP_444284.1:p.Glu280Ter) is a nonsense variant in the last exon (exon 5/5) of CCND1, predicted to escape nonsense-mediated decay and produce a truncated protein lacking the terminal 10 amino acids.

Gene
CCND1
Transcript
NM_053056.3
HGVS · transcript:coding
NM_053056.3:c.838G>T
Consequence
N/A
GRCh38
chr11:69651232 G>T
GRCh37
chr11:69466000 G>T
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 supporting; combination = 1 supporting, 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 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
CCND1 c.838G>T

NM_053056.3:c.838G>T (NP_444284.1:p.Glu280Ter) is a nonsense variant in the last exon (exon 5/5) of CCND1, predicted to escape nonsense-mediated decay and produce a truncated protein lacking the terminal 10 amino acids.1 The variant is absent from gnomAD v2.1 and v4.1 population databases, meeting PM2 at supporting strength.2 The variant is absent from ClinVar with no prior germline classifications available.3 The variant has been reported somatically in COSMIC (COSV99919608, n=3) and is classified as Likely Oncogenic by OncoKB with a gain-of-function context, but no variant-specific functional studies or germline case reports are available.4 SpliceAI predicts no splice impact (max delta score 0.00) and BayesDel score of 0.60222 provides borderline in silico evidence, insufficient to meet PP3 or BP4.5 Four CCND1 functional domain papers were reviewed (PMID:16732330, PMID:17299095, PMID:9832503, PMID:9926916); none examined the specific variant p.Glu280Ter, and thus none provide criterion-level evidence for this variant. PVS1 is not applicable because the nonsense variant in the last exon is predicted to escape NMD, and C-terminal truncations in CCND1 are associated with gain-of-function rather than loss-of-function. No other pathogenic or benign criteria were met, resulting in insufficient evidence for definitive classification under generic ACMG/AMP 2015 rules.

PM2 VUS
Gene diagram · NM_053056.3 · variants mapped to exon structure
CCND1 NM_053056.3
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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
      This variant is absent from gnomAD-Canada.
      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 = 0.00). BayesDel score = 0.60222.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      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 previously been reported in somatic cancers (COSMIC; COSV99919608, n = 3 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 4 PMIDs not cited in assessment
      16732330 ↗ Identification of mutations that disrupt phosphorylation-dependent nuclear export of cyclin D1. ONCOKB
      17299095 ↗ Point mutations and genomic deletions in CCND1 create stable truncated cyclin D1 mRNAs that are associated with increased proliferation rate and shorter survival. ONCOKB
      9832503 ↗ Glycogen synthase kinase-3beta regulates cyclin D1 proteolysis and subcellular localization. ONCOKB
      9926916 ↗ Functional domains in cyclin D1: pRb-kinase activity is not essential for transformation. ONCOKB