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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 applied · 19 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1 and v4.1 population databases, meeting the generic ACMG PM2 threshold of allele frequency below 0.1%.
Absent from gnomAD v2.1 (0 alleles across all populations)Absent from gnomAD v4.1 (0 alleles across all populations)
Assessed · not applied
Pathogenic
PS1 No nucleotide change at the same position has been previously established as pathogenic.
PS2 No de novo occurrence of NM_053056.3:c.838G>T has been reported in a patient with a CCND1-related phenotype, and no trio sequencing studies have identified this variant as de novo.
PS3 No well-established functional studies have been performed on the specific variant CCND1 p.Glu280Ter.
PS4 No case-control study comparing the frequency of c.838G>T in affected versus unaffected individuals is available.
PM1 The variant is not located within a statistically significant mutational hotspot per Cancer Hotspots analysis.
PM6 No assumed de novo occurrence of c.838G>T has been reported in the literature without confirmation of paternity and maternity.
PP1 No cosegregation data are available for c.838G>T with a CCND1-associated disease in multiple affected family members.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No specific phenotype or family history data are available for the proband carrying this variant.
PP5 No reputable source has definitively classified this variant as pathogenic.
Benign
BA1 The variant is absent from gnomAD v2.1 and v4.1, with an allele frequency of 0%, which does not meet the BA1 threshold of >1%.
BS1 The variant is absent from gnomAD v2.1 and v4.1, with an allele frequency of 0%, which does not meet the BS1 threshold of >0.3%.
BS2 No evidence that this variant has been observed in healthy adults at sufficient frequency to be considered benign.
BS3 No well-established functional studies demonstrate that CCND1 p.Glu280Ter has no damaging effect.
BS4 No lack of cosegregation data are available.
BP2 No observation of CCND1 c.838G>T in trans with a known pathogenic variant in a different gene for a dominantly inherited disorder has been reported.
BP4 Multiple lines of computational evidence do not provide a strong benign signal.
BP5 No case has been reported where this variant is found in a patient with an alternate molecular basis for disease.
BP6 No reputable source has classified this variant as benign.
N/A · 5 PVS1 · PM5 · PP2 · BP1 · 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
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