Starting
Initialising…
0%
CUX1
Final classification
VUS
CUX1 c.1657_1716+4dup · p.?
CUX1

The CUX1 c.1657_1716+4dup (NP_001189473.1:p.?) variant has not been reported in ClinVar.

Gene
CUX1
Transcript
NM_001202544.1
HGVS · transcript:coding
NM_001202544.1:c.1657_1716+4dup
Consequence
N/A
GRCh38
chr7:102280060 G>GCTGCGGTACTCGTCCCAGTACGAGGAGCGCCTGGACCCCTTCTCCTCCTTCAGCAAGCGGGTTC
GRCh37
chr7:101923352 G>GCTGCGGTACTCGTCCCAGTACGAGGAGCGCCTGGACCCCTTCTCCTCCTTCAGCAAGCGGGTTC
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
CUX1 c.1657_1716+4dup

The CUX1 c.1657_1716+4dup (NP_001189473.1:p.?) variant has not been reported in ClinVar.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, which supports rarity in population databases.2 Germline loss of function is an established disease mechanism for CUX1, but this duplication does not fall into the generic PVS1 default null-variant categories based on the available variant-level assessment.3 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.05.4

PM2 VUS
3 pvs1_gene_contextpvs1_variant_assessment
Gene diagram · NM_001202544.1 · variants mapped to exon structure
CUX1 NM_001202544.1
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.
      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.
      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 = 0.05).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      6Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC