Starting
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CUX1
Final classification
Pathogenic
CUX1 c.2983C>T · p.Arg995Ter
CUX1

NM_001202543.1:c.2983C>T (p.Arg995Ter) is a nonsense variant in exon 19 of CUX1 predicted to undergo nonsense-mediated decay, meeting PVS1 at very strong strength.

Gene
CUX1
Transcript
NM_001202543.1
HGVS · transcript:coding
NM_001202543.1:c.2983C>T
Consequence
N/A
GRCh38
chr7:102204433 C>T
GRCh37
chr7:101847713 C>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: PVS1 very strong, PM2 supporting, PP5 supporting; combination = 1 very strong + 2 supporting, which maps to 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: PVS1 very strong, PM2 supporting, PP5 supporting; combination = 1 very strong + 2 supporting, which maps to Pathogenic.
Classification rationale
PVS1PM2PP5 Pathogenic
CUX1 c.2983C>T

NM_001202543.1:c.2983C>T (p.Arg995Ter) is a nonsense variant in exon 19 of CUX1 predicted to undergo nonsense-mediated decay, meeting PVS1 at very strong strength.1 The variant is absent from gnomAD v2.1 (0/251,110 alleles) and v4.1, meeting PM2 at supporting strength.2 The variant has been classified as Pathogenic in ClinVar (Variation ID: 4532047) by a reputable clinical diagnostic laboratory (Victorian Clinical Genetics Services), meeting PP5 at supporting strength.3 Under ACMG/AMP 2015 combination rules, one Very Strong criterion (PVS1) plus two Supporting criteria (PM2, PP5) is sufficient for a Pathogenic classification.4 Heterozygous loss-of-function variants in CUX1 cause an autosomal dominant neurodevelopmental disorder characterized by global developmental delay, intellectual disability, hypotonia, and seizures, as established by Oppermann et al. (2023) in a cohort of 34 individuals.5 No benign evidence was identified: the variant is too rare for BA1/BS1, no functional studies demonstrate a benign effect, and no lack of segregation or alternate molecular basis has been reported.6 Final classification: Pathogenic. PVS1_VeryStrong + PM2_Supporting + PP5_Supporting.7

PVS1 + PM2 + PP5 Pathogenic
Gene diagram · NM_001202543.1 · variants mapped to exon structure
CUX1 NM_001202543.1
Fetching transcript structure from UCSC…
Applied criteria · 3 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 · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/251110 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/16228 alleles, homozygotes = 0).
      🇨🇦 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 / 251,110
      0 hom
      Not observed in any ancestry group.
      + 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory). (ClinVarID = 4532047)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). 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: Likely Loss-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; COSV107349027, n = 2 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 3 further PMIDs triaged but not cited — see Sources & References.
      CUX1-related neurodevelopmental disorder: deep insights into phenotype-genotype spectrum and underlying pathology.
      Found
      ClinVar Variation ID 4532047: Pathogenic criteria provided single submitter Submitter: Victorian Clinical Genetics Services Murdoch Childrens Research Institute (SCV007108443) Submission cites PMID:37644171 and PMID:25741868
      Applied to
      PP5 supports · met PVS1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 3 PMIDs not cited in assessment
      23212519 ↗ CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia. ONCOKB
      24316979 ↗ Inactivating CUX1 mutations promote tumorigenesis. ONCOKB
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR