Starting
Initialising…
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CTNNB1
Final classification
Likely Pathogenic
CTNNB1 c.802G>T · p.Gly268Ter
CTNNB1

NM_001904.4:c.802G>T (NP_001895.1:p.Gly268Ter) is a nonsense variant in exon 6 of 15 exons in CTNNB1, predicted to result in premature protein termination and nonsense-mediated decay of the transcript.

Gene
CTNNB1
Transcript
NM_001904.4
HGVS · transcript:coding
NM_001904.4:c.802G>T
Consequence
N/A
GRCh38
chr3:41225727 G>T
GRCh37
chr3:41267218 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: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely 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 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
CTNNB1 c.802G>T

NM_001904.4:c.802G>T (NP_001895.1:p.Gly268Ter) is a nonsense variant in exon 6 of 15 exons in CTNNB1, predicted to result in premature protein termination and nonsense-mediated decay of the transcript.1 CTNNB1 loss-of-function is an established disease mechanism for autosomal dominant neurodevelopmental disorder with spastic diplegia and visual defects (NEDSDV; MIM 615075), supported by ClinGen haploinsufficiency score of 3 and multiple publications describing pathogenic germline nonsense and frameshift variants.2 This variant is absent from gnomAD v2.1 and v4.1 (0 alleles across >140,000 individuals) and absent from gnomAD-Canada v1.0, consistent with a rare pathogenic variant under strong purifying selection.3 The variant is not present in ClinVar, and no functional studies, cosegregation data, or detailed clinical phenotypes for individuals carrying this variant were available in the evidence record. Applying the generic ACMG/AMP 2015 classification framework (Richards et al. 2015, PMID:25741868), the combination of one very strong criterion (PVS1) and one moderate criterion (PM2) meets the threshold for Likely Pathogenic (1 Very Strong + 1 Moderate).4

PVS1 + PM2 Likely Pathogenic
1 pvs1_generic_framework ↗pvs1_gene_context
2 pvs1_gene_context
4 generic_acmg_combination_rules
Gene diagram · NM_001904.4 · variants mapped to exon structure
CTNNB1 NM_001904.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      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 = 0.02). BayesDel score = 0.66.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      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.
      Literature · how each cited paper was used
      5papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID 33350591
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PVS1 supports · met
      PMID 36083290
      Found
      Nonsense variant NM_001904.4:c.802G>T (NP_001895.1:p.Gly268Ter) in exon 6 of 15 exons >50 nt upstream of last exon-exon junction — NMD predicted CTNNB1 loss-of-function is an established germline disease mechanism for autosomal dominant NEDSDV (MIM 615075) supported by ClinGen haploinsufficiency score of 3 Multiple publications confirm germline CTNNB1 nonsense/frameshift variants as pathogenic (PMID:41082542 PMID:36153650 PMID:36083290) ClinGen SVI PVS1 framework (PMC6185798) supports PVS1 at very strong for nonsense variants in LoF-established genes with predicted NMD
      Applied to
      PVS1 supports · met
      PMID 36153650
      Found
      Nonsense variant NM_001904.4:c.802G>T (NP_001895.1:p.Gly268Ter) in exon 6 of 15 exons >50 nt upstream of last exon-exon junction — NMD predicted CTNNB1 loss-of-function is an established germline disease mechanism for autosomal dominant NEDSDV (MIM 615075) supported by ClinGen haploinsufficiency score of 3 Multiple publications confirm germline CTNNB1 nonsense/frameshift variants as pathogenic (PMID:41082542 PMID:36153650 PMID:36083290) ClinGen SVI PVS1 framework (PMC6185798) supports PVS1 at very strong for nonsense variants in LoF-established genes with predicted NMD
      Applied to
      PVS1 supports · met
      PMID 41062690
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PVS1 supports · met
      PMID 41082542
      Found
      Nonsense variant NM_001904.4:c.802G>T (NP_001895.1:p.Gly268Ter) in exon 6 of 15 exons >50 nt upstream of last exon-exon junction — NMD predicted CTNNB1 loss-of-function is an established germline disease mechanism for autosomal dominant NEDSDV (MIM 615075) supported by ClinGen haploinsufficiency score of 3 Multiple publications confirm germline CTNNB1 nonsense/frameshift variants as pathogenic (PMID:41082542 PMID:36153650 PMID:36083290) ClinGen SVI PVS1 framework (PMC6185798) supports PVS1 at very strong for nonsense variants in LoF-established genes with predicted NMD
      Applied to
      PVS1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots