Starting
Initialising…
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LZTR1
Final classification
VUS
LZTR1 c.2412dup · p.Lys805GlnfsTer46
LZTR1

The LZTR1 c.2412dup (p.Lys805GlnfsTer46; p.K805Qfs*46) variant has not been observed in COSMIC and has been reported in ClinVar with likely pathogenic and pathogenic submissions.

Gene
LZTR1
Transcript
NM_006767.4
HGVS · transcript:coding
NM_006767.4:c.2412dup
Consequence
N/A
GRCh38
chr22:20997235 T>TC
GRCh37
chr22:21351524 T>TC
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for LZTR1 Version 1.3.0 v1.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for LZTR1 Version 1.3.0 v1.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2 VUS
LZTR1 c.2412dup

The LZTR1 c.2412dup (p.Lys805GlnfsTer46; p.K805Qfs*46) variant has not been observed in COSMIC and has been reported in ClinVar with likely pathogenic and pathogenic submissions.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting rarity in population databases and meeting the LZTR1 PM2_Supporting threshold of ≤0.0025%.2 OncoKB classifies this variant as likely oncogenic with a likely loss-of-function biological effect, but no approved RASopathy VCEP functional assay result was identified for this specific variant.3 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.02, and no REVEL or BayesDel score was available because this is not a single-nucleotide variant.4

PM2 VUS
3 oncokb ↗vcep_svi_rasopathy_vcep_v2_approved_functional_studies
Gene diagram · NM_006767.4 · variants mapped to exon structure
LZTR1 NM_006767.4
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 has been reported in ClinVar as Likely pathogenic (2 clinical laboratories) and as Pathogenic (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      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.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots