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LZTR1
Final classification
VUS
LZTR1 c.2417T>G · p.Leu806Trp
LZTR1

The LZTR1 c.2417T>G (p.Leu806Trp) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as likely pathogenic by a single clinical laboratory.

Gene
LZTR1
Transcript
NM_006767.4
HGVS · transcript:coding
NM_006767.4:c.2417T>G
Consequence
N/A
GRCh38
chr22:20997242 T>G
GRCh37
chr22:21351531 T>G
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, BP4 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, BP4 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2 BP4 VUS
LZTR1 c.2417T>G

The LZTR1 c.2417T>G (p.Leu806Trp) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as likely pathogenic by a single clinical laboratory.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, corresponding to an observed allele frequency of 0 in both datasets.2 Computational evidence supports a benign interpretation because REVEL is 0.174, below the LZTR1 BP4 threshold of 0.3, SpliceAI predicts no splice effect with a maximum delta score of 0.00, and BayesDel is -0.202983.3

PM2 + BP4 VUS
Gene diagram · NM_006767.4 · variants mapped to exon structure
LZTR1 NM_006767.4
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
      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 (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.174. BayesDel score = -0.202983.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. LZTR1, a ubiquitin ligase adaptor protein, is recurrently altered by mutation in glioblastoma, Noonan syndrome, and schwannomatosis.
      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