Genetic Information
Gene & Transcript Details
Gene
LZTR1
Transcript
NM_006767.4
MANE Select
Total Exons
—
Reference Sequence
NC_000022.10
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_006767.3 | Alternative | 4332 nt | 104–2626 |
| NM_006767.4 | MANE Select | 4282 nt | 76–2598 |
| NM_006767.2 | Alternative | 4234 nt | 6–2528 |
Variant Details
HGVS Notation
NM_006767.4:c.2417T>G
Protein Change
L806W
Location
Exon 21
(Exon 21 of )
21
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—
Clinical & Population Data
Population Frequency
gnomAD Global Frequency
0.0 in 100,000
Extremely Rare
ACMG Criteria Applied
PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).
ClinVar
OpenClassification
Likely Pathogenic
1 publications
Clinical Statement
"This variant has been reported in ClinVar as Likely pathogenic (1 clinical laboratories)."
COSMIC Somatic Evidence
OpenCOSMIC ID
Recurrence
0 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
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Functional Impact & Domains
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene LZTR1.
Functional Summary
Error in OpenAI Consolidation. OncoKB: LZTR1L806WLZTR1L806WSomaticNCBI Gene:8216|Show additional gene information Variant OverviewLZTR1, a ubiquitin ligase adaptor protein, is recurrently altered by mutation in glioblastoma, Noonan syndrome, and schwannomatosis.The LZTR1 L806W mutation has not specifically been reviewed by the OncoKB team, and therefore its biological significance is unknown. JAX-CKB: No results found
Database Previews
OncoKB
JAX-CKB
Click on previews to view full database entries. External databases may require institutional access.
Computational Analysis
Pathogenicity Predictions
SpliceAIPredictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied
SpliceAI Scores
Window: ±500bp| Effect Type | Score | Position |
|---|---|---|
| Acceptor Loss (AL) | 0.0 | -494 bp |
| Donor Loss (DL) | 0.0 | -441 bp |
| Acceptor Gain (AG) | 0.0 | -52 bp |
| Donor Gain (DG) | 0.0 | -93 bp |
High impact (≥0.5)
Medium impact (0.2-0.49)
Low impact (<0.2)
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific)
Filter Criteria:
PM2
PM2 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
PP5
PP5 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
BP4
BP4 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)