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.2219+13C>T
Protein Change
?
Location
Exon 18
(Exon 18 of )
18
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—
Clinical & Population Data
Population Frequency
gnomAD Global Frequency
1.0 in 100,000
Extremely Rare
ACMG Criteria Applied
BS1
ClinVar
OpenClassification
Likely Benign
2 publications
Clinical Statement
"This variant has been reported in ClinVar as Benign (8 clinical laboratories) and as Likely benign (1 clinical laboratories)."
COSMIC Somatic Evidence
OpenCOSMIC ID
COSN31945036
Recurrence
4 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: LZTR12219+13C>TLZTR12219+13C>TSomaticNCBI 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 2219+13c>T 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 | -397 bp |
| Donor Loss (DL) | 0.12 | -39 bp |
| Acceptor Gain (AG) | 0.01 | -124 bp |
| Donor Gain (DG) | 0.05 | 15 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:
BP4
BP4 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
BP6
BP6 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)