Genetic Information

Gene & Transcript Details

Gene
LZTR1
Transcript
NM_006767.4 MANE Select
Total Exons
Reference Sequence
NC_000022.10
Alternative Transcripts
IDStatusDetails
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.2412dup
Protein Change
K805Qfs*46
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

Open
Classification
Likely Pathogenic
2 publications
Clinical Statement

"This variant has been reported in ClinVar as Likely pathogenic (2 clinical laboratories) and as Pathogenic (1 clinical laboratories)."

COSMIC Somatic Evidence

Open
COSMIC 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 Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: LZTR1K805Qfs*46LZTR1K805Qfs*46SomaticNCBI 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 K805Qfs*46 is a truncating mutation in a tumor suppressor gene, and therefore is likely oncogenic.Hide mutation effect description The mutation effect description for truncating mutations in LZTR1 is: Truncating mutations in LZTR1 occur throughout the coding region of the protein and tend to result in loss of heterozygosity (PMID: 24362817, 23917401, 30442762). Loss-of-function truncating variants are found in patients with Noonan Syndrome, schwannomatosis, and glioblastoma (PMID: 24362817, 23917401). Inactivation of LZTR1 in hematopoietic cell lines results in increased RAS plasma membrane localization due to reduced CUL3-mediated ubiquitination degradation of RAS (PMID: 30442762). Loss of LZTR1 in HEK293T and HeLa cells results in increased expression of RIT1 and an increased MAPK response to serum stimulation (PMID: 30872527). In vitro studies with LZTR1-knockout in HeLa cells demonstrated that loss of LZTR1 results in loss of EGFR and AXL degradation, leading to aberrant growth factor signaling (PMID: 36445254). LZTR1-deleted mouse embryonic fibroblasts (MEFs) have an enhanced response to growth factors compared to wildtype MEFs (PMID: 30872527). In addition, loss of LZTR1 activity leads to imatinib, rebastinib, and ponatinib resistance but sensitivity to trametinib in cell growth assays (PMID: 30442762). Preclinical studies with E0954 schwannoma-like cells and LZTR1-knockdown mice demonstrated sensitivity to combination treatment of EGFR inhibitors afatinib or osimertinib plus AXL-specific inhibitor bemcentinib as measured by reduced clonogenicity and tumor growth (PMID: 36445254). JAX-CKB: No results found

Database Previews
OncoKB
OncoKB Preview
JAX-CKB
JAX-CKB Preview

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Computational Analysis

Pathogenicity Predictions

SpliceAI
Predictor Consensus
Unknown
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied

SpliceAI Scores

Window: ±500bp
Effect Type Score Position
- Acceptor Loss (AL) 0.02 -45 bp
- Donor Loss (DL) 0.01 -86 bp
+ Acceptor Gain (AG) 0.02 6 bp
+ Donor Gain (DG) 0.0 -438 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:
PVS1

PVS1 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PS3

PS3 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PM2

PM2 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PP5

PP5 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)