The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: LZTR1 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_006767.4(LZTR1):c.27dup (p.Gln10fs)

CA10118264

372684 (ClinVar)

Gene: LZTR1
Condition: RASopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 4732547c-19f8-4af1-9a19-ab429c51b096
Approved on: 2025-04-23
Published on: 2025-04-23

HGVS expressions

NM_006767.4:c.27dup
NM_006767.4(LZTR1):c.27dup (p.Gln10fs)
NC_000022.11:g.20982398dup
CM000684.2:g.20982398dup
NC_000022.10:g.21336687dup
CM000684.1:g.21336687dup
NC_000022.9:g.19666687dup
NG_034193.1:g.5130dup
ENST00000700578.1:c.27dup
ENST00000493460.2:n.102dup
ENST00000645935.1:c.27dup
ENST00000646124.2:c.27dup
ENST00000215739.12:c.27dup
ENST00000414985.5:c.27dup
ENST00000443265.5:c.27dup
ENST00000479606.5:n.347-629dup
ENST00000493460.1:n.102dup
NM_006767.3:c.27dup
More

Pathogenic

Met criteria codes 3
PM3 PS3_Supporting PVS1
Not Met criteria codes 3
PM2 BS1 BA1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for LZTR1 Version 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.27dup (p.Gln10fs) variant in LZTR1 is a frameshift variant predicted to cause a premature stop codon 24 amino acids downstream in biologically-relevant-exon 1 (of 21) and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0001139 (4/13466 alleles) in the East Asian population (PM2_Supporting, BS1, and BA1 are not met). This variant has been detected in 1 individual with RASopathy. They were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and which was confirmed in trans by family testing (c.1943-256C>T (p.T648fs*36), 1 PM3 point, PMID: 32623905) (PM3). ERK activation assay in patient-specific cardiomyocytes showed significantly increased levels of phosphorylated ERK supporting the abnormal impact due to loss of LZTR1 function (PMID:32623905)(PS3_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for autosomal recessive RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: PVS1, PM3, PS3_Supporting. (ClinGen RASopathy VCEP specifications version 1.3; 12/3/2024)
Met criteria codes
PM3
This variant has been detected in 1 individual with RASopathy. They were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and which was confirmed in trans by family testing (c.1943-256C>T (p.T648fs*36), 1 PM3 point, PMID: 32623905) (PM3).
PS3_Supporting
ERK activation assay in patient-specific cardiomyocytes showed significantly increased levels of phosphorylated ERK supporting the abnormal impact due to loss of LZTR1 function (PMID:32623905)(PS3_Supporting).
PVS1
The c.27dup (p.Gln10fs) variant in LZTR1 is a frameshift variant predicted to cause a premature stop codon 24 amino acids downstream in biologically-relevant-exon 1 (of 21) and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Not Met criteria codes
PM2
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0001139 (4/13466 alleles) in the East Asian population (PM2_Supporting, BS1, and BA1 are not met).
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.