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 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.1234C>T (p.Arg412Cys)

CA501019

373089 (ClinVar)

Gene: LZTR1
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: c382a894-de4a-4be7-85f1-8003be6e6f47
Approved on: 2025-07-08
Published on: 2025-12-22

HGVS expressions

NM_006767.4:c.1234C>T
NM_006767.4(LZTR1):c.1234C>T (p.Arg412Cys)
NC_000022.11:g.20992878C>T
CM000684.2:g.20992878C>T
NC_000022.10:g.21347167C>T
CM000684.1:g.21347167C>T
NC_000022.9:g.19677167C>T
NG_034193.1:g.15610C>T
ENST00000700578.1:c.1234C>T
ENST00000495142.6:n.579C>T
ENST00000642151.1:c.1065C>T
ENST00000643578.1:n.1256C>T
ENST00000646124.2:c.1234C>T
ENST00000646506.1:n.813C>T
ENST00000215739.12:c.1234C>T
ENST00000479606.5:n.1380C>T
ENST00000492480.1:n.290C>T
NM_006767.3:c.1234C>T
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Pathogenic

Met criteria codes 2
PS4 PS2_Very Strong
Not Met criteria codes 5
BA1 PP3 PM2 BS1 BP4

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 NM_006767.4:c.1234C>T (p.Arg412Cys) variant in LZTR1 is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 412. Evidence supports that this variant is associated with autosomal dominant Noonan Syndrome and is not associated with autosomal recessive Noonan Syndrome. The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003850 (1/25972 alleles) in the Ashkenazi Jewish population (PM2_Supporting, BS1, and BA1 are not met). The computational predictor REVEL gives a score of 0.351, which is neither above nor below the thresholds predicting a damaging or benign impact on LZTR1 function (no codes met). This variant has been reported in 7 with features of RASopathy that are included in this curation (PS4; > 5.0 pts.; PMID: 32981126; GeneDx (SCV000491652), Prevention Genetics (SCV004118816), and Genome Diagnostics Laboratory (Hospital for Sick Children; SCV002060883) internal data). This variant has been identified as de novo with confirmed parental relationships in 2 probands included in this curation (PS2_VeryStrong, > 4.0 pts.; Genome Diagnostics Laboratory (Hospital for Sick Children; SCV002060883) and GeneDx (SCV000491652) internal data). More cases are available, but the thresholds to apply PS4 and PS2 at the strongest levels have already been met. A heterozygous knock-in mouse model of this mutation showed, in addition to death of 75 % of mice by 2 years of age, that the mutants had reduced body lengths and weights compared to the wild-type before 10 weeks old. The mutant mice also had facial and skeletal anomalies, including smaller and more round skulls, abnormal snouts, and hypertelorism, as well as splenomegaly and renal hypertrophy, features consistent with other mouse models of RASopathies (PMID: 39352760). However, PS3 was not applied as it is not currently in the guidelines for LZTR1 variants. In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: PS4, PS2_VeryStrong (RASopathy VCEP specifications version 1.3.0; 7/8/2025).
Met criteria codes
PS4
his variant has been reported in 7 with features of RASopathy that are included in this curation (PS4; > 5.0 pts.; PMID: 32981126; GeneDx (SCV000491652), Prevention Genetics (SCV004118816), and Genome Diagnostics Laboratory (Hospital for Sick Children; SCV002060883) internal data).
PS2_Very Strong
This variant has been identified as de novo with confirmed parental relationships in 2 probands included in this curation (PS2_VeryStrong, 4.0 pts.; Genome Diagnostics Laboratory (Hospital for Sick Children; SCV002060883) and GeneDx (SCV000491652) internal data).
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
The computational predictor REVEL gives a score of 0.351, which is neither above nor below the thresholds predicting a damaging or benign impact on LZTR1 function.
PM2
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003850 (1/25972 alleles) in the Ashkenazi Jewish 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
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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