NM_006767.4(LZTR1):c.848G>A (p.Arg283Gln) AND Noonan syndrome and Noonan-related syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 8, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001813545.13

Allele description [Variation Report for NM_006767.4(LZTR1):c.848G>A (p.Arg283Gln)]

NM_006767.4(LZTR1):c.848G>A (p.Arg283Gln)

Gene:

LZTR1:leucine zipper like post translational regulator 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_006767.4(LZTR1):c.848G>A (p.Arg283Gln)

Other names:

NM_006767.4(LZTR1):c.848G>A

HGVS:

NC_000022.11:g.20991684G>A
NG_034193.1:g.14416G>A
NM_006767.4:c.848G>AMANE SELECT
NP_006758.2:p.Arg283Gln
LRG_989t1:c.848G>A
LRG_989:g.14416G>A
LRG_989p1:p.Arg283Gln
NC_000022.10:g.21345973G>A
NM_006767.3:c.848G>A

Protein change:

R283Q

Links:

dbSNP: rs1223430276

Molecular consequence:

NM_006767.4:c.848G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Noonan syndrome and Noonan-related syndrome
Identifiers:: MONDO: MONDO:0020297; MedGen: C5681679; Orphanet: 98733

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002060780	Genome Diagnostics Laboratory, The Hospital for Sick Children	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 8, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002060780

Genome Diagnostics Laboratory, The Hospital for Sick Children

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Dec 8, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genome Diagnostics Laboratory, The Hospital for Sick Children, SCV002060780.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This missense variant results in a change from arginine to glutamine at amino acid position 283. It has been reported previously in individuals with Noonan syndrome (PMIDs: 30368668, 33587123) or neurological anomaly (precise phenotype not specified – PMID: 33258288). This variant was reported to have occurred de novo in at least one individual. This variant is observed at an allele frequency of 0.000062% in population controls of the Genome Aggregation Database (gnomAD). In silico prediction programs predict this variant to impact protein function. Based on the evidence above, this variant is classified as likely pathogenic (ACMG criteria - PS4_Moderate, PM6, PP3, PP5).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 27, 2026

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