NM_006767.4(LZTR1):c.1689G>A (p.Glu563=) AND Noonan syndrome 10

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 25, 2023
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:: RCV003325239.1

Allele description [Variation Report for NM_006767.4(LZTR1):c.1689G>A (p.Glu563=)]

NM_006767.4(LZTR1):c.1689G>A (p.Glu563=)

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.1689G>A (p.Glu563=)

HGVS:

NC_000022.11:g.20994631G>A
NG_034193.1:g.17363G>A
NM_006767.4:c.1689G>AMANE SELECT
NP_006758.2:p.Glu563=
LRG_989t1:c.1689G>A
LRG_989:g.17363G>A
LRG_989p1:p.Glu563=
NC_000022.10:g.21348920G>A
NM_006767.3:c.1689G>A

Links:

dbSNP: rs977829129

NCBI 1000 Genomes Browser:

rs977829129

Molecular consequence:

NM_006767.4:c.1689G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Noonan syndrome 10 (NS10)
Identifiers:: MONDO: MONDO:0014693; MedGen: C4225280; Orphanet: 648; OMIM: 616564

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004031240	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	criteria provided, single submitter (St. Jude Assertion Criteria 2020)	Uncertain significance (Jul 25, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004031240

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

criteria provided, single submitter

(St. Jude Assertion Criteria 2020)

Uncertain significance
(Jul 25, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV004031240.1

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

Description

The LZTR1 c.1689G>A (p.Glu563=) synonymous change has a maximum frequency of 0.0028% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). Algorithms that predict the impact of sequence changes on splicing indicate that this change may impact splicing, but to our knowledge these predictions have not been confirmed by RNA studies. To our knowledge, this variant has not been reported in the literature in individuals with LZTR1-related disease. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.??

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

Last Updated: Sep 29, 2024

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