NM_006767.4(LZTR1):c.1312G>T (p.Glu438Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 29, 2024
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:: RCV005097430.1

Allele description [Variation Report for NM_006767.4(LZTR1):c.1312G>T (p.Glu438Ter)]

NM_006767.4(LZTR1):c.1312G>T (p.Glu438Ter)

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.1312G>T (p.Glu438Ter)

HGVS:

NC_000022.11:g.20993713G>T
NG_034193.1:g.16445G>T
NM_006767.4:c.1312G>TMANE SELECT
NP_006758.2:p.Glu438Ter
LRG_989t1:c.1312G>T
LRG_989:g.16445G>T
LRG_989p1:p.Glu438Ter
NC_000022.10:g.21348002G>T
NM_006767.3:c.1312G>T

Protein change:

E438*

Links:

dbSNP: rs1924687245

NCBI 1000 Genomes Browser:

rs1924687245

Molecular consequence:

NM_006767.4:c.1312G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005840661	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 29, 2024)	germline	clinical testing	PubMed (12) [See all records that cite these PMIDs] 24362817, 25335493, 25480913, 25795793, 29469822, 30368668, 30442762, 30442766, 30481304, 30859559, 25008767, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005840661

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 29, 2024)

germline

clinical testing

PubMed (12)
[See all records that cite these PMIDs]

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

Citations

PubMed

Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas.

Piotrowski A, Xie J, Liu YF, Poplawski AB, Gomes AR, Madanecki P, Fu C, Crowley MR, Crossman DK, Armstrong L, Babovic-Vuksanovic D, Bergner A, Blakeley JO, Blumenthal AL, Daniels MS, Feit H, Gardner K, Hurst S, Kobelka C, Lee C, Nagy R, Rauen KA, et al.

Nat Genet. 2014 Feb;46(2):182-7. doi: 10.1038/ng.2855. Epub 2013 Dec 22.

PubMed [citation]

PMID:: 24362817
PMCID:: PMC4352302

Expanding the mutational spectrum of LZTR1 in schwannomatosis.

Paganini I, Chang VY, Capone GL, Vitte J, Benelli M, Barbetti L, Sestini R, Trevisson E, Hulsebos TJ, Giovannini M, Nelson SF, Papi L.

Eur J Hum Genet. 2015 Jul;23(7):963-8. doi: 10.1038/ejhg.2014.220. Epub 2014 Oct 22.

PubMed [citation]

PMID:: 25335493
PMCID:: PMC4463507

See all PubMed Citations (12)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005840661.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (12)

Description

This sequence change creates a premature translational stop signal (p.Glu438*) in the LZTR1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LZTR1 are known to be pathogenic (PMID: 24362817, 25335493, 25480913, 25795793, 29469822, 30368668, 30442762, 30442766, 30481304, 30859559). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with schwannomatosis (PMID: 25008767). ClinVar contains an entry for this variant (Variation ID: 1769704). For these reasons, this variant has been classified as Pathogenic.

#	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: May 16, 2025

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