NM_006767.4(LZTR1):c.27del (p.Gln10fs) AND LZTR1-related schwannomatosis

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Mar 26, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000133460.15

Allele description [Variation Report for NM_006767.4(LZTR1):c.27del (p.Gln10fs)]

NM_006767.4(LZTR1):c.27del (p.Gln10fs)

Genes:

LOC130067016:ATAC-STARR-seq lymphoblastoid silent region 13504 [Gene]
LZTR1:leucine zipper like post translational regulator 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_006767.4(LZTR1):c.27del (p.Gln10fs)

HGVS:

NC_000022.11:g.20982398del
NG_034193.1:g.5130del
NM_006767.4:c.27delMANE SELECT
NP_006758.2:p.Gln10fs
LRG_989t1:c.27del
LRG_989:g.5130del
LRG_989p1:p.Gln10fs
NC_000022.10:g.21336681del
NC_000022.10:g.21336687del
NM_006767.3:c.27del
NM_006767.3:c.27delG
NM_006767.4:c.27delGMANE SELECT

Protein change:

Q10fs

Links:

OMIM: 600574.0004; dbSNP: rs587777613

Molecular consequence:

NM_006767.4:c.27del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: LZTR1-related schwannomatosis
Synonyms:: Schwannomatosis 2; Schwannomatosis-2, susceptibility to
Identifiers:: MONDO: MONDO:0014299; MedGen: C3810283; Orphanet: 93921; OMIM: 615670

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000188495	OMIM	no assertion criteria provided	Pathogenic (Feb 1, 2014)	unknown	literature only	PubMed (1) [See all records that cite this PMID]
SCV004193673	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 19, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004806981	Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 26, 2024)	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

SCV000188495

OMIM

no assertion criteria provided

Pathogenic
(Feb 1, 2014)

unknown

literature only

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

SCV004193673

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 19, 2023)

unknown

clinical testing

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

SCV004806981

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 26, 2024)

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	unknown	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	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

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 OMIM, SCV000188495.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a woman with schwannomatosis-2 (SWN2; 615670), Piotrowski et al. (2014) identified a germline heterozygous 1-bp deletion (27delG) in exon 1 of the LZTR1 gene, resulting in a frameshift and premature termination (Gln10ArgfsTer15). The mutation was not present in the dbSNP (build 137), 1000 Genomes Project, or Exome Sequencing Project databases. Tumor tissue also carried the heterozygous LZTR1 mutation, and showed loss of heterozygosity (LOH) at chromosome 22q11, including both the LZTR1 and NF2 (607379) genes. In addition, the tumors carried a heterozygous somatic mutation in the NF2 gene. These findings were consistent with biallelic loss of function of both LZTR1 and NF2 in all tumors.

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

From Baylor Genetics, SCV004193673.1

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

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

From Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre, SCV004806981.1

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

#	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: Jun 20, 2026

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