NM_006767.4(LZTR1):c.370GTC[1] (p.Val125del) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 20, 2021
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:: RCV001805965.2

Allele description [Variation Report for NM_006767.4(LZTR1):c.370GTC[1] (p.Val125del)]

NM_006767.4(LZTR1):c.370GTC[1] (p.Val125del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_006767.4(LZTR1):c.370GTC[1] (p.Val125del)

HGVS:

NC_000022.11:g.20987553GTC[1]
NC_000022.11:g.20987553_20987555GTC[1]
NG_034193.1:g.10285GTC[1]
NM_006767.4:c.370GTC[1]MANE SELECT
NP_006758.2:p.Val125del
LRG_989t1:c.370GTC[1]
LRG_989:g.10285GTC[1]
LRG_989p1:p.Val125del
NC_000022.10:g.21341841_21341843del
NC_000022.10:g.21341842GTC[1]
NM_006767.3:c.373_375del
NM_006767.3:c.373_375delGTC
NM_006767.4:c.373_375delMANE SELECT

Protein change:

V125del

Links:

dbSNP: rs755783378

NCBI 1000 Genomes Browser:

rs755783378

Molecular consequence:

NM_006767.4:c.370GTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002051283	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Dec 20, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 27921248, 25335493, 30481304, 30368668 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002051283

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Dec 20, 2021)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Citations

PubMed

The molecular pathogenesis of schwannomatosis, a paradigm for the co-involvement of multiple tumour suppressor genes in tumorigenesis.

Kehrer-Sawatzki H, Farschtschi S, Mautner VF, Cooper DN.

Hum Genet. 2017 Feb;136(2):129-148. doi: 10.1007/s00439-016-1753-8. Epub 2016 Dec 5. Review.

PubMed [citation]

PMID:: 27921248
PMCID:: PMC5258795

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 (4)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002051283.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

Variant summary: LZTR1 c.373_375delGTC (p.Val125del) results in an in-frame deletion that is predicted to remove one amino acids from the encoded protein. The variant allele was found at a frequency of 8e-06 in 251242 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.373_375delGTC has been reported in the literature in one individual affected with Schwannomatosis (Paganini_2015). The report does not provide unequivocal conclusions about association of the variant with Noonan Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance and likely pathogenic. Based on the evidence outlined above, the variant was classified as 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: Oct 20, 2024

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