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NM_006767.4(LZTR1):c.347C>T (p.Ala116Val) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 10, 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:
RCV003324021.2

Allele description [Variation Report for NM_006767.4(LZTR1):c.347C>T (p.Ala116Val)]

NM_006767.4(LZTR1):c.347C>T (p.Ala116Val)

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.347C>T (p.Ala116Val)
HGVS:
  • NC_000022.11:g.20987530C>T
  • NG_034193.1:g.10262C>T
  • NM_006767.4:c.347C>TMANE SELECT
  • NP_006758.2:p.Ala116Val
  • LRG_989t1:c.347C>T
  • LRG_989:g.10262C>T
  • LRG_989p1:p.Ala116Val
  • NC_000022.10:g.21341819C>T
  • NM_006767.3:c.347C>T
Protein change:
A116V
Molecular consequence:
  • NM_006767.4:c.347C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004029016Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Jul 10, 2023) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

LZTR1 molecular genetic overlap with clinical implications for Noonan syndrome and schwannomatosis.

Farncombe KM, Thain E, Barnett-Tapia C, Sadeghian H, Kim RH.

BMC Med Genomics. 2022 Jul 15;15(1):160. doi: 10.1186/s12920-022-01304-x. Review.

PubMed [citation]
PMID:
35840934
PMCID:
PMC9288044

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004029016.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: LZTR1 c.347C>T (p.Ala116Val) results in a non-conservative amino acid change located in the Kelch repeat type 1 (IPR006652) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250768 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.347C>T has been reported in the literature in at least one individual affected with Noonan Syndrome, where the variant was confirmed to have occured de novo (Farncombe_2022). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 35840934). Two ClinVar submitters have assessed this variant since 2014: both classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024