NM_006767.4(LZTR1):c.2387T>C (p.Ile796Thr) AND Noonan syndrome 2

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 27, 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:: RCV001507320.1

Allele description [Variation Report for NM_006767.4(LZTR1):c.2387T>C (p.Ile796Thr)]

NM_006767.4(LZTR1):c.2387T>C (p.Ile796Thr)

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.2387T>C (p.Ile796Thr)

HGVS:

NC_000022.11:g.20996947T>C
NG_034193.1:g.19679T>C
NM_006767.4:c.2387T>CMANE SELECT
NP_006758.2:p.Ile796Thr
LRG_989t1:c.2387T>C
LRG_989:g.19679T>C
LRG_989p1:p.Ile796Thr
NC_000022.10:g.21351236T>C
NM_006767.3:c.2387T>C

Protein change:

I796T

Links:

dbSNP: rs141672122

NCBI 1000 Genomes Browser:

rs141672122

Molecular consequence:

NM_006767.4:c.2387T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Noonan syndrome 2 (NS2)
Synonyms:: Noonan syndrome autosomal recessive
Identifiers:: MONDO: MONDO:0011531; MedGen: C1854469; Orphanet: 648; OMIM: 605275

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001712281	Department of Pediatrics, The University of Tokyo	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 27, 2021)	inherited	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 31883238

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001712281

Department of Pediatrics, The University of Tokyo

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 27, 2021)

inherited

clinical testing

PubMed (2)
[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	inherited	yes	1	not provided	not provided	1	yes	clinical testing

Citations

PubMed

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

Noonan syndrome-associated biallelic LZTR1 mutations cause cardiac hypertrophy and vascular malformations in zebrafish.

Nakagama Y, Takeda N, Ogawa S, Takeda H, Furutani Y, Nakanishi T, Sato T, Hirata Y, Oka A, Inuzuka R.

Mol Genet Genomic Med. 2020 Mar;8(3):e1107. doi: 10.1002/mgg3.1107. Epub 2019 Dec 28.

PubMed [citation]

PMID:: 31883238
PMCID:: PMC7057116

Details of each submission

From Department of Pediatrics, The University of Tokyo, SCV001712281.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	yes	clinical testing	PubMed (2)

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

Last Updated: Sep 29, 2024

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