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NM_015340.4(LARS2):c.899C>T (p.Thr300Met) AND Perrault syndrome 4

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
May 18, 2015
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:
RCV000203257.3

Allele description [Variation Report for NM_015340.4(LARS2):c.899C>T (p.Thr300Met)]

NM_015340.4(LARS2):c.899C>T (p.Thr300Met)

Gene:
LARS2:leucyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_015340.4(LARS2):c.899C>T (p.Thr300Met)
HGVS:
  • NC_000003.12:g.45476508C>T
  • NG_033907.3:g.92945C>T
  • NM_001368263.1:c.899C>T
  • NM_015340.4:c.899C>TMANE SELECT
  • NP_001355192.1:p.Thr300Met
  • NP_056155.1:p.Thr300Met
  • LRG_1353t1:c.899C>T
  • LRG_1353:g.92945C>T
  • LRG_1353p1:p.Thr300Met
  • NC_000003.11:g.45518000C>T
  • NG_033907.1:g.92926C>T
  • NG_033907.2:g.92926C>T
  • NM_015340.3:c.899C>T
Protein change:
T300M; THR300MET
Links:
OMIM: 604544.0004; dbSNP: rs864309642
NCBI 1000 Genomes Browser:
rs864309642
Molecular consequence:
  • NM_001368263.1:c.899C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015340.4:c.899C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Perrault syndrome 4 (PRLTS4)
Identifiers:
MONDO: MONDO:0014126; MedGen: C3809105; Orphanet: 2855; OMIM: 615300

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000238519Molecular Genetics and RNA Biology, Humanitas University
criteria provided, single submitter

(Submitter's publication)
Pathogenic
(May 18, 2015)
germlineresearch

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

SCV000292566OMIM
no assertion criteria provided
Pathogenic
(Dec 10, 2015)
germlineliterature only

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
Caucasiangermlineno2not providednot providednot providednot providedresearch

Citations

PubMed

First independent replication of the involvement of LARS2 in Perrault syndrome by whole-exome sequencing of an Italian family.

Soldà G, Caccia S, Robusto M, Chiereghin C, Castorina P, Ambrosetti U, Duga S, Asselta R.

J Hum Genet. 2016 Apr;61(4):295-300. doi: 10.1038/jhg.2015.149. Epub 2015 Dec 10.

PubMed [citation]
PMID:
26657938
PMCID:
PMC4817218

Details of each submission

From Molecular Genetics and RNA Biology, Humanitas University, SCV000238519.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian2not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot provided2not providednot providednot provided

From OMIM, SCV000292566.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a brother and sister, born of unrelated Italian parents, with Perrault syndrome-4 (PRLTS4; 615300), Solda et al. (2016) identified compound heterozygous missense mutations in the LARS2 gene: a c.899C-T transition (c.899C-T, NM_015340.3), resulting in a thr300-to-met (T300M) substitution in the editing domain, and a c.1912G-A transition, resulting in a glu638-to-lys (E638K; 604655.0005) substitution in the catalytic domain. The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, were filtered against the dbSNP (build 135), 1000 Genomes Project, and Exome Sequencing Project databases, and segregated with the disorder in the family. The mutations were not found in the ExAC database or in an in-house database of 3,500 ethnically matched controls. The E638 residue is highly conserved, whereas the T300 residue is conserved in mammals, but not in more distantly related species. Molecular modeling based on the E. coli structure suggested that both mutations would be deleterious. In vitro functional studies and studies on patient cells were not performed.

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

Last Updated: Sep 29, 2024