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NM_024678.6(NARS2):c.969T>A (p.Tyr323Ter) AND Combined oxidative phosphorylation defect type 24

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Aug 28, 2019
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:
RCV000779611.4

Allele description [Variation Report for NM_024678.6(NARS2):c.969T>A (p.Tyr323Ter)]

NM_024678.6(NARS2):c.969T>A (p.Tyr323Ter)

Gene:
NARS2:asparaginyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q14.1
Genomic location:
Preferred name:
NM_024678.6(NARS2):c.969T>A (p.Tyr323Ter)
HGVS:
  • NC_000011.10:g.78469304A>T
  • NG_042046.1:g.110561T>A
  • NM_001243251.2:c.288T>A
  • NM_024678.6:c.969T>AMANE SELECT
  • NP_001230180.1:p.Tyr96Ter
  • NP_078954.4:p.Tyr323Ter
  • NC_000011.9:g.78180350A>T
  • NM_024678.5:c.969T>A
Protein change:
Y323*; TYR323TER
Links:
OMIM: 612803.0003; dbSNP: rs565224393
NCBI 1000 Genomes Browser:
rs565224393
Molecular consequence:
  • NM_001243251.2:c.288T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_024678.6:c.969T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Combined oxidative phosphorylation defect type 24
Synonyms:
Combined oxidative phosphorylation deficiency 24
Identifiers:
MONDO: MONDO:0014547; MedGen: C4015643; Orphanet: 444458; OMIM: 616239

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000916290OMIM
no assertion criteria provided
Pathogenic
(May 28, 2019)
germlineliterature only

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

SCV001146806SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Aug 28, 2019)
unknowncuration

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedcuration
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations of human NARS2, encoding the mitochondrial asparaginyl-tRNA synthetase, cause nonsyndromic deafness and Leigh syndrome.

Simon M, Richard EM, Wang X, Shahzad M, Huang VH, Qaiser TA, Potluri P, Mahl SE, Davila A, Nazli S, Hancock S, Yu M, Gargus J, Chang R, Al-Sheqaih N, Newman WG, Abdenur J, Starr A, Hegde R, Dorn T, Busch A, Park E, et al.

PLoS Genet. 2015 Mar;11(3):e1005097. doi: 10.1371/journal.pgen.1005097.

PubMed [citation]
PMID:
25807530
PMCID:
PMC4373692

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, SCV000916290.2

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

Description

In 2 brothers, born of unrelated Caucasian parents (family LS06), with fatal combined oxidative phosphorylation deficiency-24 (COXPD24; 616239), Simon et al. (2015) identified compound heterozygous mutations in the NARS2 gene: a c.969T-A transversion (c.969T-A, NM_024678) in exon 10, resulting in a tyr323-to-ter (Y323X) substitution, and a c.1142A-G transition in exon 11, resulting in an asn381-to-ser (N381S; 612803.0004) substitution at a conserved residue. The mutations which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Neither variant was found in the dbSNP (build 138), 1000 Genomes Project, or Exome Variant Server databases. Both variants occurred in the catalytic domain. Patient fibroblasts showed decreased levels of NARS2 and decreased levels of aminoacylated mt-tRNA(Asn) compared to controls, although aminoacylation activity of NARS2 was normal. A truncated NARS2 protein was not detected, suggesting that the nonsense allele resulted in nonsense-mediated mRNA decay. In vitro functional expression studies in HEK293 cells showed that the N381S mutant protein was expressed at normal levels and localized normally to the mitochondria, but the mutation impaired homodimerization. The impaired oxygen consumption rate in patient cells was significantly rescued by expression of wildtype NARS2. The findings indicated that the NARS2 mutations impaired mitochondrial function.

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

From SIB Swiss Institute of Bioinformatics, SCV001146806.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (2)

Description

This variant is interpreted as a Likely pathogenic for Combined oxidative phosphorylation deficiency 24, autosomal recessive. The following ACMG Tag(s) were applied: PM2, PP1, PS3-Moderate, PVS1-Moderate.

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

Last Updated: Mar 16, 2024