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NM_018122.5(DARS2):c.1768T>G (p.Cys590Gly) AND Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 2, 2022
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:
RCV002471470.1

Allele description [Variation Report for NM_018122.5(DARS2):c.1768T>G (p.Cys590Gly)]

NM_018122.5(DARS2):c.1768T>G (p.Cys590Gly)

Gene:
DARS2:aspartyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q25.1
Genomic location:
Preferred name:
NM_018122.5(DARS2):c.1768T>G (p.Cys590Gly)
HGVS:
  • NC_000001.11:g.173857535T>G
  • NG_016138.1:g.37877T>G
  • NM_001365212.1:c.1615T>G
  • NM_018122.5:c.1768T>GMANE SELECT
  • NP_001352141.1:p.Cys539Gly
  • NP_060592.2:p.Cys590Gly
  • LRG_1270t1:c.1768T>G
  • LRG_1270:g.37877T>G
  • LRG_1270p1:p.Cys590Gly
  • NC_000001.10:g.173826673T>G
Protein change:
C539G
Molecular consequence:
  • NM_001365212.1:c.1615T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018122.5:c.1768T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome (LBSL)
Synonyms:
MITOCHONDRIAL ASPARTYL-tRNA SYNTHETASE DEFICIENCY; Leukoencephalopathy with Brainstem and Spinal Cord Involvement and Lactate Elevation; LEUKOENCEPHALOPATHY WITH BRAINSTEM AND SPINAL CORD INVOLVEMENT AND LACTATE ELEVATION, MILD
Identifiers:
MONDO: MONDO:0012622; MedGen: C1970180; Orphanet: 137898; OMIM: 611105

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002768156Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Feb 2, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical 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

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002768156.1

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

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation (MIM#611105). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from cysteine to glycine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (5 heterozygotes, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated tRNA synthetases class II domain (DECIPHER). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Dec 24, 2022