VCV002179363.4 - ClinVar

NM_018122.5(DARS2):c.173G>A (p.Arg58His)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_018122.5(DARS2):c.173G>A (p.Arg58His)

Variation ID: 2179363 Accession: VCV002179363.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1q25.1 1: 173826732 (GRCh38) [ NCBI UCSC ] 1: 173795870 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 8, 2023	May 1, 2024	Mar 7, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_018122.5:c.173G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_060592.2:p.Arg58His	missense
NM_001365212.1:c.173G>A	NP_001352141.1:p.Arg58His	missense
NM_001365213.2:c.173G>A	NP_001352142.1:p.Arg58His	missense
NM_018122.4:c.173G>A
NC_000001.11:g.173826732G>A
NC_000001.10:g.173795870G>A
NG_016138.1:g.7074G>A
LRG_1270:g.7074G>A
LRG_1270t1:c.173G>A	LRG_1270p1:p.Arg58His

... more HGVS ... less HGVS

Protein change

R58H

Other names

Canonical SPDI

NC_000001.11:173826731:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
DARS2		-	-	GRCh38 GRCh37	406	454

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Likely pathogenic (1)	criteria provided, single submitter	Jun 14, 2022	RCV002591927.3
Inborn genetic diseases	Uncertain significance (1)	criteria provided, single submitter	Mar 7, 2023	RCV003161906.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Jun 14, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003494860.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Publications: PubMed (3) PubMed: 24566671‚ 26327357‚ 33977142 Comment: This variant is present in population databases (rs773592266, gnomAD 0.006%). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data … (more) This variant is present in population databases (rs773592266, gnomAD 0.006%). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Arg58 amino acid residue in DARS2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 24566671, 26327357, 33977142). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt DARS2 protein function. This variant has not been reported in the literature in individuals affected with DARS2-related conditions. This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 58 of the DARS2 protein (p.Arg58His). (less)
Uncertain significance (Mar 07, 2023)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV003909508.2 First in ClinVar: Apr 15, 2023 Last updated: May 01, 2024	Comment: The c.173G>A (p.R58H) alteration is located in exon 2 (coding exon 2) of the DARS2 gene. This alteration results from a G to A substitution … (more) The c.173G>A (p.R58H) alteration is located in exon 2 (coding exon 2) of the DARS2 gene. This alteration results from a G to A substitution at nucleotide position 173, causing the arginine (R) at amino acid position 58 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)

Comment:

This variant is present in population databases (rs773592266, gnomAD 0.006%). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Arg58 amino acid residue in DARS2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 24566671, 26327357, 33977142). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt DARS2 protein function. This variant has not been reported in the literature in individuals affected with DARS2-related conditions. This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 58 of the DARS2 protein (p.Arg58His).

Comment:

The c.173G>A (p.R58H) alteration is located in exon 2 (coding exon 2) of the DARS2 gene. This alteration results from a G to A substitution at nucleotide position 173, causing the arginine (R) at amino acid position 58 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
LBSL: Case Series and DARS2 Variant Analysis in Early Severe Forms With Unexpected Presentations.	Stellingwerff MD	Neurology. Genetics	2021	PMID: 33977142
Early-onset leukoencephalopathy due to a homozygous missense mutation in the DARS2 gene.	Köhler C	Molecular and cellular probes	2015	PMID: 26327357
Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation: clinical and genetic characterization and target for therapy.	van Berge L	Brain : a journal of neurology	2014	PMID: 24566671

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_018122.5(DARS2):c.173G>A (p.Arg58His)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...