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NM_020320.5(RARS2):c.16C>T (p.Arg6Cys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 18, 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:
RCV002968067.2

Allele description [Variation Report for NM_020320.5(RARS2):c.16C>T (p.Arg6Cys)]

NM_020320.5(RARS2):c.16C>T (p.Arg6Cys)

Gene:
RARS2:arginyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q15
Genomic location:
Preferred name:
NM_020320.5(RARS2):c.16C>T (p.Arg6Cys)
HGVS:
  • NC_000006.12:g.87589942G>A
  • NG_008601.1:g.5076C>T
  • NG_108712.1:g.926G>A
  • NM_001318785.2:c.-675C>T
  • NM_001350505.2:c.16C>T
  • NM_001350506.2:c.-731C>T
  • NM_001350507.2:c.-854C>T
  • NM_001350508.2:c.-893C>T
  • NM_001350509.2:c.-601C>T
  • NM_001350510.2:c.-731C>T
  • NM_001350511.2:c.-850C>T
  • NM_020320.5:c.16C>TMANE SELECT
  • NP_001337434.1:p.Arg6Cys
  • NP_064716.2:p.Arg6Cys
  • NC_000006.11:g.88299660G>A
  • NR_134857.2:n.46C>T
  • NR_146738.2:n.46C>T
  • NR_146739.2:n.46C>T
  • NR_146740.2:n.46C>T
  • NR_146741.2:n.46C>T
  • NR_146742.2:n.46C>T
  • NR_146743.2:n.46C>T
  • NR_146744.2:n.46C>T
  • NR_146745.2:n.46C>T
  • NR_146746.2:n.46C>T
  • NR_146747.2:n.46C>T
  • NR_146748.2:n.46C>T
  • NR_146749.2:n.46C>T
  • NR_146750.2:n.46C>T
  • NR_146751.2:n.46C>T
  • NR_146752.2:n.46C>T
  • NR_146753.2:n.46C>T
  • NR_146754.2:n.46C>T
  • NR_146755.2:n.46C>T
  • NR_146756.2:n.46C>T
  • NR_146757.2:n.46C>T
  • NR_146758.2:n.46C>T
  • NR_146759.2:n.46C>T
Protein change:
R6C
Molecular consequence:
  • NM_001318785.2:c.-675C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350506.2:c.-731C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350507.2:c.-854C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350508.2:c.-893C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350509.2:c.-601C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350510.2:c.-731C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350511.2:c.-850C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350505.2:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020320.5:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134857.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146738.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146739.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146740.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146741.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146742.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146743.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146744.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146745.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146746.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146747.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146748.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146749.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146750.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146751.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146752.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146753.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146754.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146755.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146756.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146757.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146758.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146759.2:n.46C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003289911Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 18, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Diagnostic value of partial exome sequencing in developmental disorders.

Gieldon L, Mackenroth L, Kahlert AK, Lemke JR, Porrmann J, Schallner J, von der Hagen M, Markus S, Weidensee S, Novotna B, Soerensen C, Klink B, Wagner J, Tzschach A, Jahn A, Kuhlee F, Hackmann K, Schrock E, Di Donato N, Rump A.

PLoS One. 2018;13(8):e0201041. doi: 10.1371/journal.pone.0201041. Erratum in: PLoS One. 2020 Sep 24;15(9):e0239959. doi: 10.1371/journal.pone.0239959. PLoS One. 2022 Jun 22;17(6):e0270541. doi: 10.1371/journal.pone.0270541.

PubMed [citation]
PMID:
30091983
PMCID:
PMC6084857

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003289911.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 6 of the RARS2 protein (p.Arg6Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of pontocerebellar hypoplasia (PMID: 30091983). 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 RARS2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024