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NM_002047.4(GARS1):c.980G>C (p.Gly327Ala) AND Charcot-Marie-Tooth disease type 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 5, 2024
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:
RCV000803887.7

Allele description [Variation Report for NM_002047.4(GARS1):c.980G>C (p.Gly327Ala)]

NM_002047.4(GARS1):c.980G>C (p.Gly327Ala)

Gene:
GARS1:glycyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p14.3
Genomic location:
Preferred name:
NM_002047.4(GARS1):c.980G>C (p.Gly327Ala)
HGVS:
  • NC_000007.14:g.30612194G>C
  • NG_007942.1:g.22630G>C
  • NM_001316772.1:c.818G>C
  • NM_002047.4:c.980G>CMANE SELECT
  • NP_001303701.1:p.Gly273Ala
  • NP_002038.2:p.Gly327Ala
  • LRG_243t1:c.980G>C
  • LRG_243:g.22630G>C
  • NC_000007.13:g.30651810G>C
  • NM_002047.2:c.980G>C
Protein change:
G273A
Links:
dbSNP: rs774283805
NCBI 1000 Genomes Browser:
rs774283805
Molecular consequence:
  • NM_001316772.1:c.818G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002047.4:c.980G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Charcot-Marie-Tooth disease type 2
Synonyms:
Charcot-Marie-Tooth, Type 2
Identifiers:
MONDO: MONDO:0018993; MedGen: C0270914

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000943774Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jan 5, 2024)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Application of targeted multi-gene panel testing for the diagnosis of inherited peripheral neuropathy provides a high diagnostic yield with unexpected phenotype-genotype variability.

Antoniadi T, Buxton C, Dennis G, Forrester N, Smith D, Lunt P, Burton-Jones S.

BMC Med Genet. 2015 Sep 21;16:84. doi: 10.1186/s12881-015-0224-8.

PubMed [citation]
PMID:
26392352
PMCID:
PMC4578331

A recurrent GARS mutation causes distal hereditary motor neuropathy.

Lee DC, Meyer-Schuman R, Bacon C, Shy ME, Antonellis A, Scherer SS.

J Peripher Nerv Syst. 2019 Dec;24(4):320-323. doi: 10.1111/jns.12353. Epub 2019 Nov 22.

PubMed [citation]
PMID:
31628756
PMCID:
PMC6910989
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000943774.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 327 of the GARS protein (p.Gly327Ala). This variant is present in population databases (rs774283805, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with GARS-related conditions. ClinVar contains an entry for this variant (Variation ID: 423475). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GARS protein function. This variant disrupts the p.Gly327 amino acid residue in GARS. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 26392352, 31628756, 31985473). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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