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NM_020117.11(LARS1):c.3289A>G (p.Ile1097Val) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jan 2, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001566128.6

Allele description [Variation Report for NM_020117.11(LARS1):c.3289A>G (p.Ile1097Val)]

NM_020117.11(LARS1):c.3289A>G (p.Ile1097Val)

Gene:
LARS1:leucyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_020117.11(LARS1):c.3289A>G (p.Ile1097Val)
HGVS:
  • NC_000005.10:g.146120407T>C
  • NG_042294.1:g.67325A>G
  • NM_001317964.2:c.3151A>G
  • NM_001317965.2:c.3127A>G
  • NM_016460.4:c.3208A>G
  • NM_020117.11:c.3289A>GMANE SELECT
  • NP_001304893.1:p.Ile1051Val
  • NP_001304894.1:p.Ile1043Val
  • NP_057544.2:p.Ile1070Val
  • NP_064502.9:p.Ile1097Val
  • NC_000005.9:g.145499970T>C
  • NM_020117.9:c.3289A>G
Protein change:
I1043V
Links:
dbSNP: rs745902477
NCBI 1000 Genomes Browser:
rs745902477
Molecular consequence:
  • NM_001317964.2:c.3151A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317965.2:c.3127A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_016460.4:c.3208A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020117.11:c.3289A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001789603GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Jun 21, 2021)
germlineclinical testing

Citation Link,

SCV004528998Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jan 2, 2024)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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 GeneDx, SCV001789603.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27535533)

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004528998.1

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

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1097 of the LARS protein (p.Ile1097Val). This variant is present in population databases (rs745902477, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with LARS-related conditions. ClinVar contains an entry for this variant (Variation ID: 1200949). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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