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NM_003680.4(YARS1):c.946G>A (p.Ala316Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Jan 23, 2020
Accession:
VCV000297154.4
Variation ID:
297154
Description:
single nucleotide variant
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NM_003680.4(YARS1):c.946G>A (p.Ala316Thr)

Allele ID
282125
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p35.1
Genomic location
1: 32782500 (GRCh38) GRCh38 UCSC
1: 33248101 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.33248101C>T
NM_003680.3:c.946G>A NP_003671.1:p.Ala316Thr missense
NC_000001.11:g.32782500C>T
... more HGVS
Protein change
A316T
Other names
-
Canonical SPDI
NC_000001.11:32782499:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
1000 Genomes Project 0.00040
Trans-Omics for Precision Medicine (TOPMed) 0.00018
The Genome Aggregation Database (gnomAD) 0.00006
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
Links
ClinGen: CA745039
dbSNP: rs138454151
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Dec 2, 2016 RCV000516749.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 23, 2020 RCV000276182.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
YARS1 - - GRCh38
GRCh37
254 301

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease, dominant intermediate C
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000357240.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Dec 02, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000616301.1
Submitted: (Aug 17, 2017)
Evidence details
Uncertain significance
(Jan 23, 2020)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease, dominant intermediate C
Allele origin: germline
Invitae
Accession: SCV001382411.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces alanine with threonine at codon 316 of the YARS protein (p.Ala316Thr). The alanine residue is highly conserved and there is a … (more)

Functional evidence

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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.

Citations for this variant

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Title Author Journal Year Link
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811

Text-mined citations for rs138454151...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021