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NM_006567.5(FARS2):c.1082C>T (p.Pro361Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Mar 5, 2021)
Last evaluated:
Oct 5, 2020
Accession:
VCV000214335.7
Variation ID:
214335
Description:
single nucleotide variant
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NM_006567.5(FARS2):c.1082C>T (p.Pro361Leu)

Allele ID
211259
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6p25.1
Genomic location
6: 5613185 (GRCh38) GRCh38 UCSC
6: 5613418 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.5613418C>T
NC_000006.12:g.5613185C>T
NM_006567.5:c.1082C>T MANE Select NP_006558.1:p.Pro361Leu missense
... more HGVS
Protein change
P361L
Other names
p.P361L:CCG>CTG
Canonical SPDI
NC_000006.12:5613184:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00012
The Genome Aggregation Database (gnomAD) 0.00013
Trans-Omics for Precision Medicine (TOPMed) 0.00014
The Genome Aggregation Database (gnomAD), exomes 0.00014
Links
ClinGen: CA325392
OMIM: 611592.0008
dbSNP: rs751459058
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Oct 5, 2020 RCV000525331.8
Likely pathogenic 1 criteria provided, single submitter Sep 12, 2018 RCV000200808.4
Uncertain significance 2 criteria provided, single submitter Nov 8, 2018 RCV000578164.2
Uncertain significance 1 criteria provided, single submitter Sep 25, 2017 RCV000622524.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FARS2 - - GRCh38
GRCh37
289 357

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Sep 12, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000251375.13
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The P361L variant in the FARS2 gene has been reported previously in the compound heterozygous state with another FARS2 variant in two unrelated individuals with … (more)
Uncertain significance
(Sep 25, 2017)
criteria provided, single submitter
Method: clinical testing
Inborn genetic diseases
Allele origin: germline
Ambry Genetics
Accession: SCV000742958.2
Submitted: (Oct 09, 2020)
Evidence details
Likely pathogenic
(Oct 05, 2020)
criteria provided, single submitter
Method: clinical testing
Combined oxidative phosphorylation deficiency 14
Allele origin: germline
Invitae
Accession: SCV000652835.5
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces proline with leucine at codon 361 of the FARS2 protein (p.Pro361Leu). The proline residue is highly conserved and there is a … (more)
Uncertain significance
(Nov 08, 2018)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia 77, autosomal recessive
Allele origin: paternal
Baylor Genetics
Accession: SCV001526168.1
Submitted: (Mar 05, 2021)
Evidence details
Comment:
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Likely pathogenic
(Jun 13, 2018)
criteria provided, single submitter
Method: clinical testing
Combined oxidative phosphorylation deficiency 14
Allele origin: germline
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
Accession: SCV000845716.1
Submitted: (Jun 13, 2018)
Evidence details
Publications
PubMed (1)
Pathogenic
(Jan 30, 2018)
no assertion criteria provided
Method: literature only
SPASTIC PARAPLEGIA 77, AUTOSOMAL RECESSIVE
Allele origin: germline
OMIM
Accession: SCV000680039.1
Submitted: (Jan 30, 2018)
Evidence details
Publications
PubMed (1)
Pathogenic
(Nov 16, 2017)
no assertion criteria provided
Method: clinical testing
Combined oxidative phosphorylation deficiency 14
(Autosomal recessive inheritance)
Allele origin: maternal
Institute of Human Genetics, Klinikum rechts der Isar
Accession: SCV000680227.1
Submitted: (Dec 18, 2017)
Evidence details

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
Two types of recessive hereditary spastic paraplegia in Roma patients in compound heterozygous state; no ethnically prevalent variant found. Meszarosova AU Neuroscience letters 2020 PMID: 32007496
New insights into the phenotype of FARS2 deficiency. Vantroys E Molecular genetics and metabolism 2017 PMID: 29126765
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs751459058...

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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 Jul 13, 2021