NM_006567.5(FARS2):c.1256G>A (p.Arg419His) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 16, 2015
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:: RCV000493622.1

Allele description

NM_006567.5(FARS2):c.1256G>A (p.Arg419His)

Gene:

FARS2:phenylalanyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p25.1

Genomic location:

Preferred name:

NM_006567.5(FARS2):c.1256G>A (p.Arg419His)

HGVS:

NC_000006.12:g.5771329G>A
NG_033003.1:g.514979G>A
NG_033003.2:g.514979G>A
NM_001318872.1:c.1256G>A
NM_006567.5:c.1256G>AMANE SELECT
NP_001305801.1:p.Arg419His
NP_006558.1:p.Arg419His
NC_000006.11:g.5771562G>A
NM_006567.3:c.1256G>A

Protein change:

R419H

Links:

dbSNP: rs202183509

NCBI 1000 Genomes Browser:

rs202183509

Molecular consequence:

NM_001318872.1:c.1256G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006567.5:c.1256G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000582286	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Sep 16, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000582286

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Sep 16, 2015)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000582286.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The R419H variant has not been published as a pathogenic variant, nor has it been reported as a benign polymorphism to our knowledge. The R419H variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. A missense variants in the same residue (R419C) has been reported in the Human Gene Mutation Database in association with mitochondrial dysfunction (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, this variant is a strong candidate for a pathogenic variant, however the possibility that it is a benign variant cannot be excluded

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 27, 2021

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