NM_001040436.3(YARS2):c.616dup (p.Leu206fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 7, 2017
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:: RCV000490030.1

Allele description [Variation Report for NM_001040436.3(YARS2):c.616dup (p.Leu206fs)]

NM_001040436.3(YARS2):c.616dup (p.Leu206fs)

Gene:

YARS2:tyrosyl-tRNA synthetase 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

12p11.21

Genomic location:

Preferred name:

NM_001040436.3(YARS2):c.616dup (p.Leu206fs)

HGVS:

NC_000012.12:g.32755259dup
NG_028122.1:g.5695dup
NM_001040436.3:c.616dupMANE SELECT
NP_001035526.1:p.Leu206fs
NC_000012.11:g.32908193dup
NM_001040436.2:c.616dupC

Protein change:

L206fs

Links:

dbSNP: rs1085307738

NCBI 1000 Genomes Browser:

rs1085307738

Molecular consequence:

NM_001040436.3:c.616dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000577182	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Apr 7, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000577182

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Apr 7, 2017)

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, SCV000577182.4

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

Description

The c.616dupC variant in the YARS2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.616dupC variant causes a frameshift starting with codon Leucine 206, changes this amino acid to a Proline residue, and creates a premature Stop codon at position 23 of the new reading frame, denoted p.Leu206ProfsX23. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.616dupC variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.616dupC as a likely pathogenic variant.

#	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: Apr 23, 2022

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