NM_005548.3(KARS1):c.1784C>G (p.Thr595Ser) AND not specified

Germline classification:: Benign (2 submissions)
Last evaluated:: May 9, 2017
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:: RCV000223592.5

Allele description [Variation Report for NM_005548.3(KARS1):c.1784C>G (p.Thr595Ser)]

NM_005548.3(KARS1):c.1784C>G (p.Thr595Ser)

Gene:

KARS1:lysyl-tRNA synthetase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q23.1

Genomic location:

Preferred name:

NM_005548.3(KARS1):c.1784C>G (p.Thr595Ser)

HGVS:

NC_000016.10:g.75627905G>C
NG_028025.1:g.24783C>G
NG_050747.1:g.419C>G
NM_001130089.2:c.1868C>G
NM_001378148.1:c.1316C>G
NM_005548.3:c.1784C>GMANE SELECT
NP_001123561.1:p.Thr623Ser
NP_001123561.1:p.Thr623Ser
NP_001365077.1:p.Thr439Ser
NP_005539.1:p.Thr595Ser
LRG_366t1:c.1868C>G
LRG_366:g.24783C>G
LRG_366p1:p.Thr623Ser
NC_000016.9:g.75661803G>C
NM_001130089.1:c.1868C>G

Protein change:

T439S

Links:

dbSNP: rs6834

NCBI 1000 Genomes Browser:

rs6834

Molecular consequence:

NM_001130089.2:c.1868C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378148.1:c.1316C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005548.3:c.1784C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

120

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000269192	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Nov 24, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000729950	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (May 9, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000269192

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Nov 24, 2014)

germline

clinical testing

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

SCV000729950

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(May 9, 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
not provided	germline	not provided	122	120	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000269192.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	122	not provided	not provided	clinical testing	PubMed (1)

Description

Thr623Ser in exon 15 of KARS: This variant is not expected to have clinical sign ificance because it has been identified in 32.4% (1426/4396) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs6834).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		122	not provided	120	not provided

From GeneDx, SCV000729950.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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: Sep 29, 2024

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