NM_002047.4(GARS1):c.764C>T (p.Ala255Val) AND not specified

Germline classification:: Likely benign (2 submissions)
Last evaluated:: May 31, 2023
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:: RCV000444686.2

Allele description [Variation Report for NM_002047.4(GARS1):c.764C>T (p.Ala255Val)]

NM_002047.4(GARS1):c.764C>T (p.Ala255Val)

Gene:

GARS1:glycyl-tRNA synthetase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p14.3

Genomic location:

Preferred name:

NM_002047.4(GARS1):c.764C>T (p.Ala255Val)

HGVS:

NC_000007.14:g.30609613C>T
NG_007942.1:g.20049C>T
NM_001316772.1:c.602C>T
NM_002047.4:c.764C>TMANE SELECT
NP_001303701.1:p.Ala201Val
NP_002038.2:p.Ala255Val
LRG_243t1:c.764C>T
LRG_243:g.20049C>T
NC_000007.13:g.30649229C>T
NM_002047.2:c.764C>T

Protein change:

A201V

Links:

dbSNP: rs765478968

NCBI 1000 Genomes Browser:

rs765478968

Molecular consequence:

NM_001316772.1:c.602C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002047.4:c.764C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]
Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]
gi|15234831|ref|NP_194799.1|

Protein
acetyl-CoA acetyltransferase [Geobacillus sp. GHH01]
acetyl-CoA acetyltransferase [Geobacillus sp. GHH01]
gi|445208517|gnl|goetting|GHH_c3492 AGE23982.1|

Protein
AU128958 NT2RP2 Homo sapiens cDNA clone NT2RP2004553 5', mRNA sequence
AU128958 NT2RP2 Homo sapiens cDNA clone NT2RP2004553 5', mRNA sequence
gi|10989312|gnl|dbEST|6557732|dbj|A 58.1|

Nucleotide
HG535_0E03330 [Zygotorulaspora mrakii]
HG535_0E03330 [Zygotorulaspora mrakii]
Gene ID:59236991

Gene
GUSBP4 GUSB pseudogene 4 [Homo sapiens]
GUSBP4 GUSB pseudogene 4 [Homo sapiens]
Gene ID:375513

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000530168	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (Aug 17, 2016)	germline	clinical testing	Citation Link,
SCV003955518	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (May 31, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000530168

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(Aug 17, 2016)

germline

clinical testing

Citation Link,

SCV003955518

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(May 31, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000530168.4

#	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

From Ambry Genetics, SCV003955518.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Sep 16, 2024

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