NM_002047.4(GARS1):c.19G>T (p.Val7Leu) AND Charcot-Marie-Tooth disease type 2

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jan 17, 2024
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:: RCV000814077.9

Allele description [Variation Report for NM_002047.4(GARS1):c.19G>T (p.Val7Leu)]

NM_002047.4(GARS1):c.19G>T (p.Val7Leu)

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.19G>T (p.Val7Leu)

HGVS:

NC_000007.14:g.30594940G>T
NG_007942.1:g.5376G>T
NM_001316772.1:c.-144G>T
NM_002047.4:c.19G>TMANE SELECT
NP_002038.2:p.Val7Leu
LRG_243t1:c.19G>T
LRG_243:g.5376G>T
NC_000007.13:g.30634556G>T
NM_002047.2:c.19G>T

Protein change:

V7L

Links:

dbSNP: rs201132307

NCBI 1000 Genomes Browser:

rs201132307

Molecular consequence:

NM_001316772.1:c.-144G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_002047.4:c.19G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Charcot-Marie-Tooth disease type 2
Synonyms:: Charcot-Marie-Tooth, Type 2
Identifiers:: MONDO: MONDO:0018993; MedGen: C0270914

Recent activity

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M.musculus mitochondrial malate dehydrogenase gene 5'flank and exon 1 (and joine...
M.musculus mitochondrial malate dehydrogenase gene 5'flank and exon 1 (and joined CDS)
gi|50679|emb|X07295.1|

Nucleotide
MAG TPA_asm: Lentisphaeria bacterium UBA5239, whole genome shotgun sequencing pr...
MAG TPA_asm: Lentisphaeria bacterium UBA5239, whole genome shotgun sequencing project
gi|1248843358|tpg|DHUH00000000.1|DH 00000

Nucleotide
SH3 domain-containing protein [Caenorhabditis elegans]
SH3 domain-containing protein [Caenorhabditis elegans]
gi|115534495|ref|NP_502803.3|

Protein
Homo sapiens solute carrier family 39 member 4 (SLC39A4), RefSeqGene on chromoso...
Homo sapiens solute carrier family 39 member 4 (SLC39A4), RefSeqGene on chromosome 8
gi|2296125368|ref|NG_012234.3|

Nucleotide
plastin-1 isoform X1 [Homo sapiens]
plastin-1 isoform X1 [Homo sapiens]
gi|2217344412|ref|XP_047304282.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000954474	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 17, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000954474

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 17, 2024)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000954474.6

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

#	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 29, 2024

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