NM_020442.6(VARS2):c.2378G>A (p.Cys793Tyr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 27, 2022
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:: RCV002621623.3

Allele description [Variation Report for NM_020442.6(VARS2):c.2378G>A (p.Cys793Tyr)]

NM_020442.6(VARS2):c.2378G>A (p.Cys793Tyr)

Genes:

LOC126859646:MED14-independent group 3 enhancer GRCh37_chr6:30889690-30890889 [Gene]
VARS2:valyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.33

Genomic location:

Preferred name:

NM_020442.6(VARS2):c.2378G>A (p.Cys793Tyr)

HGVS:

NC_000006.12:g.30923417G>A
NG_034224.1:g.14210G>A
NG_084147.2:g.1835G>A
NM_001167733.3:c.1958G>A
NM_001167734.2:c.2468G>A
NM_020442.6:c.2378G>AMANE SELECT
NP_001161205.1:p.Cys653Tyr
NP_001161206.1:p.Cys823Tyr
NP_065175.4:p.Cys793Tyr
NC_000006.11:g.30891194G>A
NM_001167734.1:c.2468G>A

Protein change:

C653Y

Molecular consequence:

NM_001167733.3:c.1958G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001167734.2:c.2468G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020442.6:c.2378G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Ceropegia dinteri (3)
Identical Protein Groups
PREDICTED: Homo sapiens HPS4 biogenesis of lysosomal organelles complex 3 subuni...
PREDICTED: Homo sapiens HPS4 biogenesis of lysosomal organelles complex 3 subunit 2 (HPS4), transcript variant X29, mRNA
gi|2462585855|ref|XM_054326103.1|

Nucleotide
PREDICTED: Cervus canadensis oligodendrocyte transcription factor 2 (OLIG2), tra...
PREDICTED: Cervus canadensis oligodendrocyte transcription factor 2 (OLIG2), transcript variant X1, mRNA
gi|2090171573|ref|XM_043449148.1|

Nucleotide
bone morphogenetic protein receptor type-1A isoform 5 [Homo sapiens]
bone morphogenetic protein receptor type-1A isoform 5 [Homo sapiens]
gi|2240200210|ref|NP_001393516.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002954168	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 27, 2022)	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

SCV002954168

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 27, 2022)

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, SCV002954168.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with VARS2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 823 of the VARS2 protein (p.Cys823Tyr).

#	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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