NM_020442.6(VARS2):c.2257C>T (p.Leu753Phe) AND Combined oxidative phosphorylation defect type 20

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jan 6, 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:: RCV003139262.5

Allele description [Variation Report for NM_020442.6(VARS2):c.2257C>T (p.Leu753Phe)]

NM_020442.6(VARS2):c.2257C>T (p.Leu753Phe)

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.2257C>T (p.Leu753Phe)

HGVS:

NC_000006.12:g.30923175C>T
NG_034224.1:g.13968C>T
NG_084147.1:g.1363C>T
NG_084147.2:g.1593C>T
NM_001167733.3:c.1837C>T
NM_001167734.2:c.2347C>T
NM_020442.6:c.2257C>TMANE SELECT
NP_001161205.1:p.Leu613Phe
NP_001161206.1:p.Leu783Phe
NP_065175.4:p.Leu753Phe
NC_000006.11:g.30890952C>T
NM_001167734.1:c.2347C>T

Protein change:

L613F

Molecular consequence:

NM_001167733.3:c.1837C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001167734.2:c.2347C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020442.6:c.2257C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Combined oxidative phosphorylation defect type 20
Synonyms:: Combined oxidative phosphorylation deficiency 20
Identifiers:: MONDO: MONDO:0014397; MedGen: C4014660; Orphanet: 420728; OMIM: 615917

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003820354	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 6, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004171296	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV003820354

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 6, 2023)

germline

clinical testing

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

SCV004171296

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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	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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Revvity Omics, Revvity, SCV003820354.2

#	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

From Neuberg Centre For Genomic Medicine, NCGM, SCV004171296.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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