NM_020442.6(VARS2):c.511C>T (p.Arg171Trp) AND Combined oxidative phosphorylation defect type 20

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Nov 16, 2017
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:: RCV000578261.8

Allele description [Variation Report for NM_020442.6(VARS2):c.511C>T (p.Arg171Trp)]

NM_020442.6(VARS2):c.511C>T (p.Arg171Trp)

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.511C>T (p.Arg171Trp)

HGVS:

NC_000006.12:g.30915985C>T
NG_034224.1:g.6778C>T
NM_001167733.3:c.91C>T
NM_001167734.2:c.601C>T
NM_020442.6:c.511C>TMANE SELECT
NP_001161205.1:p.Arg31Trp
NP_001161206.1:p.Arg201Trp
NP_001161206.1:p.Arg201Trp
NP_065175.4:p.Arg171Trp
NC_000006.11:g.30883762C>T
NM_001167734.1:c.601C>T

Protein change:

R171W; ARG201TRP

Links:

OMIM: 612802.0004; dbSNP: rs139515727

NCBI 1000 Genomes Browser:

rs139515727

Molecular consequence:

NM_001167733.3:c.91C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001167734.2:c.601C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020442.6:c.511C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000680429	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	criteria provided, single submitter (Classification criteria August 2017)	Likely pathogenic (Nov 16, 2017)	paternal	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001372472	OMIM	no assertion criteria provided	Pathogenic (Jul 13, 2020)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000680429

Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München

criteria provided, single submitter

(Classification criteria August 2017)

Likely pathogenic
(Nov 16, 2017)

paternal

clinical testing

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

Citation Link,

SCV001372472

OMIM

no assertion criteria provided

Pathogenic
(Jul 13, 2020)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	paternal	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Neonatal encephalocardiomyopathy caused by mutations in VARS2.

Baertling F, Alhaddad B, Seibt A, Budaeus S, Meitinger T, Strom TM, Mayatepek E, Schaper J, Prokisch H, Haack TB, Distelmaier F.

Metab Brain Dis. 2017 Feb;32(1):267-270. doi: 10.1007/s11011-016-9890-2. Epub 2016 Aug 8.

PubMed [citation]

PMID:: 27502409

Details of each submission

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV000680429.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	paternal	yes	1	blood	not provided		1	not provided	not provided	not provided

From OMIM, SCV001372472.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

For discussion of the c.601C-T transition in the VARS2 gene, resulting in an arg201-to-trp (R201W) substitution, that was found in compound heterozygous state in a patient with combined oxidative phosphorylation deficiency-20 (COXPD20; 615917) by Baertling et al. (2017), see 612802.0003.

#	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		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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