NM_032380.5(GFM2):c.1758G>C (p.Arg586Ser) AND Combined oxidative phosphorylation deficiency 39

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 28, 2019
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:: RCV002472098.1

Allele description [Variation Report for NM_032380.5(GFM2):c.1758G>C (p.Arg586Ser)]

NM_032380.5(GFM2):c.1758G>C (p.Arg586Ser)

Gene:

GFM2:GTP dependent ribosome recycling factor mitochondrial 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q13.3

Genomic location:

Preferred name:

NM_032380.5(GFM2):c.1758G>C (p.Arg586Ser)

HGVS:

NC_000005.10:g.74726095C>G
NG_011531.1:g.46123G>C
NM_001281302.2:c.1854G>C
NM_032380.5:c.1758G>CMANE SELECT
NM_170691.3:c.1617G>C
NP_001268231.1:p.Arg618Ser
NP_115756.2:p.Arg586Ser
NP_733792.1:p.Arg539Ser
NC_000005.9:g.74021920C>G
NM_032380.4:c.1758G>C
NR_104006.2:n.1823G>C

Protein change:

R539S

Molecular consequence:

NM_001281302.2:c.1854G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_032380.5:c.1758G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_170691.3:c.1617G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_104006.2:n.1823G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Combined oxidative phosphorylation deficiency 39
Identifiers:: MONDO: MONDO:0032726; MedGen: C5193075; OMIM: 618397

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002768505	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 28, 2019)	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

SCV002768505

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 28, 2019)

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

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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002768505.1

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

Description

A heterozygous missense variant, NM_032380.4(GFM2):c.1758G>C, has been identified in exon 18 of 21 of the GFM2 gene. The variant is predicted to result in a major amino acid change from arginine to serine at position 586 of the protein (NP_115756.2(GFM2):p.(Arg586Ser)). The arginine residue at this position has low conservation (100 vertebrates, UCSC), and is located within the Elongation factor G, domain IV functional domain. In silico predictions of pathogenicity for this variant are conflicting (Polyphen, SIFT, CADD, Mutation Taster). The variant is absent in population databases (gnomAD) and has not been previously reported in clinical cases. Based on the information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS).

#	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: Dec 24, 2022

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