NM_024996.7(GFM1):c.539del (p.Gly180fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 2, 2023
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:: RCV000798894.6

Allele description [Variation Report for NM_024996.7(GFM1):c.539del (p.Gly180fs)]

NM_024996.7(GFM1):c.539del (p.Gly180fs)

Gene:

GFM1:G elongation factor mitochondrial 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q25.32

Genomic location:

Preferred name:

NM_024996.7(GFM1):c.539del (p.Gly180fs)

HGVS:

NC_000003.12:g.158646914del
NG_008441.1:g.7387del
NM_001308164.2:c.539del
NM_001308166.2:c.539del
NM_001374355.1:c.539del
NM_001374356.1:c.539del
NM_001374357.1:c.314del
NM_001374358.1:c.234+1133del
NM_001374359.1:c.5+1133del
NM_001374360.1:c.5+1133del
NM_001374361.1:c.5+1133del
NM_024996.7:c.539delMANE SELECT
NP_001295093.1:p.Gly180fs
NP_001295095.1:p.Gly180fs
NP_001361284.1:p.Gly180fs
NP_001361285.1:p.Gly180fs
NP_001361286.1:p.Gly105fs
NP_079272.4:p.Gly180fs
NC_000003.11:g.158364701del
NC_000003.11:g.158364703del
NM_024996.5:c.539del
NM_024996.5:c.539delG
NR_164499.1:n.647del
NR_164500.1:n.647del
NR_164502.1:n.647del

Protein change:

G105fs

Links:

dbSNP: rs1362847020

NCBI 1000 Genomes Browser:

rs1362847020

Molecular consequence:

NM_001308164.2:c.539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001308166.2:c.539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374355.1:c.539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374356.1:c.539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374357.1:c.314del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024996.7:c.539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374358.1:c.234+1133del - intron variant - [Sequence Ontology: SO:0001627]
NM_001374359.1:c.5+1133del - intron variant - [Sequence Ontology: SO:0001627]
NM_001374360.1:c.5+1133del - intron variant - [Sequence Ontology: SO:0001627]
NM_001374361.1:c.5+1133del - intron variant - [Sequence Ontology: SO:0001627]
NR_164499.1:n.647del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164500.1:n.647del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164502.1:n.647del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000938535	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 2, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23430926, 16632485, 17160893, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000938535

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 2, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Infantile Progressive Hepatoencephalomyopathy with Combined OXPHOS Deficiency due to Mutations in the Mitochondrial Translation Elongation Factor Gene GFM1.

Balasubramaniam S, Choy YS, Talib A, Norsiah MD, van den Heuvel LP, Rodenburg RJ.

JIMD Rep. 2012;5:113-22. doi: 10.1007/8904_2011_107. Epub 2011 Dec 21.

PubMed [citation]

PMID:: 23430926
PMCID:: PMC3509912

The molecular basis for tissue specificity of the oxidative phosphorylation deficiencies in patients with mutations in the mitochondrial translation factor EFG1.

Antonicka H, Sasarman F, Kennaway NG, Shoubridge EA.

Hum Mol Genet. 2006 Jun 1;15(11):1835-46. Epub 2006 Apr 21.

PubMed [citation]

PMID:: 16632485

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV000938535.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 644902). This premature translational stop signal has been observed in individual(s) with combined oxidative phosphorylation deficiency (PMID: 23430926). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly180Alafs*11) in the GFM1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GFM1 are known to be pathogenic (PMID: 16632485, 17160893).

#	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: Feb 20, 2024

ClinVar

Relating variation to medicine