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NM_024996.7(GFM1):c.690_693del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 1, 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:
RCV001932580.6

Allele description [Variation Report for NM_024996.7(GFM1):c.690_693del]

NM_024996.7(GFM1):c.690_693del

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.690_693del
HGVS:
  • NC_000003.12:g.158652096_158652099del
  • NG_008441.1:g.12569_12572del
  • NG_008441.2:g.12571_12574del
  • NM_001374358.1:c.235-4_235-1del
  • NM_024996.7:c.690_693delMANE SELECT
  • NC_000003.11:g.158369883_158369886del
  • NC_000003.11:g.158369885_158369888del
  • NM_001308164.1:c.747_750delTCAG
Links:
dbSNP: rs778902849
NCBI 1000 Genomes Browser:
rs778902849
Molecular consequence:
  • NM_001374358.1:c.235-4_235-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_024996.7:c.690_693del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002129045Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 1, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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

Infantile encephalopathy and defective mitochondrial DNA translation in patients with mutations of mitochondrial elongation factors EFG1 and EFTu.

Valente L, Tiranti V, Marsano RM, Malfatti E, Fernandez-Vizarra E, Donnini C, Mereghetti P, De Gioia L, Burlina A, Castellan C, Comi GP, Savasta S, Ferrero I, Zeviani M.

Am J Hum Genet. 2007 Jan;80(1):44-58. Epub 2006 Nov 15. Erratum in: Am J Hum Genet. 2007 Mar;80(3):580.

PubMed [citation]
PMID:
17160893
PMCID:
PMC1785320
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002129045.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Gln231Leufs*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). This variant is present in population databases (rs778902849, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with GFM1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1367819). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024