NM_024996.7(GFM1):c.1186C>T (p.Gln396Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 13, 2024
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:: RCV001963289.4

Allele description [Variation Report for NM_024996.7(GFM1):c.1186C>T (p.Gln396Ter)]

NM_024996.7(GFM1):c.1186C>T (p.Gln396Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

3q25.32

Genomic location:

Preferred name:

NM_024996.7(GFM1):c.1186C>T (p.Gln396Ter)

HGVS:

NC_000003.12:g.158659024C>T
NG_008441.1:g.19497C>T
NM_001308164.2:c.1243C>T
NM_001308166.2:c.1186C>T
NM_001374355.1:c.1141-1850C>T
NM_001374356.1:c.1069C>T
NM_001374357.1:c.961C>T
NM_001374358.1:c.727C>T
NM_001374359.1:c.619C>T
NM_001374360.1:c.619C>T
NM_001374361.1:c.502C>T
NM_024996.7:c.1186C>TMANE SELECT
NP_001295093.1:p.Gln415Ter
NP_001295095.1:p.Gln396Ter
NP_001361285.1:p.Gln357Ter
NP_001361286.1:p.Gln321Ter
NP_001361287.1:p.Gln243Ter
NP_001361288.1:p.Gln207Ter
NP_001361289.1:p.Gln207Ter
NP_001361290.1:p.Gln168Ter
NP_079272.4:p.Gln396Ter
NC_000003.11:g.158376813C>T
NR_164499.1:n.1209C>T
NR_164500.1:n.1294C>T
NR_164501.1:n.839C>T
NR_164502.1:n.1173C>T

Protein change:

Q168*

Links:

dbSNP: rs1332636394

NCBI 1000 Genomes Browser:

rs1332636394

Molecular consequence:

NM_001374355.1:c.1141-1850C>T - intron variant - [Sequence Ontology: SO:0001627]
NR_164499.1:n.1209C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164500.1:n.1294C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164501.1:n.839C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164502.1:n.1173C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001308164.2:c.1243C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001308166.2:c.1186C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374356.1:c.1069C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374357.1:c.961C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374358.1:c.727C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374359.1:c.619C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374360.1:c.619C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374361.1:c.502C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_024996.7:c.1186C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV002238596	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 13, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16632485, 17160893, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002238596

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 13, 2024)

germline

clinical testing

PubMed (3)
[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

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, SCV002238596.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Gln396*) 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 not present in population databases (gnomAD no frequency). 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: 1460386). For these reasons, this variant has been classified as Pathogenic.

#	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: Sep 29, 2024

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