NM_024996.7(GFM1):c.1765-2_1765-1del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 6, 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:: RCV001223407.8

Allele description [Variation Report for NM_024996.7(GFM1):c.1765-2_1765-1del]

NM_024996.7(GFM1):c.1765-2_1765-1del

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.1765-2_1765-1del

HGVS:

NC_000003.12:g.158684522_158684523del
NG_008441.1:g.44995_44996del
NM_001308164.2:c.1822-2_1822-1del
NM_001374355.1:c.1684-2_1684-1del
NM_001374356.1:c.1648-2_1648-1del
NM_001374357.1:c.1540-2_1540-1del
NM_001374358.1:c.1306-2_1306-1del
NM_001374359.1:c.1198-2_1198-1del
NM_001374360.1:c.1198-2_1198-1del
NM_001374361.1:c.1081-2_1081-1del
NM_024996.7:c.1765-2_1765-1delMANE SELECT
NC_000003.11:g.158402311_158402312del
NM_024996.5:c.1765-2_1765-1del
NM_024996.5:c.1765-2_1765-1delAG

Links:

dbSNP: rs1245712932

NCBI 1000 Genomes Browser:

rs1245712932

Molecular consequence:

NM_001308164.2:c.1822-2_1822-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001374355.1:c.1684-2_1684-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001374356.1:c.1648-2_1648-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001374357.1:c.1540-2_1540-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001374358.1:c.1306-2_1306-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001374359.1:c.1198-2_1198-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001374360.1:c.1198-2_1198-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001374361.1:c.1081-2_1081-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_024996.7:c.1765-2_1765-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001395556	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 6, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16632485, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001395556

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 6, 2023)

germline

clinical testing

PubMed (2)
[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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001395556.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in skipping of exon 15 and introduces a premature termination codon (PMID: 16632485). The resulting mRNA is expected to undergo nonsense-mediated decay. ClinVar contains an entry for this variant (Variation ID: 951478). This variant is also known as 1872-2delAG. Disruption of this splice site has been observed in individual(s) with combined oxidative phosphorylation deficiency (PMID: 16632485). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change affects a splice site in intron 14 of the GFM1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.

#	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

ClinVar

Relating variation to medicine