NM_024996.7(GFM1):c.690_693del AND Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Feb 24, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002506920.3

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)

Name:: Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1
Synonyms:: HEPATOENCEPHALOPATHY, EARLY FATAL PROGRESSIVE; Combined oxidative phosphorylation deficiency 1
Identifiers:: MONDO: MONDO:0012191; MedGen: C1836797; OMIM: 609060

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002815907	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 27, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004199341	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 24, 2024)	unknown	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

SCV002815907

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 27, 2021)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004199341

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 24, 2024)

unknown

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	unknown	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 Fulgent Genetics, Fulgent Genetics, SCV002815907.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004199341.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 8, 2024

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