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NM_024996.7(GFM1):c.539del (p.Gly180fs) AND Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jul 13, 2023
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:
RCV003232990.3

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)

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002761219Pediatric Department, Xiangya Hospital, Central South University
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenicmaternalclinical testing

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

SCV004199322Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jul 13, 2023) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalyes2not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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 Pediatric Department, Xiangya Hospital, Central South University, SCV002761219.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)

Description

This variant was observed in compound heterozygosity with variant (c.628C>G)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot provided2not providednot providednot provided

From Baylor Genetics, SCV004199322.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024