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NM_005262.3(GFER):c.258+1G>A AND Congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 25, 2020
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:
RCV002471905.1

Allele description [Variation Report for NM_005262.3(GFER):c.258+1G>A]

NM_005262.3(GFER):c.258+1G>A

Genes:
LOC130058203:ATAC-STARR-seq lymphoblastoid silent region 7014 [Gene]
GFER:growth factor, augmenter of liver regeneration [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_005262.3(GFER):c.258+1G>A
HGVS:
  • NC_000016.10:g.1984477G>A
  • NG_016288.1:g.5329G>A
  • NM_005262.3:c.258+1G>AMANE SELECT
  • NC_000016.9:g.2034478G>A
  • NM_005262.2:c.258+1G>A
Molecular consequence:
  • NM_005262.3:c.258+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome
Synonyms:
MITOCHONDRIAL COMPLEX DEFICIENCY, COMBINED; Myopathy, mitochondrial progressive, with congenital cataract, hearing loss, and developmental delay; Myopathy with cataract and combined respiratory-chain deficiency
Identifiers:
MONDO: MONDO:0013116; MedGen: C2751320; Orphanet: 330054; OMIM: 613076

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002767532Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 25, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot 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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767532.1

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

Description

A heterozygous canonical splice site variant was identified, NM_005262.2(GFER):c.258+1G>A in intron 1 of 2 of the GFER gene. This substitution is predicted to cause aberrant splicing of exon 1 in the GFER gene, affecting protein function; further testing via RNA studies are required to confirm if splicing is altered. The nucleotide at this position has high conservation (PhyloP UCSC). In silico software predicts the disruption of the donor splice site (NetGene2, Human Splicing Finder). The variant is present in the gnomAD population database at a frequency 0.0006% (1 heterozygote; 0 homozygotes). An alternative nucleotide change to cytosine at the same location has also been reported in the gnomAD database at a frequency of 0.0006%. The variant has not been previously observed in clinical cases. Based on information available at the time of curation, this variant has been classified as a VUS with POTENTIAL CLINICAL RELEVANCE.

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

Last Updated: Sep 29, 2024