NM_015560.2(OPA1):c.880G>T (p.Val294Phe) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Mar 21, 2014)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000196148.2

Allele description [Variation Report for NM_015560.2(OPA1):c.880G>T (p.Val294Phe)]

NM_015560.2(OPA1):c.880G>T (p.Val294Phe)

Gene:
OPA1:OPA1 mitochondrial dynamin like GTPase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q29
Genomic location:
Preferred name:
NM_015560.2(OPA1):c.880G>T (p.Val294Phe)
HGVS:
  • NC_000003.12:g.193637961G>T
  • NG_011605.1:g.49818G>T
  • NM_001354663.2:c.511G>T
  • NM_001354664.2:c.508G>T
  • NM_015560.2:c.880G>T
  • NM_130831.3:c.772G>T
  • NM_130832.3:c.826G>T
  • NM_130833.2:c.883G>T
  • NM_130834.3:c.934G>T
  • NM_130835.2:c.937G>T
  • NM_130836.3:c.991G>T
  • NM_130837.2:c.1045G>T
  • NP_001341592.1:p.Val171Phe
  • NP_001341593.1:p.Val170Phe
  • NP_056375.2:p.Val294Phe
  • NP_570844.1:p.Val258Phe
  • NP_570845.1:p.Val276Phe
  • NP_570846.1:p.Val295Phe
  • NP_570847.2:p.Val312Phe
  • NP_570848.1:p.Val313Phe
  • NP_570849.2:p.Val331Phe
  • NP_570850.2:p.Val349Phe
  • LRG_337t1:c.880G>T
  • LRG_337t2:c.1045G>T
  • LRG_337:g.49818G>T
  • LRG_337p1:p.Val294Phe
  • LRG_337p2:p.Val349Phe
  • NC_000003.11:g.193355750G>T
  • NM_130834.1:c.934G>T
  • p.V294F
Protein change:
V170F
Links:
dbSNP: rs863224131
NCBI 1000 Genomes Browser:
rs863224131
Molecular consequence:
  • NM_001354663.2:c.511G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354664.2:c.508G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015560.2:c.880G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130831.3:c.772G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130832.3:c.826G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130833.2:c.883G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130834.3:c.934G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130835.2:c.937G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130836.3:c.991G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130837.2:c.1045G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000251990GeneDxcriteria provided, single submitter
Likely pathogenic
(Mar 21, 2014)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000251990.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The V294F variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. This variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The V294F variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is highly conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Missense mutations in nearby residues (R290W, R290Q, A299P) have been reported in association with optic atrophy 1, supporting the functional importance of this region of the protein. Furthermore, an in-frame deletion that includes the loss of Valine 294 (p.V293_V294del) has also been reported in association with optic atrophy 1 (Ferre et al., 2009). Therefore, V294F was interpreted to be a strong candidate for a disease-causing mutation. The variant is found in OAPEO-MITOP panel(s).

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

Last Updated: Feb 27, 2021

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