NM_015560.2(OPA1):c.1384A>C (p.Thr462Pro) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: May 23, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_015560.2(OPA1):c.1384A>C (p.Thr462Pro)]

NM_015560.2(OPA1):c.1384A>C (p.Thr462Pro)

OPA1:OPA1 mitochondrial dynamin like GTPase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_015560.2(OPA1):c.1384A>C (p.Thr462Pro)
  • NC_000003.12:g.193644046A>C
  • NG_011605.1:g.55903A>C
  • NM_001354663.2:c.1015A>C
  • NM_001354664.2:c.1012A>C
  • NM_015560.2:c.1384A>C
  • NM_130831.3:c.1276A>C
  • NM_130832.3:c.1330A>C
  • NM_130833.2:c.1387A>C
  • NM_130834.3:c.1438A>C
  • NM_130835.2:c.1441A>C
  • NM_130836.3:c.1495A>C
  • NM_130837.2:c.1549A>C
  • NP_001341592.1:p.Thr339Pro
  • NP_001341593.1:p.Thr338Pro
  • NP_056375.2:p.Thr462Pro
  • NP_570844.1:p.Thr426Pro
  • NP_570845.1:p.Thr444Pro
  • NP_570846.1:p.Thr463Pro
  • NP_570847.2:p.Thr480Pro
  • NP_570848.1:p.Thr481Pro
  • NP_570849.2:p.Thr499Pro
  • NP_570850.2:p.Thr517Pro
  • LRG_337t1:c.1384A>C
  • LRG_337t2:c.1549A>C
  • LRG_337:g.55903A>C
  • LRG_337p1:p.Thr462Pro
  • LRG_337p2:p.Thr517Pro
  • NC_000003.11:g.193361835A>C
Protein change:
dbSNP: rs1553878117
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001354663.2:c.1015A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354664.2:c.1012A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015560.2:c.1384A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130831.3:c.1276A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130832.3:c.1330A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130833.2:c.1387A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130834.3:c.1438A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130835.2:c.1441A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130836.3:c.1495A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130837.2:c.1549A>C - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000589841GeneDxcriteria provided, single submitter
Likely pathogenic
(May 23, 2016)
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, SCV000589841.3

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


The T462P variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The T462P variant was not observed in approximately 6,500 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 T462P variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. A missense variant in a nearby residue (G459E) has been reported in the Human Gene Mutation Database in association with optic atrophy (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

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

Last Updated: Feb 27, 2021

Support Center