NM_001008212.2(OPTN):c.1634G>A (p.Arg545Gln) AND Open angle glaucoma

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(2) (Last evaluated: May 28, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000356568.3

Allele description [Variation Report for NM_001008212.2(OPTN):c.1634G>A (p.Arg545Gln)]

NM_001008212.2(OPTN):c.1634G>A (p.Arg545Gln)

Gene:
OPTN:optineurin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10p13
Genomic location:
Preferred name:
NM_001008212.2(OPTN):c.1634G>A (p.Arg545Gln)
HGVS:
  • NC_000010.11:g.13136766G>A
  • NG_012876.1:g.41685G>A
  • NM_001008211.1:c.1634G>A
  • NM_001008212.2:c.1634G>AMANE SELECT
  • NM_001008213.1:c.1634G>A
  • NM_021980.4:c.1634G>A
  • NP_001008212.1:p.Arg545Gln
  • NP_001008213.1:p.Arg545Gln
  • NP_001008214.1:p.Arg545Gln
  • NP_068815.2:p.Arg545Gln
  • NC_000010.10:g.13178766G>A
Protein change:
R545Q; ARG545GLN
Links:
OMIM: 602432.0003; dbSNP: rs75654767
NCBI 1000 Genomes Browser:
rs75654767
Molecular consequence:
  • NM_001008211.1:c.1634G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001008212.2:c.1634G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001008213.1:c.1634G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021980.4:c.1634G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Open angle glaucoma (POAG)
Synonyms:
Primary open angle glaucoma
Identifiers:
MONDO: MONDO:0007665; MedGen: C0339573; OMIM: 137760; Human Phenotype Ontology: HP:0012108

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000267428Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Centercriteria provided, single submitter
Uncertain significance
(Mar 18, 2016)
germlinereference population

PubMed (2)
[See all records that cite these PMIDs]

SCV000361438Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

Citation Link,

SCV001138000Mendelicscriteria provided, single submitter
Uncertain significance
(May 28, 2019)
unknownclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
East Asiangermlineunknown8not providednot providednot providednot providedreference population

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

An informatics approach to analyzing the incidentalome.

Berg JS, Adams M, Nassar N, Bizon C, Lee K, Schmitt CP, Wilhelmsen KC, Evans JP.

Genet Med. 2013 Jan;15(1):36-44. doi: 10.1038/gim.2012.112. Epub 2012 Sep 20.

PubMed [citation]
PMID:
22995991
PMCID:
PMC3538953
See all PubMed Citations (11)

Details of each submission

From Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center, SCV000267428.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1East Asian8not providednot providedreference population PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided8not providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV000361438.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (10)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

From Mendelics, SCV001138000.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 20, 2021

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