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NM_001008212.2(OPTN):c.1149-2A>G AND not provided

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Aug 14, 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:
RCV000992464.3

Allele description [Variation Report for NM_001008212.2(OPTN):c.1149-2A>G]

NM_001008212.2(OPTN):c.1149-2A>G

Gene:
OPTN:optineurin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10p13
Genomic location:
Preferred name:
NM_001008212.2(OPTN):c.1149-2A>G
HGVS:
  • NC_000010.11:g.13125944A>G
  • NG_012876.1:g.30863A>G
  • NM_001008211.1:c.1149-2A>G
  • NM_001008212.2:c.1149-2A>GMANE SELECT
  • NM_001008213.1:c.1149-2A>G
  • NM_021980.4:c.1149-2A>G
  • NC_000010.10:g.13167944A>G
  • NC_000010.10:g.13167944A>G
Links:
dbSNP: rs867368757
NCBI 1000 Genomes Browser:
rs867368757
Molecular consequence:
  • NM_001008211.1:c.1149-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001008212.2:c.1149-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001008213.1:c.1149-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_021980.4:c.1149-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001144801Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics Criteria)
Likely pathogenic
(Dec 27, 2018)
germlineclinical testing

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

SCV004028419GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely pathogenic
(Aug 14, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From Athena Diagnostics, SCV001144801.1

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

Description

The variant disrupts a canonical splice site, and is therefore predicted to result in the loss of a functional protein. Not found in the total gnomAD dataset, and the data is high quality (0/281614 chr).

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

From GeneDx, SCV004028419.1

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

Description

Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge

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

Last Updated: Sep 29, 2024