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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Arachis chloroplast sequence.
Arachis chloroplast sequence.
PopSet: 2196262766

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Encephalitozoon intestinalis ATCC 50506 transcription initiation factor TFIIIB s...
Encephalitozoon intestinalis ATCC 50506 transcription initiation factor TFIIIB subunit Brf1 (Eint_050510), partial mRNA
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001144801	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely pathogenic (Dec 27, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004028419	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Aug 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001144801

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely pathogenic
(Dec 27, 2018)

germline

clinical testing

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

SCV004028419

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Aug 14, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV004028419.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not 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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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