NC_000010.10:g.(?_13158247)_(13169923_?)dup AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 1, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003109854.5

Allele description [Variation Report for NC_000010.10:g.(?_13158247)_(13169923_?)dup]

NC_000010.10:g.(?_13158247)_(13169923_?)dup

Gene:: OPTN:optineurin [Gene - OMIM - HGNC]
Variant type:: Duplication
Cytogenetic location:: 10p13
Genomic location:: Chr10: 13158247 - 13169923 (on Assembly GRCh37)
Preferred name:: NC_000010.10:g.(?_13158247)_(13169923_?)dup
HGVS:: NC_000010.10:g.(?_13158247)_(13169923_?)dup
This HGVS expression did not pass validation

Condition(s)

Name:: Primary open angle glaucoma (POAG)
Synonyms:: OPTN-related open angle glaucoma
Identifiers:: MONDO: MONDO:0100553; MedGen: C0339573; OMIM: 137760

Name:: Amyotrophic lateral sclerosis type 12 (ALS12)
Synonyms:: AMYOTROPHIC LATERAL SCLEROSIS 12 WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA
Identifiers:: MONDO: MONDO:0013264; MedGen: C3150692; Orphanet: 803; OMIM: 613435

Name:: Glaucoma 1, open angle, E
Identifiers:: MedGen: C1842026

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791857	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 1, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25640679, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791857

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 1, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints.

Newman S, Hermetz KE, Weckselblatt B, Rudd MK.

Am J Hum Genet. 2015 Feb 5;96(2):208-20. doi: 10.1016/j.ajhg.2014.12.017. Epub 2015 Jan 29.

PubMed [citation]

PMID:: 25640679
PMCID:: PMC4320257

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003791857.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with OPTN-related conditions. This variant results in a copy number gain of the genomic region encompassing exon(s) 5-11 of the OPTN gene. While the exact position of this variant cannot be determined from the data, sub-genic copy number gains are generally in tandem (PMID: 25640679). This variant is predicted to be in-frame, and likely preserves the integrity of the reading frame.

#	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

Last Updated: Sep 29, 2024

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