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NM_130837.3(OPA1):c.2930AGA[2] (p.Lys979del) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 12, 2023
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:
RCV003555132.1

Allele description [Variation Report for NM_130837.3(OPA1):c.2930AGA[2] (p.Lys979del)]

NM_130837.3(OPA1):c.2930AGA[2] (p.Lys979del)

Gene:
OPA1:OPA1 mitochondrial dynamin like GTPase [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
3q29
Genomic location:
Preferred name:
NM_130837.3(OPA1):c.2930AGA[2] (p.Lys979del)
HGVS:
  • NC_000003.12:g.193667227AGA[2]
  • NG_011605.1:g.79084AGA[2]
  • NM_001354663.2:c.2396AGA[2]
  • NM_001354664.2:c.2393AGA[2]
  • NM_015560.3:c.2765AGA[2]
  • NM_130831.3:c.2657AGA[2]
  • NM_130832.3:c.2711AGA[2]
  • NM_130833.3:c.2768AGA[2]
  • NM_130834.3:c.2819AGA[2]
  • NM_130835.3:c.2822AGA[2]
  • NM_130836.3:c.2876AGA[2]
  • NM_130837.3:c.2930AGA[2]MANE SELECT
  • NP_001341592.1:p.Lys801del
  • NP_001341593.1:p.Lys800del
  • NP_056375.2:p.Lys924del
  • NP_056375.2:p.Lys924del
  • NP_570844.1:p.Lys888del
  • NP_570845.1:p.Lys906del
  • NP_570846.1:p.Lys925del
  • NP_570847.2:p.Lys942del
  • NP_570848.1:p.Lys943del
  • NP_570849.2:p.Lys961del
  • NP_570850.2:p.Lys979del
  • NP_570850.2:p.Lys979del
  • LRG_337t1:c.2765_2767AGA[2]
  • LRG_337t2:c.2930_2932AGA[2]
  • LRG_337:g.79084AGA[2]
  • LRG_337p1:p.Lys924del
  • LRG_337p2:p.Lys979del
  • NC_000003.11:g.193385016AGA[2]
  • NC_000003.11:g.193385016_193385018del
  • NM_015560.2:c.2765_2767AGA[2]
  • NM_130837.2:c.2930_2932AGA[2]
Protein change:
K800del
Molecular consequence:
  • NM_001354663.2:c.2396AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001354664.2:c.2393AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_015560.3:c.2765AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_130831.3:c.2657AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_130832.3:c.2711AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_130833.3:c.2768AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_130834.3:c.2819AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_130835.3:c.2822AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_130836.3:c.2876AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_130837.3:c.2930AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004292260Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 12, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Genotype-phenotype and OCT correlations in Autosomal Dominant Optic Atrophy related to OPA1 gene mutations: Report of 13 Italian families.

Pretegiani E, Rosini F, Rufa A, Gallus GN, Cardaioli E, Da Pozzo P, Bianchi S, Serchi V, Collura M, Franceschini R, Bianchi Marzoli S, Dotti MT, Federico A.

J Neurol Sci. 2017 Nov 15;382:29-35. doi: 10.1016/j.jns.2017.09.018. Epub 2017 Sep 14.

PubMed [citation]
PMID:
29111013

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 Invitae, SCV004292260.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant, c.2771_2773del, results in the deletion of 1 amino acid(s) of the OPA1 protein (p.Lys924del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs577168770, gnomAD 0.004%). This variant has been observed in individual(s) with autosomal dominant OPA1-related conditions (PMID: 29111013). This variant is also known as c.2930_2932delAGA, p.Lys979del. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

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

Last Updated: Feb 20, 2024