NM_130837.3(OPA1):c.1471A>G (p.Ile491Val) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 10, 2021
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:: RCV001985174.4

Allele description [Variation Report for NM_130837.3(OPA1):c.1471A>G (p.Ile491Val)]

NM_130837.3(OPA1):c.1471A>G (p.Ile491Val)

Gene:

OPA1:OPA1 mitochondrial dynamin like GTPase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q29

Genomic location:

Preferred name:

NM_130837.3(OPA1):c.1471A>G (p.Ile491Val)

HGVS:

NC_000003.12:g.193643621A>G
NG_011605.1:g.55478A>G
NM_001354663.2:c.937A>G
NM_001354664.2:c.934A>G
NM_015560.3:c.1306A>G
NM_130831.3:c.1198A>G
NM_130832.3:c.1252A>G
NM_130833.3:c.1309A>G
NM_130834.3:c.1360A>G
NM_130835.3:c.1363A>G
NM_130836.3:c.1417A>G
NM_130837.3:c.1471A>GMANE SELECT
NP_001341592.1:p.Ile313Val
NP_001341593.1:p.Ile312Val
NP_056375.2:p.Ile436Val
NP_570844.1:p.Ile400Val
NP_570845.1:p.Ile418Val
NP_570846.1:p.Ile437Val
NP_570847.2:p.Ile454Val
NP_570848.1:p.Ile455Val
NP_570849.2:p.Ile473Val
NP_570850.2:p.Ile491Val
LRG_337:g.55478A>G
NC_000003.11:g.193361410A>G

Protein change:

I312V

Links:

dbSNP: rs2109044723

NCBI 1000 Genomes Browser:

rs2109044723

Molecular consequence:

NM_001354663.2:c.937A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354664.2:c.934A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015560.3:c.1306A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130831.3:c.1198A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130832.3:c.1252A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130833.3:c.1309A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130834.3:c.1360A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130835.3:c.1363A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130836.3:c.1417A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130837.3:c.1471A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002224669	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 10, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002224669

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 10, 2021)

germline

clinical testing

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

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

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, SCV002224669.3

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

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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt OPA1 protein function. This variant has not been reported in the literature in individuals affected with OPA1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with valine at codon 436 of the OPA1 protein (p.Ile436Val). The isoleucine residue is highly conserved and there is a small physicochemical difference between isoleucine and valine.

#	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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