Global Variome shared LOVD
OPA1 (optic atrophy 1 (autosomal dominant))
LOVD v.3.0 Build 26 [
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Curator:
Marc Ferre
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Unique variants in the OPA1 gene
A database from the MITOchondrial DYNamics variation portal.
This database is also one of the
"Eye disease"
gene variant databases.
The variants shown are described using the
NM_130837.2
NM_015560.2
transcript reference sequence.
Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect
: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
Reported
: The number of times this variant has been reported in the database.
Exon
: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
DNA change (cDNA)
: description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.
RNA change
: description of variant at RNA level (following HGVS recommendations).
r.123c>u
r.? = unknown
r.(?) = RNA not analysed but probably transcribed copy of DNA variant
r.spl? = RNA not analysed but variant probably affects splicing
r.(spl?) = RNA not analysed but variant may affect splicing
r.0? = change expected to abolish transcription
Protein
: description of variant at protein level (following HGVS recommendations).
p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced
P-domain
: region/domain protein affected
Classification method
: The method used for the clinical classification of this variant.
All options:
ACMG
ACGS
EAHAD-CFDB
ENIGMA
InSiGHT
kConFab
other
Clinical classification
: Clinical classification of variant, preferably based on standardised criteria (e.g. ACMG), directed on the clinical consequences as published/submitted, indicated using an enriched system including inheritance: e.g. pathogenic, pathogenic (dominant), pathogenic (recessive), pathogenic (!), pathogenic (maternal), pathogenic (paternal). Standard inheritance is covered by dominant/recessive, sex-linked and imprinting by maternal/paternal. A '!' warns for exceptional circumstances to be explained in the 'Remarks' field (low penetrance, variants pathogenic in heterozygous state only, hypomorphic/hypermorphic variants, protective variants, etc.). Non-disease consequences (e.g. drug metabolism (pharmacogenetics), risk factor, blood group, tasting bitter) are indicated using additions to the benign classification; benign (dominant), benign (recessive), benign (!), etc. The value 'association' is used for variants associated with a phenotype and 'NA' for variants from in vitro/in silico records. NOTE: classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional.
All options:
pathogenic
pathogenic (dominant)
pathogenic (recessive)
pathogenic (!)
pathogenic (maternal)
pathogenic (paternal)
likely pathogenic
likely pathogenic (dominant)
likely pathogenic (recessive)
likely pathogenic (!)
likely pathogenic (maternal)
likely pathogenic (paternal)
VUS
VUS (!)
likely benign
likely benign (dominant)
likely benign (recessive)
likely benign (!)
likely benign (maternal)
likely benign (paternal)
benign
benign (dominant)
benign (recessive)
benign (!)
benign (maternal)
benign (paternal)
association
unclassified
NA
DNA change (genomic) (hg19)
: HGVS description of variant at DNA level, based on the genomic (chromosomal) DNA reference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
DNA change (hg38)
: HGVS description of variant at DNA level, based on the hg38 genomic (chromosomal) eference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
Published as
: listed only when different from "DNA change"; variant as reported originally (e.g. 521delT). Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G)
ISCN
: description of the variant according to ISCN nomenclature
DB-ID
: database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro
Variant remarks
: remarks regarding variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.
Reference
: publication describing the variant submitted, incl. links to OMIM, PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"
ClinVar ID
: ID of variant in ClinVar database
dbSNP ID
: the dbSNP ID
Origin
: Origin of variant/record: Germline = in all cells, De novo = in all cells, but not in either parent, Germline/De novo (untested) = in all cells, parents not tested (use only when De novo is likely, e.g. isolated/sporadic cases with dominant disease), Somatic = present in a subset of cells, but not in either parent, Uniparental disomy = from parental disomy (maternal or paternal), CLASSIFICATION record = submitter only sharing variant classification (note another report may share Individual data), SUMMARY record = master summary record from curator (may link to another database), In vitro (cloned) = data resulting from in vitro functional assays, animal model = data from animal model, Artefact = false positive variant call, DUPLICATE record = variant already described on another chromosome (e.g. unbalanced translocation, duplicating transposition, 2nd fusion transcript, etc.)
All options:
Germline
De novo
Germline/De novo (untested)
Somatic
Uniparental disomy
Uniparental disomy, maternal allele
Uniparental disomy, paternal allele
CLASSIFICATION record
SUMMARY record
In vitro (cloned)
In silico
animal model
Artefact
DUPLICATE record
Unknown
Not applicable
Segregation
: Indicates whether the variant segregates with the phenotype (yes), does not segregate with the phenotype (no) or segregation is unknown (?)
All options:
? = unknown
yes = segregates with phenotype
no = does not segregate with phenotype
- = not applicable
Frequency
: frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested)
Re-site
: restriction enzyme recognition site created (+) or destroyed (-); e.g. BglII+, BamHI-
VIP
: variant VIP-status was requested for matchmaking - need collaboration(s) to crack the case - please contact the submitter/curator. NOTE: to get VIP status ask the curator.
Methylation
: result of methylation test; GOM (gain of methylation), LOM (loss of methylation), 30% (30% methylated). NOTE: when several tests were done mention the method as well (e.g. MS-PCR 75%)
How to query this table
All list views have search fields which can be used to search data. You can search for a complete word or you can search for a part of a search term. If you enclose two or more words in double quotes, LOVD will search for the combination of those words only exactly in the order you specify. Note that search terms are case-insensitive and that wildcards such as * are treated as normal text! For all options, like "and", "or", and "not" searches, or searching for prefixes or suffixes, see the table below.
Operator
Column type
Example
Matches
Text
Arg
all entries containing 'Arg'
space
Text
Arg Ser
all entries containing 'Arg' and 'Ser'
|
Text
Arg|Ser
all entries containing 'Arg' or 'Ser'
!
Text
!fs
all entries not containing 'fs'
^
Text
^p.(Arg
all entries beginning with 'p.(Arg'
$
Text
Ser)$
all entries ending with 'Ser)'
=""
Text
=""
all entries with this field empty
=""
Text
="p.0"
all entries exactly matching 'p.0'
!=""
Text
!=""
all entries with this field not empty
!=""
Text
!="p.0"
all entries not exactly matching 'p.0?'
combination
Text
*|Ter !fs
all entries containing '*' or 'Ter' but not containing 'fs'
Date
2020
all entries matching the year 2020
|
Date
2020-03|2020-04
all entries matching March or April, 2020
!
Date
!2020-03
all entries not matching March, 2020
<
Date
<2020
all entries before the year 2020
<=
Date
<=2020-06
all entries in or before June, 2020
>
Date
>2020-06
all entries after June, 2020
>=
Date
>=2020-06-15
all entries on or after June 15th, 2020
combination
Date
2019|2020 <2020-03
all entries in 2019 or 2020, and before March, 2020
Numeric
23
all entries exactly matching 23
|
Numeric
23|24
all entries exactly matching 23 or 24
!
Numeric
!23
all entries not exactly matching 23
<
Numeric
<23
all entries lower than 23
<=
Numeric
<=23
all entries lower than, or equal to, 23
>
Numeric
>23
all entries higher than 23
>=
Numeric
>=23
all entries higher than, or equal to, 23
combination
Numeric
>=20 <30 !23
all entries with values from 20 to 29, but not equal to 23
Some more advanced examples:
Example
Matches
Asian
all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian
all entries containing 'Asian' but not containing 'Caucasian'
Asian|African !Caucasian
all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"
all entries containing 'South Asian', but not containing 'South East Asian'
To sort on a certain column, click on the column header or on the arrows. If that column is already selected to sort on, the sort order will be swapped. The column currently sorted on has a darker blue background color than the other columns. The up and down arrows next to the column name indicate the current sorting direction. When sorting on any field other than the default, LOVD will sort secondarily on the default sort column.
582 entries on 6 pages. Showing entries 1 - 100.
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Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
P-domain
Classification method
Clinical classification
DNA change (genomic) (hg19)
DNA change (hg38)
Published as
ISCN
DB-ID
Variant remarks
Reference
ClinVar ID
dbSNP ID
Origin
Segregation
Frequency
Re-site
VIP
Methylation
Owner
+/+?
1
-
c.(2440+1_2441-1))_(2872+1_2873-1)dup
r.?
p.?
-
-
pathogenic
g.(193376785_193377270)_(193384179_193384958)dup
-
-
-
OPA1_000523
-
PubMed: Chen 2014
-
-
Germline/De novo (untested)
-
-
-
-
-
Thomas Foulonneau
+?/., -/-?
4
-
c.?
r.(?), r.?
p.(=), p.?
Basic (exons 1-3)
-
benign, likely pathogenic
g.?
-
26+12T>G, 27-5C>T, 980G>A Arg327Gln CGG>CAG, del ex8-31
-
OPA1_000148, OPA1_000149
2 more items
PubMed: Han 2006
,
PubMed: Stone 2017
-
-
Germline
-
-
-
-
-
Marc Ferre
+/+?
1
-
c.(?_-234)_(32+1_33-1)del
r.?
p.?
-
-
pathogenic
g.(193300000_193310933)_(193311199_193332511)del
-
-
-
OPA1_000461
-
PubMed: Chen 2014
-
-
Germline/De novo (untested)
-
-
-
-
-
Thomas Foulonneau
?/.
1
-
c.-8C>T
r.(?)
p.(=)
-
-
VUS
g.193311159C>T
g.193593370C>T
-
-
OPA1_000545
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.-3G>A
r.(?)
p.(=)
-
-
VUS
g.193311164G>A
g.193593375G>A
OPA1(NM_130837.2):c.-3G>A
-
OPA1_000568
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+?
1
_1_6i
c.(?_-1)_(678+1_679-1)del
r.0?
p.0?
Basic (exons 1-3)
-
pathogenic
g.(192802437_193311166)_(193336726_193343880)del
-
del ex1-5
-
OPA1_000266
1 more item
PubMed: Fuhrmann 2009
-
-
Germline
-
-
-
-
-
Marc Ferre
+/+?
1
_1_29i
c.(?_-1)_(2983+1_2984-1)del
r.0?
p.0?
Basic (exons 1-3), GTPase (exons 10-17), Dynamin Central (exons 18-26), Putative GED (exons 29-30)
-
pathogenic
g.(191677608_193311166)_(193385070_193409851)del
-
del ex1-27
-
OPA1_000268
1 more item
PubMed: Fuhrmann 2009
-
-
Germline
yes
-
-
-
-
Marc Ferre
+/+?
1
_1_31_
c.(?_-1)_(*3211_?)del
r.0?
p.0?
Basic (exons 1-3), GTPase (exons 10-17), Dynamin Central (exons 18-26), Putative GED (exons 29-30)
-
pathogenic
g.(191677608_193311166)_(193732134_195310989)del
-
del ex1-29, c.1-?_3048+?del
-
OPA1_000270
1 more item
PubMed: Fuhrmann 2009
-
-
Germline
-
-
-
-
-
Marc Ferre
+/+?
1
_30_31_
c.(2983+1_ 2984-1)_(*3212_?)del
r.(?)
p.?
-
-
pathogenic
g.(193000000_193409851)_(193415602_194000000)del
-
Heterozygous deletion of exons 28 and 29 of OPA1
-
OPA1_000456
-
PubMed: Lynch 2017
-
-
Germline
-
-
-
-
-
Thomas Foulonneau
+/+?
7
_1_31, _1_31_
c.0
r.0
p.0
-
-
pathogenic
g.(192000000_193046853)_(194407385_195000000)del
-
193046853_194407385del, g.193046853_194407385del
-
OPA1_000431
1 more item
PubMed: Biamino 2016
-
-
Germline
yes
-
-
-
-
Thomas Foulonneau
+?/.
1
-
c.2778+521_*3211{0}
r.?
p.?
-
-
likely pathogenic
g.193383306_193420756del
-
del ex25-31 Chr3:193383306-193420756del
-
OPA1_000600
-
PubMed: Stone 2017
-
-
Germline
-
-
-
-
-
-
+/.
1
-
c.1A>T
r.(?)
p.(Met1?)
-
-
pathogenic
g.193311167A>T
g.193593378A>T
-
-
OPA1_000546
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/+?, +?/?
2
1
c.3G>A
r.(?)
p.(Met1?), p.0?
Basic (exons 1-3)
-
likely pathogenic, pathogenic
g.193311169G>A
g.193593380G>A
-
-
OPA1_000348
Mutation in start codon of gene OPA1
Amati-Bonneau P, Angers 2011 (unpublished); Le Roux 2019, submitted,
1 more item
-
-
Germline, Germline/De novo (untested)
-
-
BtsCI-, FokI-
-
-
Marc Ferre
,
Lampros Mavrogiannis
+?/?
1
1
c.3G>T
-
p.0?
Basic (exons 1-3)
-
likely pathogenic
g.193311169G>T
g.193593380G>T
-
-
OPA1_000328
Mutation in start codon of gene OPA1
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
+/+?
1
1
c.6G>A
r.(?)
p.(Trp2*)
Basic (exons 1-3)
-
pathogenic
g.193311172G>A
g.193593383G>A
-
-
OPA1_000087
1 more item
PubMed: Pesch 2001
-
-
Germline
-
-
-
-
-
Marc Ferre
+?/+?
1
1
c.7C>T
r.(?)
p.(Arg3*)
-
-
likely pathogenic (dominant)
g.193311173C>T
g.193593384C>T
-
-
OPA1_000581
-
-
-
-
Germline/De novo (untested)
?
-
-
-
-
Marc Ferre
+?/?
1
1
c.9_14del
r.(?)
p.(Leu4_Arg5del)
-
-
likely pathogenic
g.193311175_193311180del
g.193593386_193593391del
-
-
OPA1_000437
-
PubMed: Hayashi 2017
-
-
Germline
-
-
-
-
-
Thomas Foulonneau
+/+?
1
1
c.22G>T
r.(?)
p.(Ala8Ser)
Basic (exons 1-3)
-
pathogenic
g.193311188G>T
g.193593399G>T
-
-
OPA1_000117
1 more item
PubMed: Han 2006
-
-
Germline
-
-
-
-
-
Marc Ferre
+/+?
1
-
c.30del
r.(?)
p.(Cys11Valfs*7)
-
-
pathogenic
g.193311196del
g.193593407del
c.30delC
-
OPA1_000462
-
Amati-Bonneau P, Angers 2010 (unpublished); Le Roux 2019, submitted
-
-
Germline/De novo (untested)
-
-
BstNI-, PspGI-, ScrFI-, SfiI-, StyD4I-
-
-
Marc Ferre
?/.
1
1i
c.32+24C>G
r.(?)
p.(=)
-
-
VUS
g.193311222C>G
g.193593433C>G
-
-
OPA1_000390
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
?/?
1
1i
c.32+87del
r.(?)
p.(=)
Non-specific domain
-
VUS
g.193311285del
g.193593496del
-
-
OPA1_000333
-
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
-/-?
1
1i
c.32+97G>A
r.(?)
p.(=)
Basic (exons 1-3)
-
benign
g.193311295G>A
g.193593506G>A
c.1+97G>A
-
OPA1_000144
1 more item
PubMed: Han 2006
-
-
Germline
-
-
-
-
-
Marc Ferre
-?/.
1
-
c.33-4T>G
r.spl?
p.?
-
-
likely benign
g.193332508T>G
g.193614719T>G
OPA1(NM_130837.2):c.33-4T>G
-
OPA1_000547
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+?
1
-
c.33T>A
r.(?)
p.(Cys11*)
-
-
pathogenic
g.193332512T>A
g.193614723T>A
-
-
OPA1_000464
-
PubMed: Chen 2014
-
-
Germline/De novo (untested)
-
-
Hpy188I+, BtsIMutI-, TspRI-
-
-
Thomas Foulonneau
+/+?
1
-
c.(32+1_33-1)_(351+1_352-1)dup
r.?
p.?
-
-
pathogenic
g.(193311199_193332511)_(193332831_193333462)dup
-
-
-
OPA1_000463
-
PubMed: Chen 2014
-
-
Germline/De novo (untested)
-
-
-
-
-
Thomas Foulonneau
+?/+?
1
1i_3i
c.(32+1_33-1)_(448+1_449-1)del
r.spl
p.?
Basic (exons 1-3)
-
likely pathogenic
g.(193311199_193332511)_(193333560_193334966)del
-
33-?_448+?del
-
OPA1_000349
-
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
+?/+?
1
1i_29i
c.(32+1_33-1)_(2983+1_2984-1)dup
r.?
p.?
Basic (exons 1-3), GTPase (exons 10-17), Dynamin Central (exons 18-26), Putative GED (exons 29-30)
-
likely pathogenic
g.(193311199_193332511)_(193385070_193409851)dup
-
33-?_2983+?dup
-
OPA1_000273
1 more item
Mavrogiannis LA, Prescott K, Charlton RS (unpublished)
-
-
Germline
yes
-
-
-
-
Lampros Mavrogiannis
+/-?, -/., -?/?
3
2
c.43C>A
r.(?)
p.(Gln15Lys)
Basic (exons 1-3)
-
benign, likely benign
g.193332522C>A
g.193614733C>A
OPA1(NM_130837.2):c.43C>A (p.Q15K)
-
OPA1_000318
VKGL data sharing initiative Nederland
Amati-Bonneau P, (unpublished); Le Roux 2019, submitted, Mavrogiannis LA, Charlton RS (unpublished)
-
-
CLASSIFICATION record, Germline, Germline/De novo (untested)
-
-
HpyCH4V+, BsrI-
-
-
Marc Ferre
,
Lampros Mavrogiannis
,
VKGL-NL_Utrecht
+/+?
1
-
c.50T>G
r.(?)
p.(Leu17*)
-
-
pathogenic
g.193332529T>G
g.193614740T>G
-
-
OPA1_000465
-
Amati-Bonneau P, Angers2014 (unpublished); Le Roux 2019, submitted
-
-
Germline/De novo (untested)
-
-
BpuEI+, SmlI+
-
-
Marc Ferre
+?/.
1
2
c.60_61del
r.(?)
p.(His20Glnfs*52)
Basic
ACMG
pathogenic (dominant)
g.193332539_193332540del
g.193614750_193614751del
-
-
OPA1_000604
-
-
-
-
Germline
yes
-
-
-
-
Xingyu Xu
-?/., -?/?
4
2
c.70A>G
r.(?)
p.(Ile24Val)
Basic (exons 1-3)
-
likely benign
g.193332549A>G
g.193614760A>G
OPA1(NM_130837.2):c.70A>G (p.I24V)
-
OPA1_000321
VKGL data sharing initiative Nederland
Mavrogiannis LA, Charlton RS (unpublished)
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Lampros Mavrogiannis
,
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
,
VKGL-NL_AMC
+/+?
1
-
c.71_73delinsAG
r.(?)
p.(Ile24Lysfs*25)
-
-
pathogenic
g.193332550_193332552delinsAG
g.193614761_193614763delinsAG
-
-
OPA1_000466
-
PubMed: Chen 2014
-
-
Germline/De novo (untested)
-
-
HpyAV+
-
-
Thomas Foulonneau
-?/.
1
-
c.88C>T
r.(?)
p.(Leu30=)
-
-
likely benign
g.193332567C>T
g.193614778C>T
OPA1(NM_130837.2):c.88C>T (p.L30=)
-
OPA1_000548
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+?
1
2
c.91C>T
r.(?)
p.(Gln31*)
-
-
pathogenic
g.193332570C>T
g.193614781C>T
-
-
OPA1_000438
-
PubMed: Ścieżyńska 2017
-
-
Germline
-
-
-
-
-
Thomas Foulonneau
+/+?, +?/.
2
2
c.112C>T
r.(?), r.?
p.(Arg38*)
Basic, Basic (exons 1-3)
ACMG
pathogenic, pathogenic (dominant)
g.193332591C>T
g.193614802C>T
-
-
OPA1_000236
1 more item
PubMed: Nakamura 2006
-
-
Germline
yes
-
-
-
-
Marc Ferre
,
Xingyu Xu
+/+?, +?/+?, -/., -?/., ?/., ?/?
11
2
c.113_130del
r.(?)
p.(Arg38_Ser43del)
Basic (exons 1-3)
-
benign, likely benign, likely pathogenic, pathogenic, VUS
g.193332592_193332609del
g.193614803_193614820del
112_139del18, 113_130del18, OPA1(NM_130837.2):c.113_130delGAAGCATTTATCATTCAC (p.R38_S43del),
1 more item
-
OPA1_000082, OPA1_000397
VKGL data sharing initiative Nederland,
2 more items
Amati-Bonneau P, Angers 2012 (unpublished); Le Roux 2019, submitted, Le Roux 2019, submitted,
3 more items
-
rs761926672
CLASSIFICATION record, Germline, Germline/De novo (untested)
-
-
Hpy188III-
-
-
Johan den Dunnen
,
Marc Ferre
,
Erik-Jan Kamsteeg
,
Lampros Mavrogiannis
,
VKGL-NL_Rotterdam
,
Angelique Caignard
,
Bjorn Oskarsson
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
,
Bastien Le Roux
+/+
1
2
c.132dup
r.(?)
p.(His45Serfs*28)
-
-
pathogenic (dominant)
g.193332611dup
g.193614822dup
-
-
OPA1_000542
-
-
-
-
Germline
yes
-
-
-
-
Marc Ferre
+/+?
1
-
c.143T>G
r.(?)
p.(Leu48*)
-
-
pathogenic
g.193332622T>G
g.193614833T>G
-
-
OPA1_000467
-
Amati-Bonneau P, Angers 2013 (unpublished); Le Roux 2019, submitted
-
-
Germline/De novo (untested)
-
-
LpnPI+
-
-
Marc Ferre
+/+?
1
2
c.154C>T
r.(?)
p.(Arg52*)
Basic (exons 1-3)
-
pathogenic
g.193332633C>T
g.193614844C>T
-
-
OPA1_000166
1 more item
PubMed: Ban 2007
-
-
Germline
-
-
-
-
-
Yuriko Ban
+/+?
2
2
c.181C>T
r.(?)
p.(Gln61*), p.(Gln61Ter)
Basic (exons 1-3)
-
pathogenic
g.193332660C>T
g.193614871C>T
-
-
OPA1_000158
VKGL data sharing initiative Nederland,
1 more item
PubMed: Nakamura 2006
-
-
CLASSIFICATION record, Germline
yes
-
-
-
-
Marc Ferre
,
VKGL-NL_Nijmegen
-?/.
1
-
c.182A>G
r.(?)
p.(Gln61Arg)
-
-
likely benign
g.193332661A>G
g.193614872A>G
OPA1(NM_130837.2):c.182A>G (p.Q61R)
-
OPA1_000549
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+?
2
2
c.190del
r.(?)
p.(Ser64Leufs*2)
Basic (exon 1-3), Basic (exons 1-3)
-
pathogenic
g.193332669del
g.193614880del
-
-
OPA1_000165
1 more item
PubMed: Ferre 2009
-
-
Germline
-
-
-
-
-
Marc Ferre
,
Bastien Le Roux
+?/+?, -/-?
2
-
c.190_194del
r.(?)
p.(Ser64Aspfs*7)
-
-
benign, likely pathogenic
g.193332669_193332673del
g.193614880_193614884del
-
-
OPA1_000459
-
PubMed: Nasca 2017
-
-
Germline/De novo (untested)
-
-
EarI-,MboII-
-
-
Thomas Foulonneau
+/+
1
2
c.193_194del
r.(?)
p.(Leu65Aspfs*7)
-
-
pathogenic (dominant)
g.193332672_193332673del
g.193614883_193614884del
-
-
OPA1_000544
-
-
-
-
Germline/De novo (untested)
?
-
-
-
-
Marc Ferre
+/+
1
2
c.209T>A
r.(?)
p.(Leu70*)
-
-
pathogenic
g.193332688T>A
g.193614899T>A
-
-
OPA1_000566
-
-
-
-
Germline/De novo (untested)
?
-
-
-
-
Marc Ferre
+/+
2
2
c.224del
r.(?)
p.(Phe75Serfs*19)
-
-
pathogenic
g.193332703del
g.193614914del
-
-
OPA1_000423
-
Le Roux 2019, submitted
-
-
Germline/De novo (untested)
-
-
-
-
-
Marc Ferre
,
Bastien Le Roux
-?/.
1
-
c.237A>G
r.(?)
p.(Lys79=)
-
-
likely benign
g.193332716A>G
g.193614927A>G
OPA1(NM_130837.2):c.237A>G (p.K79=)
-
OPA1_000569
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.238T>C
r.(?)
p.(Tyr80His)
-
-
likely benign
g.193332717T>C
-
OPA1(NM_130837.2):c.238T>C (p.Y80H)
-
OPA1_000598
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+?, -?/.
3
2
c.239A>G
r.(?)
p.(Tyr80Cys)
Basic (exons 1-3)
-
likely benign, pathogenic
g.193332718A>G
g.193614929A>G
OPA1(NM_130837.2):c.239A>G (p.Y80C)
-
OPA1_000139
VKGL data sharing initiative Nederland,
1 more item
PubMed: Han 2006
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Marc Ferre
,
VKGL-NL_AMC
,
Bastien Le Roux
+/+?, ?/.
2
-
c.245A>G
r.(?)
p.(Tyr82Cys)
-
-
pathogenic, VUS
g.193332724A>G
g.193614935A>G
OPA1(NM_130837.2):c.245A>G (p.Y82C)
-
OPA1_000468
VKGL data sharing initiative Nederland
Amati-Bonneau P, Angers 2016 (unpublished); Le Roux 2019, submitted
-
-
CLASSIFICATION record, Germline/De novo (untested)
-
-
ApeKI+, BbvI+, Cac8I+, Fnu4HI+, MwoI+, TseI+
-
-
Marc Ferre
,
VKGL-NL_Groningen
-?/.
1
-
c.254G>A
r.(?)
p.(Arg85His)
-
-
likely benign
g.193332733G>A
-
OPA1(NM_130837.2):c.254G>A (p.R85H)
-
OPA1_000589
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+
1
2
c.262_263delinsC
r.(?)
p.(Phe88Leufs*6)
-
-
pathogenic (dominant)
g.193332741_193332742delinsC
g.193614952_193614953delinsC
-
-
OPA1_000543
-
-
-
-
Germline/De novo (untested)
?
-
-
-
-
Marc Ferre
+/+?
1
2
c.267G>A
r.(?)
p.(Trp89*)
Basic (exons 1-3)
-
pathogenic
g.193332746G>A
g.193614957G>A
-
-
OPA1_000327
-
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
+/+?, ?/.
2
2
c.284C>T
r.(?)
p.(Thr95Met)
Basic (exons 1-3)
-
pathogenic, VUS
g.193332763C>T
g.193614974C>T
OPA1(NM_130837.2):c.284C>T (p.T95M)
-
OPA1_000167
VKGL data sharing initiative Nederland,
1 more item
PubMed: Ferre 2009
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Marc Ferre
,
VKGL-NL_Rotterdam
+/+?
2
2
c.305A>G
r.(?)
p.(Tyr102Cys)
Basic (exon 1-3), Basic (exons 1-3)
-
pathogenic
g.193332784A>G
g.193614995A>G
-
-
OPA1_000218
1 more item
PubMed: Ferre 2009
-
-
Germline
-
-
-
-
-
Marc Ferre
,
Bastien Le Roux
-/-?, -?/-?
2
2
c.321G>A
r.(?)
p.(=)
Basic (exons 1-3)
-
benign, likely benign
g.193332800G>A
g.193615011G>A
-
-
OPA1_000041
1 more item
PubMed: Pesch 2001
-
-
Germline
-
-
-
-
-
Marc Ferre
,
Lampros Mavrogiannis
+/+?, ?/.
3
2
c.344C>T
r.(?)
p.(Ala115Val)
Basic (exons 1-3)
-
pathogenic, VUS
g.193332823C>T
g.193615034C>T
-
-
OPA1_000253
1 more item
Amati-Bonneau P, Angers 2017 (unpublished); Le Roux 2019, submitted,
PubMed: Comander 2017
,
1 more item
-
-
Germline, Germline/De novo (untested)
-
-
HpyCH4III+
-
-
Marc Ferre
?/.
1
3
c.356T>C
r.(?)
p.(Phe119Ser)
Basic
ACMG
VUS
g.193333467T>C
g.193615678T>C
-
-
OPA1_000605
-
-
-
-
Germline
-
-
-
-
-
Xingyu Xu
+?/+?
1
3
c.356_357del
r.(?)
p.(Phe119*)
Basic (exons 1-3)
-
likely pathogenic
g.193333467_193333468del
g.193615678_193615679del
-
-
OPA1_000290
-
PubMed: Almind 2012
-
-
Germline
-
-
-
-
-
Angelique Caignard
+/?
1
3
c.357del
r.(?)
p.(Phe119Leufs*7)
Basic (exons 1-3)
-
pathogenic
g.193333468del
g.193615679del
-
-
OPA1_000323
-
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
+/+?
1
3
c.361C>T
r.(?)
p.(Gln121*)
Basic (exons 1-3)
-
pathogenic
g.193333472C>T
g.193615683C>T
-
-
OPA1_000168
1 more item
PubMed: Ferre 2009
-
-
Germline
-
-
-
-
-
Marc Ferre
+?/+?
1
3
c.374T>C
r.(?)
p.(Met125Thr)
-
-
VUS
g.193333485T>C
-
-
-
OPA1_000592
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Marc Ferre
?/.
3
3
c.380C>T
r.(?), r.?
p.(Pro127Leu)
Basic
ACMG
likely pathogenic (dominant), VUS
g.193333491C>T
g.193615702C>T
OPA1(NM_130837.2):c.380C>T (p.P127L)
-
OPA1_000389
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record, Germline
?
-
-
-
-
Andreas Laner
,
VKGL-NL_Rotterdam
,
Xingyu Xu
-?/?
1
3
c.381G>A
r.(?)
p.(=)
Basic (exons 1-3)
-
likely benign
g.193333492G>A
g.193615703G>A
-
-
OPA1_000336
-
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
+/+?
1
-
c.419del
r.(?)
p.(Val140Glyfs*24)
-
-
pathogenic
g.193333530del
g.193615741del
c.419delT
-
OPA1_000469
-
Amati-Bonneau P, Angers 2012 (unpublished); Le Roux 2019, submitted
-
-
Germline/De novo (untested)
-
-
BslI+
-
-
Marc Ferre
-/-?, -/., -?/.
4
3
c.420G>T
r.(?)
p.(=), p.(Val140=)
Basic (exons 1-3)
-
benign, likely benign
g.193333531G>T
g.193615742G>T
OPA1(NM_130837.2):c.420G>T (p.V140=)
-
OPA1_000042
VKGL data sharing initiative Nederland,
1 more item
PubMed: Toomes 2001
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Marc Ferre
,
VKGL-NL_Rotterdam
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
+/+?
1
-
c.422G>A
r.(?)
p.(Trp141*)
-
-
pathogenic
g.193333533G>A
g.193615744G>A
-
-
OPA1_000470
-
Amati-Bonneau P, Angers 2015 (unpublished); Le Roux 2019, submitted
-
-
Germline/De novo (untested)
-
-
-
-
-
Marc Ferre
+/+?
1
3i
c.448+1G>C
r.spl
p.?
Basic (exons 1-3)
-
pathogenic
g.193333560G>C
g.193615771G>C
-
-
OPA1_000076
1 more item
PubMed: Thiselton 2002
-
-
Germline
-
-
-
-
-
Marc Ferre
+/.
1
-
c.448+1G>T
r.spl?
p.?
-
-
pathogenic
g.193333560G>T
g.193615771G>T
-
-
OPA1_000418
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/+?
1
3i
c.448+2T>G
r.spl
p.?
Basic (exons 1-3)
-
pathogenic
g.193333561T>G
g.193615772T>G
-
-
OPA1_000169
1 more item
PubMed: Ferre 2009
-
-
Germline
-
-
-
-
-
Marc Ferre
+/?
1
-
c.449-34dup
r.(?)
p.(=)
-
-
pathogenic
g.193334933dup
g.193617144dup
-
-
OPA1_000471
-
PubMed: Li 2017
-
-
Germline/De novo (untested)
-
-
AflII+, MseI+, SmlI+, DdeI-
-
-
Thomas Foulonneau
+?/?
1
3i_10i
c.(448+1_449-1)_(1035+1_1036-1)dup
r.?
p.?
GTPase (exons 10-17)
-
likely pathogenic
g.(193333560_193334966)_(193355071_193355740)dup
-
449-?_1035+?dup
-
OPA1_000279
Large duplication of exons 4-8 (reference: OPA1 transcript variant 1, NM_015560.1) detected by MLPA
Mavrogiannis LA, Robertson L, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
-/-?, -/.
2
4
c.473G>A
r.(?)
p.(Ser158Asn)
Non-specific domain
-
benign
g.193334991G>A
g.193617202G>A
473A>G (Asn158Ser)
-
OPA1_000043
VKGL data sharing initiative Nederland,
1 more item
PubMed: Toomes 2001
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Marc Ferre
,
VKGL-NL_Nijmegen
-/-?
1
4
c.478G>C
r.(?)
p.(Glu160Gln)
Non-specific domain
-
benign
g.193334996G>C
g.193617207G>C
-
-
OPA1_000044
1 more item
PubMed: Toomes 2001
-
-
Germline
-
-
-
-
-
Marc Ferre
-/-?
1
4
c.500C>T
r.(?)
p.(Pro167Leu)
Non-specific domain
-
benign
g.193335018C>T
g.193617229C>T
-
-
OPA1_000045
1 more item
PubMed: Thiselton 2002
-
-
Germline
-
-
-
-
-
Marc Ferre
?/.
1
-
c.517G>A
r.(?)
p.(Val173Ile)
-
-
VUS
g.193335035G>A
g.193617246G>A
OPA1(NM_130837.2):c.517G>A (p.V173I)
-
OPA1_000550
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/-?
1
4
c.534A>G
r.(?)
p.(=)
Non-specific domain
-
likely benign
g.193335052A>G
g.193617263A>G
-
-
OPA1_000341
-
-
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
-/-?
1
4i
c.556+178G>T
r.(?)
p.(=)
Non-specific domain
-
benign
g.193335252G>T
g.193617463G>T
-
-
OPA1_000047
1 more item
PubMed: Delettre 2001
-
-
Germline
-
-
-
-
-
Marc Ferre
?/.
2
-
c.592G>A
r.(?)
p.(Asp198Asn)
-
-
VUS
g.193335608G>A
g.193617819G>A
OPA1(NM_130837.2):c.592G>A (p.D198N)
-
OPA1_000398
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_AMC
+/+?
4
5i
c.610+360G>A
r.(?)
p.(=)
Non-specific domain
-
pathogenic
g.193335986G>A
g.193618197G>A
-
-
OPA1_000283
-
PubMed: Bonifert 2014
-
-
Germline
-
-
-
-
-
Tobias Bonifert
+/+?
4
5i
c.610+364G>A
r.(?)
p.(=)
Non-specific domain
-
pathogenic
g.193335990G>A
g.193618201G>A
-
-
OPA1_000282
-
PubMed: Bonifert 2014
-
-
Germline
-
-
-
-
-
Tobias Bonifert
-/-?, -/.
2
4i
c.611-19T>C
r.(=)
p.(=)
Non-specific domain
-
benign
g.193336639T>C
g.193618850T>C
-
-
OPA1_000046
VKGL data sharing initiative Nederland,
1 more item
PubMed: Toomes 2001
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Marc Ferre
,
VKGL-NL_Nijmegen
+/+
1
6
c.619dup
r.(?)
p.(Glu207Glyfs*6)
-
-
pathogenic (dominant)
g.193336666dup
g.193618877dup
-
-
OPA1_000585
-
-
-
-
De novo
yes
-
-
-
-
Marc Ferre
-/-?, -/., -?/.
5
6
c.629C>T
r.(?)
p.(Ala210Val)
Non-specific domain
-
benign, likely benign
g.193336676C>T
g.193618887C>T
OPA1(NM_130837.2):c.629C>T (p.A210V)
-
OPA1_000048
83 heterozygous, no homozygous;
Clinindb (India)
, VKGL data sharing initiative Nederland,
1 more item
PubMed: Narang 2020
,
Journal: Narang 2020
,
PubMed: Pesch 2001
-
rs34307082
CLASSIFICATION record, Germline
-
83/2795 individuals
-
-
-
Marc Ferre
,
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
Mohammed Faruq
+/+?
1
6
c.665_666insACTGGAGAATGTAAAGGGCTTT
r.(?)
p.(His223Leufs*10)
-
-
pathogenic
g.193336712_193336713insACTGGAGAATGTAAAGGGCTTT
g.193618923_193618924insACTGGAGAATGTAAAGGGCTTT
-
-
OPA1_000439
-
PubMed: Bolognini 2017
-
-
Germline
-
-
-
-
-
Thomas Foulonneau
?/?
1
6i
c.678+1G>T
-
p.?
Non-specific domain
-
VUS
g.193336726G>T
g.193618937G>T
-
-
OPA1_000358
-
PubMed: Liskova 2016
-
-
Germline
-
-
-
-
-
Lubica Dudakova
+?/?
1
6i
c.678+2T>G
-
p.?
Non-specific domain
-
likely pathogenic
g.193336727T>G
g.193618938T>G
-
-
OPA1_000330
-
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
-/.
2
-
c.679-8C>T
r.(=)
p.(=)
-
-
benign
g.193343873C>T
g.193626084C>T
OPA1(NM_130837.2):c.679-8C>T
-
OPA1_000399
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_AMC
+/+?
1
7
c.740G>A
-
p.(Arg247His)
Non-specific domain
-
pathogenic
g.193343942G>A
g.193626153G>A
-
-
OPA1_000235
1 more item
PubMed: Cornille 2008
-
-
Germline
no
-
-
-
-
Marc Ferre
+/?, -/-?
3
7
c.768C>G
r.(?)
p.(Ser256Arg)
Non-specific domain
-
benign, pathogenic
g.193343970C>G
g.193626181C>G
-
-
OPA1_000254
Variation in an alternative exon,
2 more items
PubMed: Yu-Wai-Man 2010
,
PubMed: Yu-Wai-Man 2014
-
-
Germline
-
-
-
-
-
Marc Ferre
,
Thomas Foulonneau
+?/.
1
-
c.785G>C
r.(?)
p.(Arg262Pro)
-
-
likely pathogenic (dominant)
g.193343987G>C
g.193626198G>C
-
-
OPA1_000597
-
PubMed: Zhou 2018
-
-
Germline
-
-
-
-
-
-
-/.
1
-
c.790-12T>A
r.(=)
p.(=)
-
-
benign
g.193349389T>A
g.193631600T>A
OPA1(NM_130837.2):c.790-12T>A
-
OPA1_000551
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+, +/+?, +?/?
3
8
c.794C>A
r.(?)
p.(Ser265*)
Non-specific domain
-
likely pathogenic, pathogenic, pathogenic (dominant)
g.193349405C>A
g.193631616C>A
-
-
OPA1_000088
1 more item
PubMed: Pesch 2001
-
-
Germline, Germline/De novo (untested)
?
-
-
-
-
Marc Ferre
,
Angelique Caignard
+/+?
2
8
c.796_799del
r.(?)
p.(Asp266Lysfs*16)
Non-specific domain
-
pathogenic
g.193349407_193349410del
g.193631618_193631621del
c.631-634del
-
OPA1_000248
1 more item
Amati-Bonneau P, Angers 2016 (unpublished); Le Roux 2019, submitted,
PubMed: Cohn 2007
-
-
Germline, Germline/De novo (untested)
-
-
Hpy188I-
-
-
Marc Ferre
+/+?
1
8
c.799A>T
r.(?)
p.(Lys267*)
Non-specific domain
-
pathogenic
g.193349410A>T
g.193631621A>T
-
-
OPA1_000337
-
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
+/+?, +/.
3
8
c.800_801del
r.(?)
p.(Lys267Argfs*4)
Non-specific domain
ACMG
pathogenic
g.193349411_193349412del
g.193631622_193631623del
800_801delAA
-
OPA1_000026
2 more items
PubMed: de Castro-Miró 2016
,
PubMed: Toomes 2001
,
PubMed: Yu-Wai-Man 2010
-
-
Germline
yes
-
-
-
-
Marc Ferre
,
Marta de Castro-Miró
+/+?
1
8
c.800_803del
r.(?)
p.(Lys267Argfs*15)
Non-specific domain
-
pathogenic
g.193349411_193349414del
g.193631622_193631625del
-
-
OPA1_000010
1 more item
PubMed: Baris 2003
-
-
Germline
-
-
-
-
-
Marc Ferre
+/+?
1
8
c.802del
r.(?)
p.(Glu268Argfs*15)
-
-
likely pathogenic (dominant)
g.193349413del
g.193631624del
-
-
OPA1_000567
Variant inherited from the asymptomatic father
-
-
-
De novo
no
-
-
-
-
Marc Ferre
+/+?, +/.
2
8
c.804_805del
r.(?)
p.(Lys269Asnfs*2), p.(Lys269AsnfsTer2)
Non-specific domain
-
pathogenic
g.193349415_193349416del
g.193631626_193631627del
OPA1(NM_130837.2):c.804_805delGA (p.K269Nfs*2)
-
OPA1_000263
VKGL data sharing initiative Nederland,
1 more item
PubMed: Yu-Wai-Man 2010
-
-
CLASSIFICATION record, Germline
yes
-
-
-
-
Marc Ferre
,
VKGL-NL_AMC
+/+?
1
8
c.814C>T
r.(?)
p.(Gln272*)
Non-specific domain
-
pathogenic
g.193349425C>T
g.193631636C>T
-
-
OPA1_000320
-
Mavrogiannis LA, Charlton RS (unpublished)
-
-
Germline
-
-
-
-
-
Lampros Mavrogiannis
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