NDDVD - Neurodegenerative Diseases Variation Database
TOR1A (torsin family 1, member A (torsin A))
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Curator:
Y Yang
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Unique variants in the TOR1A gene
The variants shown are described using the NM_000113.2 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 = exons 3 to 7, 8i_9 = border intron 8/exon 9.
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.
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
Variant/VariO/DNA
: VariO of DNA
Variant/VariO/protein
: VariO of protein
DNA change (genomic) (hg19)
: Description of variant at DNA level, based on the genomic DNA reference sequence (following HGVS recommendations).
g.12345678C>T
g.12345678_12345890del
g.12345678_12345890dup
Reference
: Reference to publication describing the variant, including links to OMIM (when available), PubMed or or other source, e.g. "den Dunnen ASHG2003 P2346".
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.
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).
How to query this table
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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.
11 entries on 1 page. Showing entries 1 - 11.
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How to query
Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
Variant/VariO/DNA
Variant/VariO/protein
DNA change (genomic) (hg19)
Reference
DB-ID
Frequency
Owner
./.
1
2
c.246C>T
r.(?)
p.(=)
-
-
g.132585058G>A
Wang L et al. (2016)
dbSNP
TOR1A_000011
-
XY Liu
./.
1
2
c.361G>A
r.(?)
p.(Glu121Lys)
VariO:0136 DNA substitution; VariO:0313 transition; VariO:0315 purine transition
VariO:0021 amino acid substitution
g.132584943C>T
1 more item
TOR1A_000007
-
Y Yang
./.
1
2
c.385G>A
r.(?)
p.(Val129Ile)
-
-
g.132584919C>T
Dobričić V et al. (2015)
TOR1A_000010
-
XY Liu
./.
1
3
c.581A>T
r.(?)
p.(Asp194Val)
VariO:0136 DNA substitution; VariO:0316 transversion
VariO:0021 amino acid substitution
g.132581063T>A
Cheng FB1, Feng JC, Ma LY, Miao J, Ott T, Wan XH, Grundmann K.(2014)
TOR1A_000004
-
Y Yang
./.
2
3
c.613T>A
r.(?)
p.(Phe205Ile)
VariO:0136 DNA substitution; VariO:0316 transversion
VariO:0021 amino acid substitution
g.132581031A>T
2 more items
TOR1A_000002
-
Y Yang
./.
2
4
c.646G>C
r.(?)
p.(Asp216His)
VariO:0136 DNA substitution; VariO:0316 transversion
VariO:0021 amino acid substitution
g.132580901C>G
Wang L et al. (2016)
dbSNP
,
1 more item
TOR1A_000001
-
Y Yang
,
XY Liu
./.
1
5
c.863G>A
r.(?)
p.(Arg288Gln)
VariO:0136 DNA substitution; VariO:0313 transition; VariO:0315 purine transition
VariO:0021 amino acid substitution
g.132576387C>T
1 more item
TOR1A_000006
-
Y Yang
./.
4
5
c.904_906delGAG
r.(?)
p.(Glu303del)
VariO:0141 DNA deletion
VariO:0016 sequence retaining amino acid deletion
g.132576344_132576346delCTC
Narayanan R, McGrath A, Tritschler C, Manning JM, Harrington MG.(1979)
,
3 more items
TOR1A_000003
-
Y Yang
./.
2
5
c.907_909delGAG
r.(?)
p.(Glu303del)
VariO:0141 DNA deletion
VariO:0016 sequence retaining amino acid deletion
g.132576341_132576343delCTC
Camargo CH1, Camargos ST2, Raskin S3, Cardoso FE2, Teive HA1.(2014)
,
1 more item
TOR1A_000005
-
Y Yang
./.
1
5
c.934_937delAGAG
r.(?)
p.(Arg312Phefs*14)
VariO:0141 DNA deletion
VariO:0023 amphigoric amino acid indel
g.132576313_132576316delCTCT
1 more item
TOR1A_000008
-
Y Yang
./.
1
5
c.967_984del18
r.(?)
p.(Phe323_Tyr328del)
VariO:0141 DNA deletion
VariO:0016 sequence retaining amino acid deletion
g.132576266_132576283del18
1 more item
TOR1A_000009
-
Y Yang
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