Iran Variome MPS Database
GALNS (galactosamine (N-acetyl)-6-sulfatase)
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Unique variants in the GALNS gene
The variants shown are described using the
NM_000512.4
XM_005256302.1
XM_005256301.1
XM_005256303.1
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
Clinical classification
: Drop down selection
All options:
pathogenic
likely pathogenic
VUS
likely benign
benign
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.
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'
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66 entries on 1 page. Showing entries 1 - 66.
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Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
Clinical classification
DNA change (genomic) (hg19)
Reference
DB-ID
Owner
./.
1
-
c.-70_319del
r.?
p.?
pathogenic
g.88908305_88923355del
-
GALNS_000057
Variome.ir
+/+, ./.
3
-
c.29G>A
r.(?)
p.(Trp10*)
pathogenic
g.88923257C>T
-
GALNS_000025
Variome.ir
./.
1
-
c.83dupC
r.(?)
p.(Gln29Alafs*17)
likely pathogenic
g.88923203dupG
-
GALNS_000041
Variome.ir
./.
1
-
c.84del
r.(?)
p.(Gln29Serfs*100)
pathogenic
g.88923202del
-
GALNS_000006
Variome.ir
./.
1
-
c.85C>T
r.(?)
p.(Gln29*)
pathogenic
g.88923201G>A
-
GALNS_000049
Variome.ir
./.
1
-
c.95A>C
r.(?)
p.(Asn32Thr)
likely pathogenic
g.88923191T>G
-
GALNS_000048
Variome.ir
./.
1
-
c.107T>G
r.(?)
p.(Leu36Arg)
likely pathogenic
g.88923179A>C
-
GALNS_000054
Variome.ir
./.
2
-
c.120+1G>C
r.spl?
p.?
pathogenic
g.88923165C>G
-
GALNS_000033
Variome.ir
./.
1
-
c.121A>T
r.(?)
p.(Met41Leu)
pathogenic
g.88909237T>A
-
GALNS_000051
Variome.ir
+/+
1
-
c.121_422del
r.(?)
p.(Met41Alafs*16)
pathogenic
g.88907400_88909237del
-
GALNS_000029
Variome.ir
+/+, ./.
2
-
c.139G>A
r.(?)
p.(Gly47Arg)
pathogenic
g.88909219C>T
-
GALNS_000038
Variome.ir
./+
1
-
c.148G>A
r.(?)
p.(Gly50Arg)
likely pathogenic
g.88909210C>T
-
GALNS_000010
Variome.ir
./.
2
-
c.230C>G
r.(?)
p.(Pro77Arg)
likely pathogenic, pathogenic
g.88909128G>C
-
GALNS_000037
Variome.ir
./.
1
-
c.230delC
r.(?)
p.(Pro77Leufs*52)
pathogenic
g.88909128delG
-
GALNS_000061
Variome.ir
./.
1
-
c.244T>C
r.(?)
p.(Ser82Pro)
pathogenic
g.88909114A>G
-
GALNS_000047
Variome.ir
./.
1
-
c.263C>T
r.(?)
p.(Thr88Ile)
likely pathogenic
g.88908361G>A
-
GALNS_000058
Variome.ir
./.
1
-
c.266G>A
r.(?)
p.(Gly89Glu)
likely pathogenic
g.88908358C>T
-
GALNS_000044
Variome.ir
./.
1
-
c.284delA
r.(?)
p.(Asn95Metfs*34)
pathogenic
g.88908340delT
-
GALNS_000034
Variome.ir
./+
1
-
c.313A>G
r.(?)
p.(Arg105Gly)
likely pathogenic
g.88908311T>C
-
GALNS_000012
Variome.ir
+/+, ./+, ./.
4
-
c.319G>A
r.(?)
p.(Ala107Thr)
pathogenic
g.88908305C>T
-
GALNS_000003
Variome.ir
./.
1
-
c.326C>T
r.(?)
p.(Thr109Ile)
likely pathogenic
g.88907496G>A
-
GALNS_000031
Variome.ir
./.
3
-
c.346G>A
r.(?)
p.(Gly116Ser)
pathogenic
g.88907476C>T
-
GALNS_000026
Variome.ir
./.
2
-
c.374C>T
r.(?)
p.(Pro125Leu)
pathogenic
g.88907448G>A
-
GALNS_000039
Variome.ir
./.
1
-
c.416G>A
r.(?)
p.(Gly139Asp)
likely pathogenic
g.88907406C>T
-
GALNS_000067
Variome.ir
+/+, ./.
2
-
c.421T>A
r.(?)
p.(Trp141Arg)
pathogenic
g.88907401A>T
-
GALNS_000019
Variome.ir
./+
1
-
c.423-7_898+45del
r.(?)
p.(His142Trpfs*15)
pathogenic
g.88901576_88904180del
-
GALNS_000002
Variome.ir
+/+, ./.
2
-
c.424_565del
r.(?)
p.(His142Aspfs*10)
pathogenic
g.88904031_88904172del
-
GALNS_000028, GALNS_000030
Variome.ir
+/+
1
-
c.442C>T
r.(?)
p.(Gln148*)
pathogenic
g.88904154G>A
-
GALNS_000008
Variome.ir
./.
1
-
c.535C>T
r.(?)
p.(Pro179Ser)
pathogenic
g.88904061G>A
-
GALNS_000064
Variome.ir
./+, ./.
3
-
c.542A>G
r.(?)
p.(Tyr181Cys)
likely pathogenic, pathogenic
g.88904054T>C
-
GALNS_000005
Variome.ir
./.
2
-
c.602G>A
r.(?)
p.(Gly201Glu)
likely pathogenic
g.88902640C>T
-
GALNS_000011
Variome.ir
./.
1
-
c.609delC
r.(?)
p.(Asn204Thrfs*115)
pathogenic
g.88902633delG
-
GALNS_000032
Variome.ir
+/+
1
-
c.647T>C
r.(?)
p.(Phe216Ser)
pathogenic
g.88902244A>G
-
GALNS_000018
Variome.ir
./.
1
-
c.680del
r.(?)
p.(Phe227Serfs*92)
pathogenic
g.88902211del
-
GALNS_000023
Variome.ir
./.
1
-
c.680T>C
r.(?)
p.(Phe227Ser)
likely pathogenic
g.88902211A>G
-
GALNS_000059
Variome.ir
./.
1
-
c.688T>C
r.(?)
p.(Trp230Arg)
likely pathogenic
g.88902203A>G
-
GALNS_000052
Variome.ir
./.
1
-
c.722C>A
r.(?)
p.(Ala241Asp)
likely pathogenic
g.88902169G>T
-
GALNS_000020
Variome.ir
+/+, ./+, ./.
6
-
c.860C>T
r.(?)
p.(Ser287Leu)
pathogenic
g.88901659G>A
-
GALNS_000014
Variome.ir
+/+
1
-
c.866A>G
r.(?)
p.(Asn289Ser)
likely pathogenic
g.88901653T>C
-
GALNS_000001
Variome.ir
./+
1
-
c.868G>A
r.(?)
p.(Gly290Ser)
pathogenic
g.88901651C>T
-
GALNS_000013
Variome.ir
./.
1
-
c.869G>C
r.(?)
p.(Gly290Ala)
likely pathogenic
g.88901650C>G
-
GALNS_000045
Variome.ir
./+
1
-
c.916T>G
r.(?)
p.(Phe306Val)
likely pathogenic
g.88898492A>C
-
GALNS_000004
Variome.ir
./+
1
-
c.934A>G
r.(?)
p.(Thr312Ala)
likely pathogenic
g.88898474T>C
-
GALNS_000017
Variome.ir
./.
1
-
c.941T>C
r.(?)
p.(Phe314Ser)
likely pathogenic
g.88898467A>G
-
GALNS_000009
Variome.ir
./.
1
-
c.947G>A
r.(?)
p.(Gly316Glu)
likely pathogenic
g.88898461C>T
-
GALNS_000024
Variome.ir
./.
1
-
c.949G>C
r.(?)
p.(Gly317Arg)
likely pathogenic
g.88898459C>G
-
GALNS_000060
Variome.ir
./.
2
-
c.956G>C
r.(?)
p.(Arg319Thr)
likely pathogenic
g.88898452C>G
-
GALNS_000053
Variome.ir
./+, ./.
3
-
c.965C>T
r.(?)
p.(Ala322Val)
likely pathogenic
g.88898443G>A
-
GALNS_000027
Variome.ir
./.
1
-
c.974G>A
r.(?)
p.(Trp325*)
pathogenic
g.88898434C>T
-
GALNS_000065
Variome.ir
./.
1
-
c.1002+1G>A
r.spl?
p.?
pathogenic
g.88898405C>T
-
GALNS_000055
Variome.ir
+/+, ./.
2
-
c.1019G>A
r.(?)
p.(Gly340Asp)
likely pathogenic, pathogenic
g.88893230C>T
-
GALNS_000046
Variome.ir
./.
4
-
c.1042A>G
r.(?)
p.(Thr348Ala)
likely pathogenic
g.88893207T>C
-
GALNS_000042
Variome.ir
./.
1
-
c.1073C>T
r.(?)
p.(Pro358Leu)
likely pathogenic
g.88893176G>A
-
GALNS_000035
Variome.ir
./.
1
-
c.1156C>T
r.(?)
p.(Arg386Cys)
likely pathogenic
g.88891261G>A
-
GALNS_000036
Variome.ir
./.
1
-
c.1157G>A
r.(?)
p.(Arg386His)
likely pathogenic
g.88891260C>T
-
GALNS_000022
Variome.ir
./+
1
-
c.1219A>C
r.(?)
p.(Asn407His)
pathogenic
g.88891198T>G
-
GALNS_000040
Variome.ir
./.
2
-
c.1259C>G
r.(?)
p.(Pro420Arg)
likely pathogenic
g.88889102G>C
-
GALNS_000015
Variome.ir
./.
1
-
c.1265A>G
r.(?)
p.(Gln422Arg)
VUS
g.88889096T>C
-
GALNS_000066
Variome.ir
./+
1
-
c.1279del
r.(?)
p.(Val427Serfs*14)
likely pathogenic
g.88889082del
-
GALNS_000007
Variome.ir
./.
1
-
c.1365_1482del
r.(?)
p.(Ser455Argfs*11)
pathogenic
g.88884415_88884532del
-
GALNS_000056
Variome.ir
./.
1
-
c.1480A>G
r.(?)
p.(Met494Val)
likely pathogenic
g.88884417T>C
-
GALNS_000050
Variome.ir
./.
1
-
c.1482+1G>A
r.spl?
p.?
pathogenic
g.88884414C>T
-
GALNS_000043
Variome.ir
./.
1
-
c.1493C>T
r.(?)
p.(Pro498Leu)
likely pathogenic
g.88880923G>A
-
GALNS_000062
Variome.ir
./.
1
-
c.1496C>T
r.(?)
p.(Pro499Leu)
likely pathogenic
g.88880920G>A
-
GALNS_000063
Variome.ir
./.
1
-
c.1519T>C
r.(?)
p.(Cys507Arg)
likely pathogenic
g.88880897A>G
-
GALNS_000016
Variome.ir
./.
1
-
c.1568A>G
r.(?)
p.(*523Trpext*92)
VUS
g.88880848T>C
-
GALNS_000021
Variome.ir
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