Global Variome shared LOVD
GK (glycerol kinase)
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Curators:
Johan den Dunnen
and
Global Variome, with Curator vacancy
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Unique variants in the GK gene
This database is one of the gene variant databases from the
Leiden Muscular Dystrophy pages
The variants shown are described using the NM_001205019.1 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 = 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
Classification method
: The method used for the clinical classification of this variant.
All options:
ACMG
ACGS
EAHAD-CFDB
ENIGMA
IARC
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, 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.
67 entries on 1 page. Showing entries 1 - 67.
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Legend
How to query
Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
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
1_21
c.(?_-179)_(*1866_?)del
r.0
p.0
-
pathogenic (recessive)
g.?
-
-
-
GK_000022
contiguous gene syndrome
PubMed: Hellerud 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/+, +/.
5
-1-21_, _1_21_
c.(?_-1)_(*1_?)del
r.0, r.0?
p.0, p.0?
-
pathogenic, pathogenic (recessive)
g.(25034000_28807460)_(31645980_31676106)del, g.(28606165_28771534)_(30746860_31140035)del,
3 more items
g.(?_31119228)_(33339609_?)del
-
-
DMD_040078, DMD_040261, DMD_050080, GK_010028, NR0B1_000002
658 kb deletion incl. GKD_3'DMD, deletion incl. IL1RAPL1, NR0B1 (DAX1), GK, DMD (partial),
2 more items
L Medne ASHG 2010 A1669,
PubMed: Carrie 1999
,
PubMed: Guo 1995
,
PubMed: Zhang 2004
,
1 more item
-
-
Germline, Germline/De novo (untested), Unknown
yes
-
-
-
-
Johan den Dunnen
,
Bert Bakker
+/.
1
_1_21_
c.-179_*2720{0}
r.0
p.0
-
pathogenic (recessive)
g.29949219_31144301del
g.29931102_31126184del
-
-
DMD_000533
breakpoint in intron 8 IL1RAPL1 gene (antisense strand), RNA contains new 3' sequence replacing ex79
PubMed: Jin 2000
,
PubMed: Greener 2002
,
GenBank AF181286.1
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
1
_1_21_
c.-179_*{0}
r.0
p.0
-
pathogenic (recessive)
g.(?_30322539)_(33357493_?)del
g.(?_30304422)_(33339377_?)del
-
-
DMD_010080
deletion incl. GK, NR0B1 and DMD gene
PubMed: Tao 2022
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/+, +/.
16
_1_21_
c.0
r.0
p.0
-
pathogenic (recessive)
g.(25000000_28500000)_(33357726_37000000)del, g.(25040000_28600000)_(31241239_31279071)del,
11 more items
g.(28180000_28480000)_(31968515_32216915)del, g.(29668505_29917463)_(31348635_31444480)del,
2 more items
hg19 25878399_31987991del, hg19 29008175–31496701del
-
DMD_003415, DMD_003416, DMD_003417, DMD_040079, DMD_040080, DMD_040081, DMD_040082, DMD_050380,
5 more items
2.49 Mb deletion including IL1RAPL1, DAX1, GK and last 22 exons DMD, deletion incl. GK and DMD,
9 more items
PubMed: Heide 2015
,
PubMed: Korkut 2016
,
PubMed: Loke 2009
,
PubMed: Tomar 2019
,
PubMed: Piko 2009
,
1 more item
-
-
De novo, Germline, Germline/De novo (untested), Unknown
-, yes
-
-
-
X-inactivation CpG island 5' CAG repeat AR gene 59%:41%,
1 more item
Johan den Dunnen
,
Poh San Lai
+/.
2
1_21
c.?
r.(?)
p.?
-
pathogenic (recessive)
g.?
-
-
-
GK_000000
carries GPD2:[791A>G];[791A>G] (His264Arg), unknown variant
PubMed: Hellerud 2003
,
PubMed: Sjarif 2004
-
-
Germline
-
-
-
-
-
Johan den Dunnen
./.
1
-
c.78+164G>C
r.(=)
p.(=)
-
VUS
g.30671896G>C
g.30653779G>C
-
-
GK_010026
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
-/., -?/., ./.
6
3
c.165G>A
r.(=), r.(?)
p.(=)
-
benign, likely benign, VUS
g.30686141G>A
g.30668024G>A
Q55Q
-
GK_000009, GK_010016
recurrent, found 22 times; for details contact Lucy Raymond (flr24 @ cam.ac.uk)
PubMed: Gaudet 2000
,
PubMed: Sargent 2000
,
PubMed: Tarpey 2009
-
-
Germline
-
4/40
AvaII-
-
-
Johan den Dunnen
,
Yu Sun
+/.
1
3
c.182T>C
r.182u>c
p.Leu61Pro
-
pathogenic (recessive)
g.30686158T>C
g.30668041T>C
-
-
GK_000025
not in100 normal chromosomes
PubMed: Sjarif 2004
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3i
c.259+1G>A
r.153_259del
p.Trp52Tyrfs*29
-
pathogenic (recessive)
g.30686236G>A
g.30668119G>A
IVS3+1G>A
-
GK_000026
nonsense mediated mRNA decay
PubMed: Zhang 2006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.259+1354G>A
r.(=)
p.(=)
-
benign
g.30687589G>A
g.30669472G>A
-
-
GK_010041
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
2
3i
c.259+2254G>A
r.[259_260ins259+2256_259+2467, 153_59delins259+2256_259+2467]
p.[Ala87Valfs*3, Trp52Tyrfs*24]
-
pathogenic (recessive)
g.30688489G>A
g.30670372G>A
-
-
GK_000012
not in100 normal chromosomes
PubMed: Sargent 2000
,
PubMed: Sjarif 2004
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.259+2333G>T
r.(=)
p.(=)
-
benign
g.30688568G>T
-
-
-
GK_010050
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
4
c.287C>T
r.(?)
p.(Thr96Ile)
-
pathogenic (recessive)
g.30695519C>T
g.30677402C>T
-
-
GK_000027
not in100 normal chromosomes
PubMed: Hellerud 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
./.
1
-
c.337+385dup
r.(=)
p.(=)
-
VUS
g.30695954dup
g.30677837dup
-
-
GK_010019
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
+?/.
1
4i
c.338-43_338-42ins316; 338-52_338-43dup
r.[=, 338_414del]
p.[=, Trp114Glnfs*7]
-
likely pathogenic (recessive)
g.?
-
IVS4-52ins316alu
-
GK_000007
insertion reverse AluY sequence (74bp T-tail); not in 167 control chromosomes;
PubMed: Zhang 2000
,
PubMed: Zhang 2006
,
OMIM:var0007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
4i
c.338-1G>A
r.338_414del
p.Trp114Glnfs*7
-
pathogenic (recessive)
g.30709239G>A
g.30691122G>A
IVS4-1G>A
-
GK_000028
nonsense mediated mRNA decay
PubMed: Zhang 2006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.367G>A
r.(?)
p.(Val123Ile)
-
likely benign
g.30709269G>A
g.30691152G>A
GK(NM_001205019.1):c.367G>A (p.V123I)
-
GK_010042
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.380G>T
r.(?)
p.(Ser127Ile)
-
likely benign
g.30709282G>T
-
GK(NM_001205019.1):c.380G>T (p.S127I)
-
GK_010055
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
./.
2
-
c.552+142G>C
r.(=)
p.(=)
-
VUS
g.30712796G>C
g.30694679G>C
-
-
GK_010020
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
./.
2
-
c.553-102C>T
r.(=)
p.(=)
-
VUS
g.30714057C>T
g.30695940C>T
-
-
GK_010023
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
+/.
1
7
c.553-1G>C
r.553_554del
p.Ser184Phefs*17
-
pathogenic (recessive)
g.30714158G>C
g.30696041G>C
IVS6-1G>C
-
GK_000001
strongly reduced levels all 3 GK-transcricpts
PubMed: Walker 1996
,
OMIM:var0001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7
c.593A>G
r.(?)
p.(Asp198Gly)
-
pathogenic (recessive)
g.30714199A>G
g.30696082A>G
593A>G (D198G)
-
GK_000017
not in >100 normal chromosomes
PubMed: Dipple 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7
c.601A>G
r.(?)
p.(Asn201Asp)
-
pathogenic (recessive)
g.30714207A>G
g.30696090A>G
601A>G (D201N)
-
GK_000029
-
PubMed: Hellerud 2004
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.661G>A
r.(?)
p.(Glu221Lys)
-
likely benign
g.30714267G>A
g.30696150G>A
GK(NM_001205019.1):c.661G>A (p.E221K)
-
GK_010034
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/.
1
8i
c.729+17C>A
r.(?)
p.(=)
-
benign
g.30714817C>A
g.30696700C>A
IVS8+17C>A
-
GK_000030
-
PubMed: Sargent 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.729+21_729+24del
r.(=)
p.(=)
-
likely benign
g.30714821_30714824del
g.30696704_30696707del
GK(NM_001205019.1):c.729+21_729+24delCAAA
-
GK_010046
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
./.
1
-
c.730-252T>C
r.(=)
p.(=)
-
VUS
g.30715597T>C
g.30697480T>C
-
-
GK_010025
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
./.
2
-
c.730-22C>T
r.(=)
p.(=)
-
VUS
g.30715827C>T
g.30697710C>T
-
-
GK_010004
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
?/.
1
-
c.745G>A
r.(?)
p.(Val249Met)
-
VUS
g.30715864G>A
g.30697747G>A
GK(NM_001205019.1):c.745G>A (p.(Val249Met))
-
GK_010036
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-?/.
1
-
c.748-9T>C
r.(=)
p.(=)
-
likely benign
g.30718522T>C
g.30700405T>C
GK(NM_001205019.1):c.748-9T>C
-
GK_010037
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/., -?/.
2
-
c.748-5A>T
r.spl?
p.?
-
benign, likely benign
g.30718526A>T
g.30700409A>T
GK(NM_000167.5):c.730-5A>T (p.?), GK(NM_001205019.1):c.748-5A>T
-
GK_010038
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_Rotterdam
./.
4
-
c.784-78_784-75dup
r.(=)
p.(=)
-
VUS
g.30718877_30718880dup
g.30700760_30700763dup
-
-
GK_010007, GK_010027
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
+/.
1
11
c.784T>C
r.784u>c
p.262CysArg
-
pathogenic (recessive)
g.30718955T>C
g.30700838T>C
766T>C (C256R)
-
GK_000013
not in 40 normal chromosomes
PubMed: Sargent 2000
-
-
Germline
-
-
TspRI-
-
-
Johan den Dunnen
+/., +?/.
2
11
c.851C>T
r.(?), r.(spl?)
p.(Thr284Met)
-
likely pathogenic, pathogenic
g.30719022C>T
g.30700905C>T
833C>T (Thr278Met), GK(NM_000167.5):c.833C>T (p.T278M)
-
GK_010033
VKGL data sharing initiative Nederland
PubMed: Romero 1997
-
-
CLASSIFICATION record, Germline
yes
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Utrecht
./.
1
-
c.851+334A>G
r.(=)
p.(=)
-
VUS
g.30719356A>G
g.30701239A>G
-
-
GK_010009
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
+/.
2
11i
c.852-1G>A
r.spl
p.?
-
pathogenic (recessive)
g.30725672G>A
g.30707555G>A
IVS9A-1G>A
-
GK_000031
not in100 normal chromosomes
PubMed: Hellerud 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
4
11i
c.(851+1_852-1)_(*1866_?)del
r.?
p.?
-
pathogenic (recessive)
g.?
-
del Ex9-end
-
GK_000004
-
PubMed: Sjarif 1998
,
OMIM:var0004
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.855T>C
r.(?)
p.(Tyr285=)
-
likely benign
g.30725676T>C
g.30707559T>C
GK(NM_001205019.1):c.855T>C (p.Y285=)
-
GK_010048
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
12
c.857G>C
r.(?)
p.(Gly286Ala)
-
pathogenic (recessive)
g.30725678G>C
g.30707561G>C
Gly280Ala
-
GK_000011
-
PubMed: Wibmer 2005
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
12
c.880A>G
r.(?)
p.(Asn294Asp)
-
pathogenic (recessive)
g.30725701A>G
g.30707584A>G
862A>G (N288D), N288D
-
GK_000008
not in >100 normal chromosomes, shared haplotype DXS8039-DXS997
PubMed: Dipple 2001
,
PubMed: Gaudet 2000
,
OMIM:var0007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
12i
c.894+1G>T
r.852_894del
p.Tyr845Valfs*30
-
pathogenic (recessive)
g.30725716G>T
g.30707599G>T
IVS10+1G>T
-
GK_000032
nonsense mediated mRNA decay
PubMed: Zhang 2006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.895-7C>T
r.(=)
p.(=)
-
likely benign
g.30726164C>T
g.30708047C>T
GK(NM_000167.5):c.877-7C>T (p.(=))
-
GK_010044
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
1
13
c.932C>T
r.(?)
p.(Ala311Val)
-
pathogenic (recessive)
g.30726208C>T
g.30708091C>T
914C>T (A305V)
-
GK_000018
not in >100 normal chromosomes
PubMed: Dipple 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
13
c.946A>T
r.(?)
p.(Arg316*)
-
pathogenic (recessive)
g.30726222A>T
g.30708105A>T
1042T>A (R310X)
-
GK_000014
-
PubMed: Sargent 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
1
-
c.1054+2T>C
r.spl?
p.?
-
likely pathogenic
g.30736735T>C
g.30718618T>C
-
-
GK_010049
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
./.
2
-
c.1054+22G>T
r.(=)
p.(=)
-
VUS
g.30736755G>T
g.30718638G>T
-
-
GK_010010
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
-/.
1
14i
c.1055+22G>T
r.(?)
p.(=)
-
benign
g.30737558G>T
-
-
-
GK_000010
1 more item
PubMed: Gaudet 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
15
c.1091G>A
r.(?)
p.(Cys364Tyr)
-
pathogenic (recessive)
g.30737572G>A
g.30719455G>A
1073G>A (C358Y)
-
GK_000023
not in100 normal chromosomes
PubMed: Hellerud 2003
-
-
Germline
-
-
Fnu4H-
-
-
Johan den Dunnen
+/.
1
16
c.1212A>C
r.1212a>c
p.Glu404Asp
-
pathogenic (recessive)
g.30738188A>C
g.30720071A>C
1194A>C (E398D)
-
GK_000024
not in100 normal chromosomes
PubMed: Sjarif 2004
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
16
c.1225C>T
r.(?)
p.(Gln409*)
-
pathogenic (recessive)
g.30738201C>T
g.30720084C>T
1207C>T (Q403X)
-
GK_000015
-
PubMed: Sargent 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.1231C>T
r.(?)
p.(Arg411Ter)
-
pathogenic
g.30738207C>T
g.30720090C>T
GK(NM_203391.3):c.1231C>T (p.R411*)
-
GK_010039
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
1
16
c.1232G>A
r.(?)
p.(Arg411Gln)
-
pathogenic (recessive)
g.30738208G>A
g.30720091G>A
1214G>A (R405Q)
-
GK_000019
not in >100 normal chromosomes
PubMed: Dipple 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.1236+1G>A
r.spl?
p.?
-
VUS
g.30738213G>A
g.30720096G>A
GK(NM_001205019.1):c.1236+1G>A
-
GK_010040
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
1
17
c.1255C>T
r.(?)
p.(Arg419*)
-
pathogenic (recessive)
g.30738756C>T
g.30720639C>T
C1351T (R413X)
-
GK_000005
-
PubMed: Sjarif 1998
,
OMIM:var0005
-
-
Germline
-
-
TaqI-
-
-
Johan den Dunnen
?/.
1
-
c.1288G>A
r.(?)
p.(Val430Ile)
-
VUS
g.30738789G>A
-
GK(NM_001205019.1):c.1288G>A (p.V430I)
-
GK_010052
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+/.
1
17
c.1301T>C
r.(?)
p.(Met434Thr)
-
pathogenic (recessive)
g.30738802T>C
g.30720685T>C
1283T>C (M428T)
-
GK_000020
not in >100 normal chromosomes
PubMed: Dipple 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
17
c.1331A>G
r.(?)
p.(Gln444Arg)
-
pathogenic (recessive)
g.30738832A>G
g.30720715A>G
1313A>G (Q438R)
-
GK_000021
not in >100 normal chromosomes
PubMed: Dipple 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
17
c.1337A>T
r.1337a>u
p.Asp446Val
-
pathogenic (recessive)
g.30738838A>T
g.30720721A>T
D440V
-
GK_000003
reduced GK-transcripts; not in 100 control chromosomes
PubMed: Walker 1996
,
OMIM:var0003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/., ./.
3
17i
c.1357+20T>C
r.(=)
p.(=)
-
benign, VUS
g.30738878T>C
g.30720761T>C
NM_000167.5:c.1339+20T>C
-
GK_000034, GK_010013
-
from website {DBsub-Emory}
-
-
Germline, Unknown
-
-
-
-
-
Yu Sun
,
Madhuri Hegde
-?/.
1
-
c.1374C>T
r.(?)
p.(Pro458=)
-
likely benign
g.30738985C>T
-
GK(NM_001205019.1):c.1374C>T (p.P458=)
-
GK_010051
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.1417G>A
r.(?)
p.(Glu473Lys)
-
likely benign
g.30739028G>A
-
GK(NM_001205019.1):c.1417G>A (p.E473K)
-
GK_010053
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.1438C>T
r.(?)
p.(Leu480Phe)
-
VUS
g.30739049C>T
-
GK(NM_000167.6):c.1420C>T (p.L474F)
-
GK_010054
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/.
3
18i
c.(1501+1_1502-1)_(1582+1_1583-1)del
r.(?), r.1502_1582del
p.Ser502_Gly528del
-
pathogenic (recessive)
g.?
-
del Ex17
-
GK_000002
5 Kb deletion; normal GK transcript levels, extra 4.7Kb transcript,
1 more item
PubMed: Hellerud 2004
,
PubMed: Walker 1996
,
OMIM:var0002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
19
c.1525T>C
r.(?)
p.(Trp509Arg)
-
pathogenic (recessive)
g.30742241T>C
g.30724124T>C
T1651C (W503R)
-
GK_000006
not in 100 control chromosomes
PubMed: Sjarif 1998
,
OMIM:var0006
-
rs2893548
Germline
-
-
NlaIII-
-
-
Johan den Dunnen
-?/.
1
-
c.1651G>A
r.(?)
p.(Gly551Arg)
-
likely benign
g.30745651G>A
g.30727534G>A
GK(NM_001205019.1):c.1651G>A (p.G551R)
-
GK_010045
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
./.
2
-
c.*340C>T
r.(=)
p.(=)
-
VUS
g.30747199C>T
g.30729082C>T
-
-
GK_010001
-
-
-
-
Germline
-
-
-
-
-
Yu Sun
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