Global Variome shared LOVD
HMGCL (3-hydroxymethyl-3-methylglutaryl-CoA lyase)
LOVD v.3.0 Build 30b [
Current LOVD status
]
Register as submitter
|
Log in
Curator:
Global Variome, with Curator vacancy
View all genes
View HMGCL gene homepage
View graphs about the HMGCL gene database
Create a new gene entry
View all transcripts
View all transcripts of gene HMGCL
Create a new transcript information entry
View all variants
View all variants affecting transcripts
View unique variants in gene HMGCL
View all variants in gene HMGCL
Full data view for gene HMGCL
Create a new data submission
View active genomic custom columns
Enable more genomic custom columns
View all individuals
View all individuals with variants in gene HMGCL
Create a new data submission
View active custom columns
Enable more custom columns
View all diseases
View all diseases associated with gene HMGCL
Create a new disease information entry
View available phenotype columns
View all screenings
View all screenings for gene HMGCL
Create a new data submission
View active custom columns
Enable more custom columns
Submit new data
Unique variants in the HMGCL gene
The variants shown are described using the NM_000191.2 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
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)
conflicting
association
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.
77 entries on 1 page. Showing entries 1 - 77.
10 per page
25 per page
50 per page
100 per page
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
-
c.?
r.61_144del
p.Val21_Lys48del
-
pathogenic (recessive)
g.?
-
r.61-144del
-
NPHS2_000000
-
PubMed: Alfadhel 2022
,
Journal: Alfadhel 2022
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
-
c.27del
r.(?)
p.(Arg10Glyfs*24), p.(Arg10GlyfsTer24)
-
pathogenic (recessive)
g.24151879del
g.23825389del
27delG, c.27_27delG
-
HMGCL_000033
-
PubMed: Grunert 2017
,
PubMed: Pospisilova 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
5
1
c.31C>T
r.(?)
p.(Arg11*), p.(Arg11Ter)
ACMG
pathogenic (recessive)
g.24151875G>A
g.23825385G>A
-
-
HMGCL_000050
Grünert 2017:28583327, Aoyama 2015:25872961, Puisac 2013:23465862
PubMed: Aoyama 2015
,
PubMed: Grunert 2017
ClinVar-521752
rs1212444447
Germline
yes
-
-
-
-
Johan den Dunnen
,
Miriam Erandi Reyna-Fabián
+/.
1
1i_4i
c.61-540_348+22del
r.?
p.?
-
pathogenic (recessive)
g.24143146_24147626del
g.23816656_23821136del
NG_013061 g.9326-13806del
-
HMGCL_000051
-
PubMed: Aoyama 2015
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
_1i_6i
c.(?_61-1)_(561+1_562-1)del
r.?
p.?
-
pathogenic (recessive)
g.(24134814_24137225)_(24147084_?)del
g.(23808324_23810735)_(23820594_?)del
del ex(1_2)-6
-
HMGCL_000018
-
PubMed: Wang 1996
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.88C>T
r.(?)
p.(Pro30Ser)
-
likely benign
g.24147056G>A
g.23820566G>A
HMGCL(NM_000191.2):c.88C>T (p.(Pro30Ser))
-
HMGCL_000006
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
6
2
c.109G>A
r.(?), r.[109c>u,61_144del,61_252del]
p.(Glu37Lys), p.[Glu37*,Val21_Lys48del,Val21_Gln84del]
-
pathogenic (recessive)
g.24147035C>T
g.23820545C>T
-
-
HMGCL_000069
-
PubMed: Casale 1998
,
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
20
2
c.109G>T
r.(?), r.[109c>u,61_144del]
p.(Glu37*), p.(Glu37Ter), p.[Glu37*,Val21_Lys48del]
ACMG
pathogenic, pathogenic (recessive)
g.24147035C>A
g.23820545C>A
E37X, HMGCL(NM_000191.3):c.109G>T (p.E37*)
-
HMGCL_000024
HMGCL activity 0.00, HMGCL activity 0.00 (compound heterozygous), HMGCL activity 0.08,
3 more items
PubMed: Cardoso 2004
,
PubMed: Grünert 2017
PubMed: Muñoz-Bonet 2017
PubMed: Puisac 2013
,
4 more items
ClinVar-195033
rs763494292
CLASSIFICATION record, Germline
yes
-
-
-
-
Johan den Dunnen
,
VKGL-NL_VUmc
,
Miriam Erandi Reyna-Fabián
+?/.
1
2
c.112G>T
r.(?)
p.(Val38Phe)
ACMG
likely pathogenic (!)
g.24147032C>A
g.23820542C>A
-
-
HMGCL_000071
1 more item
-
ClinVar-2075645
-
Germline
yes
-
-
-
-
Miriam Erandi Reyna-Fabián
+/.
2
2
c.121C>T
r.(?)
p.(Arg41*)
ACMG
pathogenic (recessive)
g.24147023G>A
g.23820533G>A
-
-
HMGCL_000023
Mitchel 1998:9463337, Pié 2007:17692550, Menao 2009:19177531, no variant 2nd chromosome
PubMed: Mitchell 1998
ClinVar-553933
rs770225915
Germline
yes
-
-
-
-
Johan den Dunnen
,
Miriam Erandi Reyna-Fabián
+/.
60
-
c.122G>A
r.(?)
p.(Arg41Gln)
-
pathogenic, pathogenic (recessive)
g.24147022C>T
g.23820532C>T
HMGCL(NM_000191.3):c.122G>A (p.R41Q)
-
HMGCL_000004
no variant 2nd chromosome, VKGL data sharing initiative Nederland
PubMed: Al-Sayed 2006
,
PubMed: Alfadhel 2022
,
Journal: Alfadhel 2022
,
PubMed: Mitchell 1998
,
1 more item
-
-
CLASSIFICATION record, Germline
-
32/36 cases
-
-
-
Johan den Dunnen
,
VKGL-NL_Groningen
,
Muhammad Umair
+/.
1
-
c.124G>A
r.(?)
p.(Asp42Asn)
-
pathogenic (recessive)
g.24147020C>T
-
D42N
-
HMGCL_000044
-
PubMed: Vargas 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.124G>C
r.(?)
p.(Asp42His)
-
pathogenic (recessive)
g.24147020C>G
-
-
-
HMGCL_000022
no variant 2nd chromosome
PubMed: Mitchell 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.125A>G
r.(?)
p.(Asp42Gly)
-
pathogenic (recessive)
g.24147019T>C
-
-
-
HMGCL_000020
-
PubMed: Mitchell 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.126T>G
r.(?)
p.(Asp42Glu)
-
pathogenic (recessive)
g.24147018A>C
-
-
-
HMGCL_000021
-
PubMed: Mitchell 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.137dup
r.(?)
p.(Asn46Lysfs*2)
-
pathogenic (recessive)
g.24147010dup
g.23820520dup
134-137insA
-
HMGCL_000016
-
PubMed: Mitchell 1995
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.144G>T
r.(?)
p.(Lys48Asn)
-
pathogenic
g.24147000C>A
-
g.144G>T
-
HMGCL_000043
2nd variant not reported
PubMed: Carrasco 2007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
2i_4i
c.(144+1_145-1)_(348+1_349-1)del
r.?
p.?
-
pathogenic (recessive)
g.(24140829_24143164)_(24144074_24146999)del
g.(23814339_23816674)_(23817584_23820509)del
del ex3-4
-
HMGCL_000049
-
PubMed: Koksal 2015
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
2i_6i
c.(144+1_145-1)_(561+1_562-1)del
r.?
p.?
-
pathogenic (recessive)
g.(24134814_24137225)_(24144074_24146999)del
g.(23808324_23810735)_(23817584_23820509)del
del ex3-6
-
HMGCL_000017
-
PubMed: Wang 1996
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.163G>C
r.(?)
p.(Val55Leu)
-
likely benign
g.24144055C>G
g.23817565C>G
HMGCL(NM_000191.2):c.163G>C (p.V55L)
-
HMGCL_000009
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
6
-
c.206_207del
r.(?), r.206_207del
p.(Ser69CysfsTer11), p.Ser69Cysfs*11
-
pathogenic (recessive)
g.24144015_24144016del
g.23817525_23817526del
-
-
HMGCL_000011
-
PubMed: Alfadhel 2022
,
Journal: Alfadhel 2022
,
PubMed: Mitchell 1993
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
,
Muhammad Umair
+/.
1
-
c.225C>G
r.(?)
p.(Ser75Arg)
-
pathogenic (recessive)
g.24143993G>C
-
-
-
HMGCL_000038
-
PubMed: Casals 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3
c.230del
r.(?)
p.(Val77Glyfs*16)
ACMG
pathogenic (recessive)
g.24143988del
g.23817498del
-
-
HMGCL_000072
1 more item
-
ClinVar-1685878
rs1638632303
Germline
yes
-
-
-
-
Miriam Erandi Reyna-Fabián
+?/.
1
3
c.233C>T
r.(?)
p.(Ser78Phe)
ACMG
likely pathogenic (recessive)
g.24143985G>A
g.23817495G>A
-
-
HMGCL_000070
1 more item
-
ClinVar-2083770
rs754253328
Germline
yes
-
-
-
-
Miriam Erandi Reyna-Fabián
+/.
3
3
c.242G>A
r.(?)
p.(Trp81*), p.(Trp81Ter)
-
pathogenic (recessive)
g.24143976C>T
g.23817486C>T
-
-
HMGCL_000052
paternal uniparental disomy of chromosome 1
PubMed: Aoyama 2015
,
PubMed: Menao 2009
-
-
Germline, Uniparental disomy, paternal allele
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.252G>A
r.145_252del
p.Asn49_Gln84del
-
pathogenic (recessive)
g.24143966C>T
g.23817476C>T
-
-
HMGCL_000068
-
PubMed: Grunert 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3i
c.252+1del
r.145_252del
p.Asn49_Gln84del
-
pathogenic (recessive)
g.24143966del
g.23817476del
252+1delG
-
HMGCL_000030
-
PubMed: Muroi 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3i
c.252+1G>A
r.145_252del
p.Asn49_Gln84del
-
pathogenic (recessive)
g.24143965C>T
-
IVS3+1G>A
-
HMGCL_000047
-
PubMed: Lin 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
3i
c.252+34=
r.(?)
p.?
-
benign
g.24143932=
g.23817442=
-
-
HMGCL_000067
-
PubMed: Menao 2009
-
rs2076344
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.272T>A
r.(?)
p.(Val91Asp)
-
pathogenic (recessive)
g.24143241A>T
g.23816751A>T
-
-
HMGCL_000066
-
PubMed: Grunert 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.286C>T
r.286c>u
p.Gln96*
-
pathogenic (recessive)
g.24143227G>A
-
-
-
HMGCL_000032
-
PubMed: Funghini 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.308_317dup
r.(?)
p.(Thr107ProfsTer48)
-
pathogenic (recessive)
g.24143198_24143207dup
g.23816708_23816717dup
-
-
HMGCL_000065
-
PubMed: Alfadhel 2022
,
Journal: Alfadhel 2022
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.323C>T
r.(?)
p.(Pro108Leu)
-
pathogenic (recessive)
g.24143190G>A
-
-
-
HMGCL_000054
-
PubMed: Grunert 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.344C>T
r.(?)
p.(Ala115Val)
-
VUS
g.24143169G>A
g.23816679G>A
HMGCL(NM_000191.2):c.344C>T (p.A115V)
-
HMGCL_000005
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
2
-
c.349-3C>A
r.spl?
p.?
-
VUS
g.24140831G>T
g.23814341G>T
HMGCL(NM_000191.2):c.349-3C>A, HMGCL(NM_000191.3):c.349-3C>A
-
HMGCL_000008
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_Rotterdam
+/.
3
-
c.374_375del
r.(?)
p.(Val125Aspfs*26), p.(Val125AspfsTer26)
-
pathogenic (recessive)
g.24140802_24140803del
g.23814312_23814313del
374_375delTC, c.374_375delTC
-
HMGCL_000041
-
PubMed: Grunert 2017
,
PubMed: Zafeiriou 2007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5
c.425C>T
r.(?)
p.(Ser142Phe)
-
pathogenic (recessive)
g.24140752G>A
g.23814262G>A
-
-
HMGCL_000064
-
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.434A>T
r.433_561del
p.Gln145_Glu187del
-
pathogenic (recessive)
g.24140743T>A
-
A434T
-
HMGCL_000029
-
PubMed: Muroi 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
-
c.493C>T
r.(?)
p.(Arg165Trp)
-
pathogenic (recessive)
g.24140684G>A
g.23814194G>A
-
-
HMGCL_000063
-
PubMed: Grunert 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
-
c.494G>A
r.(?)
p.(Arg165Gln)
-
pathogenic (recessive)
g.24140683C>T
-
-
-
HMGCL_000045
-
PubMed: Lin 2009
,
PubMed: Pierron 2010
-
-
De novo, Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5i
c.497+4A>G
r.[349_497del,349_561del]
p.[Ala118Arfs*10,Val117_Glu187del]
-
pathogenic (recessive)
g.24140676T>C
g.23814186T>C
-
-
HMGCL_000062
-
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
6
6
c.505_506del
r.(?), r.[505_506del,498_561del,349_561del]
p.(Ser169Leufs*8), p.[Ser169Leufs*8,Tyr167Serfs*27,Ala118_Val188del]
ACMG
pathogenic (recessive)
g.24137283_24137284del
g.23810793_23810794del
504_505delCT, V168fs(−2)
-
HMGCL_000019
HMGCL activity 0.07 (compound heterozygous),
1 more item
PubMed: Cardoso 2004
,
PubMed: Casals 1997
,
PubMed: Vargas 2008
ClinVar-521753
rs764264834
Germline
yes
-
-
-
-
Johan den Dunnen
,
Miriam Erandi Reyna-Fabián
+/.
1
6
c.521G>A
r.(?)
p.(Cys174Tyr)
-
pathogenic (recessive)
g.24137266C>T
g.23810776C>T
-
-
HMGCL_000061
-
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
6
c.559G>T
r.(?)
p.(Glu187Ter)
-
pathogenic (recessive)
g.24137228C>A
g.23810738C>A
-
-
HMGCL_000060
-
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.561+1G>A
r.spl
p.?
-
pathogenic (recessive)
g.24137225C>T
-
IVS6+1GA
-
HMGCL_000040
-
PubMed: Al-Sayed 2006
-
-
Germline
-
1/36 cases
-
-
-
Johan den Dunnen
+/.
1
6i
c.562-1G>A
r.(562_750del)
p.(Val188_Gln250del)
-
pathogenic (recessive)
g.24134814C>T
g.23808324C>T
IVS6-1G>A
-
HMGCL_000046
Fig.1C show other variant (654A>G)
PubMed: Lin 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
6i_7i
c.(561+1_562-1)_(750+1_751-1)del
r.562_750del
p.Val188_Gln250del
-
pathogenic (recessive)
g.(24131016_24134624)_(24134814_24137225)del
g,(23804526_23808134)_(23808324_23810735)del
ex del7
-
HMGCL_000031
2.2 kb deletion
PubMed: Muroi 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7
c.575T>C
r.(?)
p.(Phe192Ser)
-
pathogenic (recessive)
g.24134800A>G
g.23808310A>G
-
-
HMGCL_000059
-
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
7
c.598A>T
r.(?)
p.(Ile200Phe)
-
pathogenic (recessive)
g.24134777T>A
g.23808287T>A
-
-
HMGCL_000058
-
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.599T>A
r.(?)
p.(Ile200Asn)
-
pathogenic (recessive)
g.24134776A>T
g.23808286A>T
-
-
HMGCL_000013
-
PubMed: Alfadhel 2022
,
Journal: Alfadhel 2022
-
-
Germline
-
-
-
-
-
Muhammad Umair
+/.
1
-
c.602C>A
r.(?)
p.(Ser201Tyr)
-
pathogenic (recessive)
g.24134773G>T
-
-
-
HMGCL_000037
-
PubMed: Casals 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.608G>A
r.(?)
p.(Gly203Glu)
-
pathogenic (recessive)
g.24134767C>T
-
-
-
HMGCL_000039
-
PubMed: Mir 2006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
-
c.610G>A
r.(?)
p.(Asp204Asn)
-
pathogenic (recessive)
g.24134765C>T
-
-
-
HMGCL_000036
HMGCL activity 0.00 (compound heterozygous)
PubMed: Cardoso 2004
,
PubMed: Casals 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.650T>G
r.(?)
p.(Met217Arg)
-
VUS
g.24134725A>C
g.23808235A>C
HMGCL(NM_000191.2):c.650T>G (p.(Met217Arg))
-
HMGCL_000007
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-/., -?/.
4
-
c.654A>G
r.(=), r.(?)
p.(=), p.(Leu218=)
-
benign, likely benign
g.24134721T>C
g.23808231T>C
HMGCL(NM_000191.3):c.654A>G (p.L218=)
-
HMGCL_000003
shown in Fig.1C (not reported), VKGL data sharing initiative Nederland
PubMed: Lin 2009
,
PubMed: Pie 1997
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
+/.
1
-
c.658del
r.(?)
p.(Ala220LeufsTer27)
-
pathogenic (recessive)
g.24134717del
g.23808227del
c.658_658delG
-
HMGCL_000057
-
PubMed: Grunert 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.663C>T
r.(?)
p.(Val221=)
-
likely benign
g.24134712G>A
-
HMGCL(NM_000191.2):c.663C>T (p.V221=)
-
HMGCL_000010
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
-
c.697C>G
-
p.His233Asp
-
NA
g.24134678G>C
-
-
-
HMGCL_000034
functional analysis shows <0.01 specific activity
PubMed: Roberts 1996
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.697_698delinsGC
-
p.His233Ala
-
NA
g.24134677_24134678delinsGC
-
-
-
HMGCL_000035
functional analysis shows <0.01 specific activity
PubMed: Roberts 1996
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
4
-
c.698A>G
-, r.(?), r.698a>g
p.(His233Arg), p.His233Arg
-
NA, pathogenic (recessive)
g.24134677T>C
-
A698G
-
HMGCL_000025
functional analysis shows <0.01 specific activity
PubMed: Pospisilova 2003
,
PubMed: Roberts 1996
,
PubMed: Zapater 1998
-
-
Germline, In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.727G>A
r.(?)
p.(Ala243Thr)
-
benign
g.24134648C>T
-
-
-
HMGCL_000053
-
PubMed: Pie 1997
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
7i
c.750+1G>A
r.(?)
p.?
-
pathogenic (recessive)
g.24134624C>T
g.23808134C>T
-
-
HMGCL_000056
-
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.751-3T>C
r.spl?
p.?
-
likely benign
g.24131018A>G
g.23804528A>G
HMGCL(NM_000191.2):c.751-3T>C
-
HMGCL_000015
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
-
c.788T>C
r.788u>c
p.Leu263Pro
-
pathogenic (recessive)
g.24130978A>G
-
T788C
-
HMGCL_000026
-
PubMed: Zapater 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.796T>C
r.(?)
p.(Cys266Arg)
-
pathogenic (recessive)
g.24130970A>G
-
796C>T (C266R)
-
HMGCL_000042
-
PubMed: Zafeiriou 2007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.805G>A
r.(?)
p.(Ala269Thr)
-
VUS
g.24130961C>T
g.23804471C>T
HMGCL(NM_000191.3):c.805G>A (p.A269T)
-
HMGCL_000002
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/.
1
-
c.820G>A
r.(?)
p.(Gly274Arg)
-
pathogenic (recessive)
g.24130946C>T
-
-
-
HMGCL_000048
-
PubMed: Pierron 2010
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
-
c.835G>A
r.835g>a
p.Glu279Lys
-
pathogenic (recessive)
g.24130931C>T
-
G835A
-
HMGCL_000027
-
PubMed: Muroi 2000
-
rs28934894
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
8
c.853del
r.853del
p.Leu285Ter
-
pathogenic (recessive)
g.24130913del
g.23804423del
853delC
-
HMGCL_000055
-
PubMed: Menao 2009
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
7
8i
c.876+1G>C
r.spl, r.spl?, r.[751_876del,876_877ins[c;876+1_876+78]]
p.?, p.[Met231_Thr292del,Gly393Leufs*18]
-
pathogenic, pathogenic (recessive)
g.24130889C>G
g.23804399C>G
-
-
HMGCL_000014
VKGL data sharing initiative Nederland
PubMed: Buesa 1996
,
PubMed: Grunert 2017
,
PubMed: Koling 2000
,
PubMed: Grunert 2017
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Nijmegen
+/.
6
-
c.914_915del
r.(?)
p.(Arg41Gln), p.(Phe305Tyrfs*10), p.(Phe305TyrfsTer10)
-
pathogenic (recessive)
g.24129017_24129018del
g.23802527_23802528del
914_915delTT, F305fs(-2), g.913-15delTT
-
HMGCL_000012
study includes functional analysis variant
PubMed: Al-Sayed 2006
,
PubMed: Alfadhel 2022
,
Journal: Alfadhel 2022
,
PubMed: Carrasco 2007
,
1 more item
-
-
Germline
-
1/36 cases
-
-
-
Johan den Dunnen
,
Muhammad Umair
+/.
1
-
c.922C>T
r.922c>u
p.Gln308*
-
pathogenic (recessive)
g.24129009G>A
-
C922T
-
HMGCL_000028
-
PubMed: Muroi 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.950A>G
r.(?)
p.(Lys317Arg)
-
VUS
g.24128981T>C
g.23802491T>C
HMGCL(NM_000191.2):c.950A>G (p.(Lys317Arg))
-
HMGCL_000001
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
?/.
1
-
c.*3474G>C
r.(=)
p.(=)
-
VUS
g.24125479C>G
-
GALE(NM_000403.3):c.19G>C (p.V7L)
-
GALE_000011
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
-
c.*4745C>T
r.(=)
p.(=)
-
pathogenic
g.24124208G>A
-
-
-
GALE_000019
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.*5306C>T
r.(=)
p.(=)
-
likely benign
g.24123647G>A
-
GALE(NM_000403.3):c.529-10C>T
-
GALE_000009
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.*5525C>T
r.(=)
p.(=)
-
VUS
g.24123428G>A
-
GALE(NM_001008216.2):c.647C>T (p.(Ala216Val))
-
GALE_000020
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
10 per page
25 per page
50 per page
100 per page
Legend
How to query
Screenscraping/webscraping (downloading large amounts of data using scripts) is strictly prohibited.
Use our
APIs
to retrieve data.
Powered by
LOVD v.3.0
Build 30b
LOVD software ©2004-2024
Leiden University Medical Center
Database contents © by their respective submitters and curators