Global Variome shared LOVD
CBS (cystathionine-beta-synthase)
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Unique variants in the CBS gene
The variants shown are described using the NM_000071.2 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.
Haplotype
: haplotype on which variant was found
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
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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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229 entries on 3 pages. Showing entries 1 - 100.
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Effect
Reported
Exon
DNA change (cDNA)
Haplotype
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
12
c.[1105C>T;1471C>T]
-
-
p.[Arg369Cys;Arg491Cys]
-
NA
g.[44476994G>A;44480591G>A]
g.[43056884G>A;43060481G>A]
-
-
CBS_000064
expression cloning in E.coli, CBs activity 0.10
Kluijtmans 1998, PhD thesis
-
-
In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
-/.
1
_1
c.(-3469_-3466del)
CTTT[5]
r.(=)
p.(=)
-
benign
g.44499284_44499287del
g.43079174_43079177del
-3469_-3466del -6921TTTC
-
CBS_000056
-
PubMed: Kraus 1998
-
-
Germline
-
20/30 chromosomes
-
-
-
Johan den Dunnen
+/.
1
5
c.[172C>T;341C>T]
-
-
p.[Arg58Trp;Ala114Val]
-
NA
g.[44486463G>A;44492132G>A]
g.[43066353G>A;43072022G>A]
-
-
CBS_000057
expression cloning in E.coli, CBs activity 0.013
PubMed: de Franchis 1999
-
-
In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
+/.
1
4
c.[233C>G;306G>C]
-
-
p.[Pro78Arg;Lys12Asn]
-
NA
g.[44488629C>G;44488702G>C]
g.[43068519C>G;43068592G>C]
-
-
CBS_000058
expression cloning in E.coli, CBs activity 0
PubMed: de Franchis 1994
-
-
In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
+/.
1
5
c.[374G>A;393G>C]
-
-
p.[Arg125Gln;Glu131Asp]
-
NA
g.[44486411C>G;44486430C>T]
g.[43066301C>G;43066320C>T]
-
-
CBS_000059
expression cloning in E.coli, CBs activity 0.015
PubMed: Marble 1994
-
-
In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
+/.
1
5
c.[430G>A;1316G>A]
-
-
p.[Glu144Lys;Arg439Gln]
-
NA
g.[44478986C>T;44486374C>T]
g.[43058876C>T;43066264C>T]
-
-
CBS_000060
expression cloning in E.coli, CBs activity <0.01
PubMed: Dawson 1997
-
-
In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
+/.
7
3
c.19dup
-
r.(?)
p.(Gln7Profs*30)
-
pathogenic
g.44492290dup
g.43072180dup
19insC
-
CBS_000218
CBS activity 0.33 nM/mg/h, CBS activity 0.46 nM/mg/h
PubMed: Gaustadnes 2002
,
PubMed: Janosik 2001
,
PubMed: Janosik 2001
,
PubMed: Linnebank 2004
,
2 more items
-
-
Germline
-
3/9770000 chromosomes
-
-
-
Johan den Dunnen
+/., +?/.
4
3
c.28del
-
r.(?)
p.(Val10Trpfs*72), p.(Val10TrpfsTer72)
-
likely pathogenic, pathogenic
g.44492276del
g.43072166del
28delG, CBS(NM_001178008.2):c.28delG (p.V10Wfs*72)
-
CBS_000217
CBS activity 0.03 nM/mg/h, VKGL data sharing initiative Nederland
PubMed: Janosik 2001
,
PubMed: Sokolova 2001
-
-
CLASSIFICATION record, Germline
-
1/9770000 chromosomes
-
-
-
Johan den Dunnen
,
VKGL-NL_Rotterdam
-/., -?/.
4
?
c.52C>T
-
r.(?)
p.(Arg18Cys)
-
benign, likely benign
g.44492252G>A
g.43072142G>A
CBS(NM_000071.2):c.52C>T (p.(Arg18Cys), p.R18C), CBS(NM_001178008.2):c.52C>T (p.R18C)
-
CBS_000030
VKGL data sharing initiative Nederland
PubMed: Lee 2005
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Leiden
,
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
+/.
1
3
c.103G>A
-
r.(?)
p.(Asp35Asn)
-
pathogenic
g.44492201C>T
g.43072091C>T
103G>A;129G>A
-
CBS_000216
-
PubMed: Katsushima 2006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3
c.129G>A
-
r.(?)
p.(Trp43*)
-
pathogenic
g.44492175C>T
g.43072065C>T
103G>A;129G>A
-
CBS_000215
-
PubMed: Katsushima 2006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.133C>T
-
r.(?)
p.(Arg45Trp)
-
VUS
g.44492171G>A
g.43072061G>A
CBS(NM_001178008.3):c.133C>T (p.R45W)
-
CBS_000053
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/.
1
?
c.141T>A
-
r.(?)
p.(Asp47Glu)
-
pathogenic
g.44492163A>T
g.43072053A>T
-
-
CBS_000214
-
PubMed: Cheng 2007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., ?/.
7
3, ?
c.146C>T
-
r.(?)
p.(Pro49Leu)
-
pathogenic, VUS
g.44492158G>A
g.43072048G>A
CBS(NM_001178008.2):c.146C>T (p.P49L)
-
CBS_000052
VKGL data sharing initiative Nederland
PubMed: Cozar 2011
,
PubMed: de Franchis 1998
,
PubMed: Evangelisti 2008
,
PubMed: Gaustadnes 2002
,
1 more item
-
-
CLASSIFICATION record, Germline
-
-
DdeI+
-
-
Johan den Dunnen
,
VKGL-NL_Rotterdam
+/., ?/.
4
3, ?
c.172C>T
-
r.(?)
p.(Arg58Trp), p.Arg58Trp
-
NA, pathogenic, VUS
g.44492132G>A
g.43072022G>A
CBS(NM_001178008.2):c.172C>T (p.R58W)
-
CBS_000213
expression cloning in E.coli, CBs activity 0.013, VKGL data sharing initiative Nederland
PubMed: de Franchis 1998
,
PubMed: de Franchis 1999
,
PubMed: de Franchis 1999
,
PubMed: Kraus 1999
-
-
CLASSIFICATION record, Germline, In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Rotterdam
+/.
1
3
c.194A>C
-
r.(?)
p.(His65Pro)
-
pathogenic
g.44492110T>G
g.43072000T>G
-
-
CBS_000212
-
CBS mutation database, Linnebank
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
3
c.194A>G
-
r.(?)
p.(His65Arg)
-
pathogenic
g.44492110T>C
g.43072000T>C
-
-
CBS_000211
CBS activity 0.02 nM/mg/h; no variant 2nd allele identified
CBS mutation database, Linnebank,
PubMed: Chen 1999
,
PubMed: Janosik 2001
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3_3i
c.208_209+8del
-
r.spl
p.0?
-
pathogenic
g.44492089_44492098del
g.43071979_43071988del
69_70+8del
-
CBS_000209
-
PubMed: Urreizti 2006
-
-
Germline
-
-
FokI+
-
-
Johan den Dunnen
-?/.
1
-
c.209C>T
-
r.(?)
p.(Pro70Leu)
-
likely benign
g.44492095G>A
-
CBS(NM_001178008.2):c.209C>T (p.P70L)
-
CBS_000228
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
6
3i
c.209+1G>A
-
r.spl?, r.[-8_209del,153_209del], r.[153_209del,-8_209del]
p.?
-
pathogenic
g.44492094C>T
g.43071984C>T
CBS(NM_000071.2):c.209+1G>A (p.?), IVS1+1G>A
-
CBS_000029
VKGL data sharing initiative Nederland
CBS mutation database, Linnebank,
PubMed: Gaustadnes 2002
,
PubMed: Gordon 1997
,
PubMed: Urreizti 2003
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Leiden
+/.
1
3i
c.209+1_209+2insC
-
r.spl
p.?
-
pathogenic
g.44492093_44492094insG
g.43071983_43071984insG
IVS1+1insC
-
CBS_000210
-
PubMed: Gaustadnes 2002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
3i
c.210-1G>C
-
r.spl
p.?
-
pathogenic
g.44488726C>G
g.43068616C>G
IVS1-1G>C, IVS2-1G>C
-
CBS_000208
CBS activity 0.03 nM/mg/h
PubMed: Janosik 2001
,
PubMed: Sokolova 2001
-
-
Germline
-
1/9770000 chromosomes
-
-
-
Johan den Dunnen
-?/.
1
-
c.215A>T
-
r.(?)
p.(Lys72Ile)
-
likely benign
g.44488720T>A
-
CBS(NM_000071.2):c.215A>T (p.(Lys72Ile))
-
CBS_000224
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
3
4
c.233C>G
-
r.(?), r.233c>g
p.Pro78Arg
-
NA, pathogenic
g.44488702G>C
g.43068592G>C
-
-
CBS_000207
both 0,5 activity, expression cloning in E.coli, CBs activity 0.126-0.609
PubMed: de Franchis 1994
-
-
Germline, In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
+/.
7
4, ?
c.253G>A
-
r.(?)
p.(Gly85Arg)
-
pathogenic
g.44488682C>T
g.43068572C>T
-
-
CBS_000206
1 heterozygous, no homozygous;
Clinindb (India)
CBS mutation database, De Lucca,
PubMed: Cozar 2011
,
PubMed: De Lucca 2004
,
PubMed: Maclean 2002
,
2 more items
-
rs863223435
Germline
-
1/2792 individuals
-
-
-
Johan den Dunnen
,
Mohammed Faruq
+/.
1
4
c.256del
-
r.(?)
p.(Asp86Thrfs*16)
-
pathogenic
g.44488682del
g.43068572del
G253del
-
CBS_000205
-
CBS mutation database, Linnebank
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
4
c.260C>A
-
r.(?)
p.(Thr87Asn)
-
pathogenic
g.44488675G>T
g.43068565G>T
-
-
CBS_000204
-
CBS mutation database, De Lucca
-
-
Germline
-
-
MslI-
-
-
Johan den Dunnen
+/.
4
4, ?
c.262C>T
-
r.(?)
p.(Pro88Ser)
-
pathogenic
g.44488673G>A
g.43068563G>A
-
-
CBS_000203
-
PubMed: de Franchis 1998
,
PubMed: Sebastio 1995
-
-
Germline
-
-
MnlI+
-
-
Johan den Dunnen
+/.
5
4
c.302T>C
-
r.(?)
p.(Leu101Pro)
-
pathogenic
g.44488633A>G
g.43068523A>G
-
-
CBS_000202
no variant 2nd allele identified
PubMed: Gallagher 1998
,
PubMed: Gaustadnes 2002
,
PubMed: Kruger 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., -/., -?/., ?/.
7
4
c.304A>C
-
r.(?)
p.(Lys102Gln)
-
benign, likely benign, pathogenic, VUS
g.44488631T>G
g.43068521T>G
304A>C;IVS4-29del129, CBS(NM_000071.2):c.304A>C (p.K102Q, p.(Lys102Gln))
-
CBS_000001
VKGL data sharing initiative Nederland
CBS mutation database, Linnebank,
PubMed: Kozich 1997
-
-
CLASSIFICATION record, Germline
-
-
PstI+
-
-
Gerard C.P. Schaafsma
,
Johan den Dunnen
,
VKGL-NL_Leiden
,
VKGL-NL_Utrecht
,
VKGL-NL_AMC
+/.
3
4
c.306G>C
-
r.(?), r.306g>c
p.Lys102Asn, p.Lys12Asn
-
NA, pathogenic
g.44488629C>G
g.43068519C>G
-
-
CBS_000201
both 0,5 activity, expression cloning in E.coli, CBs activity 0.333-0.387
PubMed: de Franchis 1994
-
-
Germline, In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
+/.
1
4
c.313_316del
-
r.(?)
p.(Leu105Trpfs*13)
-
pathogenic
g.44488619_44488622del
g.43068509_43068512del
-
-
CBS_000200
-
PubMed: Kraus 1999
, V Shih
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.316+728C>T
-
r.(=)
p.(=)
-
benign
g.44487891G>A
g.43067781G>A
CBS(NM_000071.2):c.316+728C>T, CBSL(NM_001354006.1):c.316+728C>T
-
CBS_000028
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/.
4
5
c.325T>C
-
r.(?)
p.(Cys109Arg)
-
pathogenic
g.44486479A>G
g.43066369A>G
CBS(NM_001321072.1):c.10T>C (p.C4R)
-
CBS_000051
VKGL data sharing initiative Nederland
PubMed: Gaustadnes 2002
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Groningen
-?/.
1
-
c.339C>T
-
r.(?)
p.(Asn113=)
-
likely benign
g.44486465G>A
-
CBS(NM_000071.2):c.339C>T (p.(=))
-
CBS_000235
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
23
5, ?
c.341C>T
-
r.(?)
p.(Ala114Val), p.Ala114Val
-
NA, pathogenic
g.44486463G>A
g.43066353G>A
-
-
CBS_000199
CBS activity 0.13 nM/mg/h, expression cloning in E.coli, CBs activity 0-0.545, no var allele 2,
1 more item
CBS mutation database, Kraus,
PubMed: de Franchis 1998
,
PubMed: de Franchis 1999
,
PubMed: Janosik 2001
,
7 more items
-
-
Germline, In vitro (cloned)
-
1/9770000 chromosomes
FokI+, MaeII+
-
-
Johan den Dunnen
+/.
8
5, ?
c.346G>A
-
r.(?), r.346g>a
p.(Gly116Arg), p.Gly116Arg
-
pathogenic
g.44486458C>T
g.43066348C>T
-
-
CBS_000198
no var allele 2
CBS mutation database, Sebastio, Redonnet-Vernhet 2005 (abstract J Inherit Metab Dis 28 sup1),
3 more items
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5
c.361C>A
-
r.(?)
p.(Arg121Ser)
-
pathogenic
g.44486443G>T
g.43066333G>T
-
-
CBS_000197
-
CBS mutation database, Linnebank
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
4
5
c.361C>T
-
r.(?)
p.(Arg121Cys)
-
pathogenic
g.44486443G>A
g.43066333G>A
-
-
CBS_000196
-
CBS mutation database, Shih,
PubMed: Cozar 2011
,
PubMed: Katsushima 2006
,
PubMed: Kraus 1999
, V Shih
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
7
5
c.362G>A
-
r.(?)
p.(Arg121His)
-
pathogenic
g.44486442C>T
g.43066332C>T
-
-
CBS_000195
-
CBS mutation database, Linnebank,
PubMed: Bermudez 2006
,
PubMed: Katsushima 2006
,
2 more items
-
-
Germline
-
-
FokI+
-
-
Johan den Dunnen
+/.
1
5
c.362G>T
-
r.(?)
p.(Arg121Leu)
-
pathogenic
g.44486442C>A
g.43066332C>A
-
-
CBS_000194
-
PubMed: Kraus 1999
, V Shih
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
5
5
c.373C>T
-
r.(?)
p.(Arg125Trp)
-
pathogenic
g.44486431G>A
g.43066321G>A
-
-
CBS_000193
-
CBS mutation database, Linnebank,
PubMed: Kluijtmans 1999
,
PubMed: Urreizti 2003
-
-
Germline
-
-
AciI-
-
-
Johan den Dunnen
+/.
15
5, ?
c.374G>A
-
r.(?), r.374g>a
p.(Arg125Gln), p.Arg125Gln
-
NA, pathogenic
g.44486430C>T
g.43066320C>T
G374A
-
CBS_000191
expression cloning in E.coli, CBs activity 0.019
CBS mutation database, Kraus, CBS mutation database, Linnebank,
PubMed: Cozar 2011
,
6 more items
-
-
Germline, In vitro (cloned)
-
-
PstI+
-
-
Johan den Dunnen
+/.
1
5
c.374G>C
-
r.(?)
p.(Arg125Pro)
-
pathogenic
g.44486430C>G
g.43066320C>G
-
-
CBS_000192
-
PubMed: Castro 2001
-
-
Germline
-
-
HpaII+
-
-
Johan den Dunnen
+/.
2
5, ?
c.376A>G
-
r.(?)
p.(Met126Val)
-
pathogenic
g.44486428T>C
g.43066318T>C
-
-
CBS_000190
-
PubMed: de Franchis 1998
,
PubMed: de Franchis 1999
,
PubMed: Kraus 1999
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.381T>G
-
r.(?)
p.(Ile127Met)
-
VUS
g.44486423A>C
g.43066313A>C
CBS(NM_000071.2):c.381T>G (p.(Ile127Met))
-
CBS_000050
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
1
5
c.384G>C
-
r.(?)
p.(Glu128Asp)
-
pathogenic
g.44486420C>G
g.43066310C>G
-
-
CBS_000189
no variant 2nd allele identified
PubMed: Coude 1998
-
-
Germline
-
-
MulI-,FokI-
-
-
Johan den Dunnen
+/.
2
5
c.393G>C
-
r.(?), r.393g>c
p.Glu131Asp
-
NA, pathogenic
g.44486411C>G
g.43066301C>G
-
-
CBS_000188
expression cloning in E.coli, CBs activity 0
PubMed: Marble 1994
-
-
Germline, In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.396C>T
-
r.(?)
p.(Arg132=)
-
likely benign
g.44486408G>A
-
CBS(NM_001321072.1):c.81C>T (p.R27=)
-
CBS_000227
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.400G>A
-
r.(?)
p.(Gly134Arg)
-
VUS
g.44486404C>T
g.43066294C>T
CBS(NM_001321072.1):c.85G>A (p.G29R)
-
CBS_000049
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
5
c.415G>A
-
r.(?)
p.(Gly139Arg)
-
pathogenic
g.44486389C>T
g.43066279C>T
-
-
CBS_000187
-
PubMed: Shih 1995
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
5, ?
c.429C>G
-
r.(?)
p.(Ile143Met)
-
pathogenic
g.44486375G>C
g.43066265G>C
-
-
CBS_000186
-
PubMed: Linnebank 2004
,
PubMed: Orendae 2004
-
-
Germline
-
-
TaqI-
-
-
Johan den Dunnen
+/.
13
5
c.430G>A
-
r.(?)
p.(Glu144Lys), p.Glu144Lys
-
NA, pathogenic
g.44486374C>T
g.43066264C>T
-
-
CBS_000185
CBS activity 0.00 nM/mg/h, CBS activity 0.10 nM/mg/h, no variant 2nd allele identified,
1 more item
CBS mutation database, Kraus,
PubMed: Dawson 1997
,
PubMed: Gaustadnes 2002
,
PubMed: Gordon 1997
,
4 more items
-
-
Germline, In vitro (cloned)
-
2/9770000 chromosomes
TaqI-
-
-
Johan den Dunnen
+/.
2
5
c.434C>T
-
r.(?)
p.(Pro145Leu), p.Pro145Leu
-
NA, pathogenic
g.44486370G>A
g.43066260G>A
-
-
CBS_000184
expression cloning in E.coli, CBs activity 0
PubMed: Kozich 1993
-
-
Germline, In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
+/.
4
5
c.442G>A
-
r.(?)
p.(Gly148Arg)
-
pathogenic
g.44486362C>T
g.43066252C>T
-
-
CBS_000183
-
PubMed: Katsushima 2006
,
PubMed: Kraus 1999
, T Ohura,
PubMed: Orendae 2004
,
PubMed: Urreizti 2006
-
-
Germline
-
-
FokI+, MspI-,BstNI+
-
-
Johan den Dunnen
+/.
1
5
c.443G>A
-
r.(?)
p.(Gly148Glu)
-
pathogenic
g.44486361C>T
g.43066251C>T
-
-
CBS_000182
-
CBS mutation database, Linnebank
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5
c.444dup
-
r.(?)
p.(Asn149Glufs*39)
-
pathogenic
g.44486362dup
g.43066252dup
-
-
CBS_000181
-
PubMed: Gaustadnes 2002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
6
5, ?
c.451G>A
-
r.spl?
p.(Gly151Arg)
-
pathogenic
g.44486353C>T
g.43066243C>T
-
-
CBS_000180
-
CBS mutation database, Linnebank, CBS mutation database, Shih,
PubMed: Katsushima 2006
,
3 more items
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
?
c.452_478del
-
r.(?)
p.(Gly151_Ala159del)
-
pathogenic
g.44485782_44485808del
g.43065672_43065698del
452del27
-
CBS_000172
-
PubMed: de Franchis 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5i_6i
c.(451+1_452-1)_(531+1_532-1)del
-
r.452_531del
p.?
-
pathogenic
g.(44485632_44485725)_(44485806_44486352)del
g.(43065522_43065615)_(43065696_43066242)del
452del80
-
CBS_000062
-
PubMed: Kraus 1999
, V Shih
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., -?/.
2
6
c.453G>A
-
r.(?), r.453g>a
p.(Pro145=), p.Pro145=
-
likely benign, pathogenic
g.44485804C>T
g.43065694C>T
-
-
CBS_000179
-
PubMed: Marble 1994
,
PubMed: Urreizti 2006
-
-
Germline
-
-
FokI+
-
-
Johan den Dunnen
+/.
3
6
c.456C>G
-
r.(?)
p.(Ile152Met), p.Ile152Met
-
NA, pathogenic
g.44485801G>C
g.43065691G>C
-
-
CBS_000178
expression cloning in E.coli, CBs activity 0.003
Kluijtmans 1998, PhD thesis,
PubMed: Kluijtmans 1999
-
-
Germline, In vitro (cloned)
-
-
Sau3AI-
-
-
Johan den Dunnen
+/.
4
6, ?
c.457G>A
-
r.(?)
p.(Gly153Arg)
-
pathogenic
g.44485800C>T
g.43065690C>T
-
-
CBS_000177
-
CBS mutation database, Linnebank, Redonnet-Vernhet 2005 (abstract J Inherit Metab Dis 28 sup1),
1 more item
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
?
c.461T>A
-
r.(?)
p.(Leu154Gln)
-
pathogenic
g.44485796A>T
g.43065686A>T
-
-
CBS_000176
-
PubMed: Lee 2005
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., ?/.
6
6, ?
c.463G>A
-
r.(?)
p.(Ala155Thr)
-
pathogenic, VUS
g.44485794C>T
g.43065684C>T
CBS(NM_001321072.1):c.148G>A (p.A50T), CBSL(NM_001354006.1):c.463G>A (p.A155T)
-
CBS_000175
CBS activity 0.00 nM/mg/h, CBS activity 0.10 nM/mg/h, VKGL data sharing initiative Nederland
PubMed: Janosik 2001
,
PubMed: Janosik 2001
,
PubMed: Linnebank 2004
,
PubMed: Kraus 1999
, V Kozich,
1 more item
-
-
CLASSIFICATION record, Germline
-
2/9770000 chromosomes
Sau96I+
-
-
Johan den Dunnen
,
VKGL-NL_Rotterdam
+/.
1
?
c.464C>T
-
r.(?)
p.(Ala155Val)
-
pathogenic
g.44485793G>A
g.43065683G>A
-
-
CBS_000174
-
PubMed: Lee 2005
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
6
c.469G>C
-
r.(?)
p.(Ala157Pro)
-
pathogenic
g.44485788C>G
g.43065678C>G
-
-
CBS_000173
-
PubMed: Evangelisti 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
6
c.493_514del
-
r.(?)
p.(Cys165Argfs*2)
-
pathogenic
g.44485743_44485764del
g.43065633_43065654del
493del22
-
CBS_000169
-
PubMed: Gaustadnes 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
9
6, ?
c.494G>A
-
r.(?)
p.(Cys165Tyr), p.Cys165Tyr
-
NA, pathogenic
g.44485763C>T
g.43065653C>T
CBS(NM_000071.2):c.494G>A (p.C165Y)
-
CBS_000027
CBS activity 0.46 nM/mg/h, expression cloning in E.coli, CBs activity 0.013,
1 more item
Kluijtmans 1998, PhD thesis,
PubMed: Gaustadnes 2002
,
PubMed: Gordon 1997
,
PubMed: Janosik 2001
,
2 more items
-
-
CLASSIFICATION record, Germline, In vitro (cloned)
-
-
BsoFI-
-
-
Johan den Dunnen
,
VKGL-NL_Utrecht
-?/.
1
-
c.501C>T
-
r.(?)
p.(Ile167=)
-
likely benign
g.44485756G>A
g.43065646G>A
CBS(NM_001321072.1):c.186C>T (p.I62=)
-
CBS_000219
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
2
6
c.502G>A
-
r.(?)
p.(Val168Met)
-
pathogenic
g.44485755C>T
g.43065645C>T
-
-
CBS_000171
-
CBS mutation database, Linnebank,
PubMed: Kruger 1995
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
?
c.503T>C
-
r.(?)
p.(Val168Ala)
-
pathogenic
g.44485754A>G
g.43065644A>G
-
-
CBS_000170
-
PubMed: Porto 2005
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
6
c.517A>G
-
r.(?)
p.(Met173Val)
-
pathogenic
g.44485740T>C
g.43065630T>C
-
-
CBS_000168
-
PubMed: Urreizti 2006
-
-
Germline
-
-
FokI+
-
-
Johan den Dunnen
+/.
2
6
c.518_520del
-
r.(?)
p.(Met173del)
-
pathogenic
g.44485739_44485741del
g.43065629_43065631del
518delTGA
-
CBS_000167
-
PubMed: Cozar 2011
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., +?/.
4
6
c.526G>A
-
r.(?)
p.(Glu176Lys)
-
likely pathogenic, pathogenic
g.44485731C>T
g.43065621C>T
CBS (NM_001178009.1):c.526G>A(p.E176K)/c.949A>G(p.R317G)
-
CBS_000166
CBS activity 0.03 nM/mg/h, different transcript: CBS (NM_001178009.1):c.526G>A(p.E176K)
PubMed: Janosik 2001
,
PubMed: Kozich 1997
,
PubMed: Sokolova 2001
,
PubMed: Sun 2018
-
-
Germline, Germline/De novo (untested)
?
195, 2/9770000 chromosomes
BstXI+
-
-
Johan den Dunnen
+/.
2
6i
c.531+1G>A
-
r.spl
p.?
-
pathogenic
g.44485725C>T
g.43065615C>T
IVS4+1G>A
-
CBS_000165
-
CBS mutation database, Skovby
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/., -?/.
3
-
c.531+11G>A
-
r.(=)
p.(=)
-
benign, likely benign
g.44485715C>T
g.43065605C>T
CBS(NM_000071.2):c.531+11G>A (, p.(=))
-
CBS_000048
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
+/.
1
6i_8i
c.532-38del796
-
r.spl
p.?
-
pathogenic
g.44485669del796
g.43065559del796
IVS4-38del796 (V178GfsX23 )
-
CBS_000164
1 more item
PubMed: Cozar 2011
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
6i
c.532-30_532-2del
-
r.spl
p.?
-
pathogenic
g.44485634_44485662del
g.43065524_43065552del
532-32del30
-
CBS_000162
-
PubMed: Kozich 1997
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
6i
c.532-29_631del
-
r.532_666del
p.?
-
pathogenic
g.44485533_44485661del
g.43065423_43065551del
304A>C;IVS4-29del129
-
CBS_000157
-
CBS mutation database, Linnebank
-
-
Germline
-
-
PstI+
-
-
Johan den Dunnen
+/.
2
6i
c.532-14_532-7del
-
r.spl?
p.(?)
-
pathogenic
g.44485639_44485646del
g.43065529_43065536del
IVS5-14_-7del8
-
CBS_000163
-
PubMed: Cozar 2011
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
7
c.536_553del
-
r.(?)
p.(Asp179_Leu184del)
-
pathogenic
g.44485613_44485630del
g.43065503_43065520del
533del18
-
CBS_000160
-
PubMed: Gaustadnes 2002
,
PubMed: Shih 1995
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
7
c.539T>C
-
r.(?)
p.(Val180Ala), p.Val18Ala
-
NA, pathogenic
g.44485624A>G
g.43065514A>G
-
-
CBS_000161
expression cloning in E.coli, CBs activity 0.03, no variant 2nd allele identified
Kluijtmans 1998, PhD thesis,
PubMed: Kluijtmans 1999
-
-
Germline, In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
+/.
52
7, ?
c.572C>T
-
r.(?)
p.(Thr191Met), p.Thr191Met
-
NA, pathogenic
g.44485591G>A
g.43065481G>A
-
-
CBS_000159
2 heterozygous, no homozygous;
Clinindb (India)
, expression cloning in E.coli, CBs activity 0.01,
1 more item
Kluijtmans 1998, PhD thesis, Redonnet-Vernhet 2005 (abstract J Inherit Metab Dis 28 sup1),
8 more items
-
rs121964973
Germline, In vitro (cloned)
-
2/2788 individuals
FokI+
-
-
Johan den Dunnen
,
Mohammed Faruq
-/., -?/.
3
-
c.573G>A
-
r.(?)
p.(Thr191=)
-
benign, likely benign
g.44485590C>T
g.43065480C>T
CBS(NM_000071.2):c.573G>A (p.T191=, p.(Thr191=))
-
CBS_000026
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
-?/.
1
-
c.582T>C
-
r.(?)
p.(Asn194=)
-
likely benign
g.44485581A>G
g.43065471A>G
CBS(NM_001321072.1):c.267T>C (p.N89=), CBSL(NM_001354006.1):c.582T>C (p.N194=)
-
CBS_000223
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
7
c.593A>T
-
r.(?)
p.(Asp198Val)
-
pathogenic
g.44485570T>A
g.43065460T>A
-
-
CBS_000158
-
PubMed: Kraus 1999
, V Shih
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., ?/.
3
7
c.599C>T
-
r.(?)
p.(Pro200Leu)
-
pathogenic, VUS
g.44485564G>A
g.43065454G>A
CBS(NM_000071.2):c.599C>T (p.(Pro200Leu), p.P200L)
-
CBS_000025
VKGL data sharing initiative Nederland
PubMed: Cozar 2011
-
-
CLASSIFICATION record, Germline
-
-
MspI-
-
-
Johan den Dunnen
,
VKGL-NL_Leiden
,
VKGL-NL_Groningen
-/.
2
-
c.636C>T
-
r.(?)
p.(Asn212=)
-
benign
g.44485527G>A
g.43065417G>A
CBS(NM_000071.2):c.636C>T (p.(Asn212=)), CBS(NM_001321072.1):c.321C>T (p.N107=)
-
CBS_000024
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_Rotterdam
+/.
1
7
c.650C>T
-
r.(?)
p.(Ser217Phe)
-
pathogenic
g.44485513G>A
g.43065403G>A
-
-
CBS_000156
-
PubMed: Katsushima 2006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.667-6A>G
-
r.(=)
p.(=)
-
likely benign
g.44485388T>C
g.43065278T>C
CBS(NM_000071.2):c.667-6A>G (p.(=))
-
CBS_000047
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
1
8
c.671G>A
-
r.(?)
p.(Arg224His)
-
pathogenic
g.44485378C>T
g.43065268C>T
-
-
CBS_000155
-
PubMed: Kruger 1995
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
7
8, ?
c.676G>A
-
r.(?)
p.(Ala226Thr)
-
pathogenic
g.44485373C>T
g.43065263C>T
-
-
CBS_000154
-
CBS mutation database, Linnebank,
PubMed: Cozar 2011
,
PubMed: Kraus 1999
, L Elsas,
PubMed: Kruger 2003
,
2 more items
-
-
Germline
-
-
FokI+
-
-
Johan den Dunnen
+/.
1
8
c.683A>G
-
r.(?)
p.(Asn228Ser)
-
pathogenic
g.44485366T>C
g.43065256T>C
-
-
CBS_000153
-
PubMed: Kruger 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
8
c.684C>A
-
r.(?)
p.(Asn228Lys)
-
pathogenic
g.44485365G>T
g.43065255G>T
-
-
CBS_000152
-
PubMed: Gaustadnes 2002
,
PubMed: Orendae 2004
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
8
c.684C>G
-
r.(?)
p.(Asn228Lys)
-
pathogenic
g.44485365G>C
g.43065255G>C
-
-
CBS_000151
-
PubMed: Gallagher 1998
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
8
c.689del
-
r.(?)
p.(Leu230Argfs*39)
-
pathogenic
g.44485360del
g.43065250del
689delT
-
CBS_000150
-
PubMed: Cozar 2011
-
-
Germline
-
-
MspI+
-
-
Johan den Dunnen
+/.
2
8
c.691G>C
-
r.(?)
p.(Ala231Pro)
-
pathogenic
g.44485358C>G
g.43065248C>G
-
-
CBS_000149
-
PubMed: Kruger 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
8
c.694C>G
-
r.(?)
p.(His232Asp)
-
pathogenic
g.44485355G>C
g.43065245G>C
-
-
CBS_000148
-
PubMed: Katsushima 2006
,
PubMed: Yokoi 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., -/., -?/.
5
8
c.699C>T
-
r.(?)
p.(Tyr233=)
-
benign, likely benign, pathogenic
g.44485350G>A
g.43065240G>A
CBS(NM_000071.2):c.699C>T (p.Y233=), CBSL(NM_001354006.1):c.699C>T (p.Y233=)
-
CBS_000032
VKGL data sharing initiative Nederland
PubMed: Janosikova 2005
-
-
CLASSIFICATION record, Germline
-
128/400 chroosomes
-
-
-
Johan den Dunnen
,
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
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