Global Variome shared LOVD
DPYD (dihydropyrimidine dehydrogenase)
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Unique variants in the DPYD gene
DPYD reference haplotypes
The variants shown are described using the NM_000110.3 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
Haplotype
: haplotype on which variant was found
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'
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.
73 entries on 1 page. Showing entries 1 - 73.
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Legend
How to query
Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
Haplotype
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.-1427187_*543783del
r.?
p.?
-
-
pathogenic
g.97000749_99813665del
g.96535193_99348109del
-
-
DPYD_000018
decreased gene dosage
PubMed: DDDS 2015
,
Journal: DDDS 2015
-
-
De novo
-
-
-
-
-
Johan den Dunnen
./.
1
-
c.-463957_*3733049del
r.?
p.?
-
-
pathogenic
g.93811483_98850435del
-
-
-
DPYD_000017
decreased gene dosage
PubMed: DDDS 2015
,
Journal: DDDS 2015
-
-
De novo
-
-
-
-
-
Johan den Dunnen
+/.
2
8i_12i
c.[850+31531_1525-15893inv;1525-15892_1525-15889del]
r.?, r.spl
p.?
-
-
pathogenic (recessive)
g.[97997390_98113120inv;97997386_97997389del]
-
g.[98113121_97997390inv;97997386_97997389del]
-
DPYD_000030
-
PubMed: van Kuilenburg 2018
,
Journal: van Kuilenburg 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Maja Tarailo-Graovac
-?/.
1
-
c.5C>T
r.(?)
p.(Ala2Val)
-
-
likely benign
g.98386474G>A
-
DPYD(NM_000110.3):c.5C>T (p.A2V)
-
DPYD_000060
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.37G>A
r.(?)
p.(Glu13Lys)
-
-
likely benign
g.98386442C>T
-
DPYD(NM_000110.3):c.37G>A (p.E13K)
-
DPYD_000059
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+?/.
1
2
c.62G>A
r.62g>a
p.Arg21Gln
DPYD*12
-
likely pathogenic
g.98348908C>T
g.97883352C>T
G62A (R21Q)
-
DPYD_000014
reference haplotype DPYD*12 [62G>A; 1156G>T]
PubMed: Mattison 2002
-
rs80081766
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.73C>T
r.(?)
p.(His25Tyr)
-
-
likely benign
g.98348897G>A
g.97883341G>A
DPYD(NM_000110.3):c.73C>T (p.H25Y)
-
DPYD_000046
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/.
1
-
c.85=
r.(=)
p.(Cys29=)
-
-
benign
g.98348885G>A
-
DPYD(NM_000110.3):c.85C>T (p.R29C)
-
DPYD_000011
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/., +?/+?, +?/., -?/.
5
2
c.85C=
-, r.(=), r.85c=
p.Arg29=
DPYD*9A, DPYD*9B
-
likely benign, likely pathogenic, NA, pathogenic
g.98348885=, g.98348885G=
-
T85C
-
DPYD_000000
5 more items
PubMed: Johnson 2002
,
PubMed: McLeod 1998
,
PubMed: Vreken 1997
-
-
Germline, In vitro (cloned), Unknown
-, yes
-
-
-
-
Johan den Dunnen
-/-, ?/.
3
2
c.85C>T
r.85c>u
p.Arg29Cys
DPYD*1
-
benign, VUS
g.98348885G>A
g.97883329G>A
-
-
DPYD_000011
2 more items
PubMed: McLeod 1998
,
PubMed: van Kuilenburg 2018
,
Journal: van Kuilenburg 2018
-
rs1801265
Germline
-
-
-
-
-
Johan den Dunnen
+/+?, +/.
2
4
c.299_302del
r.(?), r.299_302del
p.(Phe100SerfsTer15), p.Phe100Serfs*15
DPYD*7
-
pathogenic
g.98205971_98205974del
g.97740415_97740418del
delTCAT295-298, DPYD(NM_000110.3):c.299_302delTCAT (p.F100Sfs*15)
-
DPYD_000009
reference haplotype DPYD*7 [299_302del], VKGL data sharing initiative Nederland
PubMed: McLeod 1998
-
rs72549309
CLASSIFICATION record, Germline
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Groningen
+/.
1
-
c.321+2T>C
r.spl?
p.?
-
-
pathogenic
g.98205946A>G
-
DPYD(NM_000110.3):c.321+2T>C
-
DPYD_000070
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.465G>A
r.(?)
p.(Leu155=)
-
-
likely benign
g.98187084C>T
g.97721528C>T
DPYD(NM_000110.3):c.465G>A (p.L155=)
-
DPYD_000045
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.484-5C>T
r.spl?
p.?
-
-
likely benign
g.98165108G>A
g.97699552G>A
DPYD(NM_000110.3):c.484-5C>T (p.?)
-
DPYD_000044
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-?/.
1
-
c.484-4G>A
r.spl?
p.?
-
-
likely benign
g.98165107C>T
-
DPYD(NM_000110.3):c.484-4G>A
-
DPYD_000069
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/., -?/., ./., ?/.
20
6
c.496A>G
r.(?), r.496a>g
p.(Met166Val), p.Met166Val
-
-
benign, likely benign, VUS
g.98165091T>C
g.97699535T>C
A496G (M166V), DPYD(NM_000110.3):c.496A>G (p.M166V), M166V
-
DPYD_000002
normal enzyme activity (PBM cells), VKGL data sharing initiative Nederland
PubMed: Bell 2011
,
PubMed: Johnson 2002
,
PubMed: van Kuilenburg 2018
,
Journal: van Kuilenburg 2018
-
-
CLASSIFICATION record, Germline, Unknown
-, no
-
-
-
-
Gerard C.P. Schaafsma
,
Johan den Dunnen
,
VKGL-NL_Groningen
-?/., ?/.
3
-
c.557A>G
r.(?)
p.(Tyr186Cys)
-
-
likely benign, VUS
g.98165030T>C
g.97699474T>C
DPYD(NM_000110.3):c.557A>G (p.Y186C)
-
DPYD_000005
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Gerard C.P. Schaafsma
,
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
+?/+?
1
7
c.703C>T
r.703c>u
p.Arg235Trp
DPYD*8
-
likely pathogenic
g.98157332G>A
g.97691776G>A
C703T
-
DPYD_000010
reference haplotype DPYD*8 [703C>T]
PubMed: McLeod 1998
-
rs1801266
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.731A>C
r.(?)
p.(Glu244Ala)
-
-
VUS
g.98157304T>G
g.97691748T>G
DPYD(NM_000110.3):c.731A>C (p.E244A)
-
DPYD_000050
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
?/.
1
-
c.768T>G
r.(?)
p.(Ile256Met)
-
-
VUS
g.98144733A>C
g.97679177A>C
DPYD(NM_000110.3):c.768T>G (p.(Ile256Met))
-
DPYD_000029
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-/., -?/., ?/.
3
-
c.775A>G
r.(?)
p.(Lys259Glu)
-
-
benign, likely benign, VUS
g.98144726T>C
g.97679170T>C
DPYD(NM_000110.3):c.775A>G (p.K259E)
-
DPYD_000043
21 heterozygous, no homozygous;
Clinindb (India)
, VKGL data sharing initiative Nederland
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs45589337
CLASSIFICATION record, Germline
-
21/2773 individuals
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
,
Mohammed Faruq
-?/.
1
-
c.868A>G
r.(?)
p.(Lys290Glu)
-
-
likely benign
g.98060705T>C
-
DPYD(NM_000110.3):c.868A>G (p.K290E)
-
DPYD_000068
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
10
c.1003G>T
r.1003g>u
p.Val335Leu
DPYD*11
-
VUS
g.98058899C>A
g.97593343C>A
G1003T (V335L)
-
DPYD_000013
reference haplotype DPYD*11 [1003G>T]
PubMed: Mattison 2002
-
rs72549306
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.1129-15T>C
r.(=)
p.(=)
-
-
benign
g.98039541A>G
g.97573985A>G
DPYD(NM_000110.3):c.1129-15T>C
-
DPYD_000027
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
1
-
c.1140T>C
r.(?)
p.(Ala380=)
-
-
likely benign
g.98039515A>G
g.97573959A>G
DPYD(NM_000110.3):c.1140T>C (p.A380=)
-
DPYD_000042
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+
1
11
c.1156G>T
r.1156g>u
p.Glu386*
DPYD*12
-
pathogenic
g.98039499C>A
g.97573943C>A
G1156T (E386X)
-
DPYD_000015
reference haplotype DPYD*12 [62G>A; 1156G>T]
PubMed: Mattison 2002
-
rs78060119
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.1210G>T
r.(?)
p.(Val404Phe)
-
-
VUS
g.98039445C>A
g.97573889C>A
DPYD(NM_000110.3):c.1210G>T (p.V404F)
-
DPYD_000049
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.1217T>C
r.(?)
p.(Met406Thr)
-
-
VUS
g.98039438A>G
g.97573882A>G
DPYD(NM_000110.3):c.1217T>C (p.M406T)
-
DPYD_000041
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/+, +/., -/.
12
11
c.1236G>A
r.(=), r.spl?
p.(=), p.(Glu412=)
DPYD 1236GA
-
benign, benign (!), benign (!)Â , pathogenic
g.98039419C>T
g.97573863C>T
E412E, Glu412Glu
-
DPYD_000019
3 homozygous;
Clinindb (India)
, 71 heterozygous;
Clinindb (India)
,
3 more items
IP3 project, submitted,
PubMed: Henricks 2018
,
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs56038477
Germline, SUMMARY record
-
3/2795 individuals, 51/1103 patients, 71/2795 individuals
-
-
-
Johan den Dunnen
,
Jesse Swen
,
Mohammed Faruq
+/.
1
-
c.1256G>A
r.(?)
p.(Trp419Ter)
-
-
pathogenic
g.98039399C>T
g.97573843C>T
DPYD(NM_000110.3):c.1256G>A (p.W419*)
-
DPYD_000040
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
1
-
c.1360A>G
r.(?)
p.(Ile454Val)
-
-
likely benign
g.98015280T>C
-
DPYD(NM_000110.3):c.1360A>G (p.I454V)
-
DPYD_000063
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.1475C>T
r.(?)
p.(Ser492Leu)
-
-
VUS
g.98015165G>A
g.97549609G>A
-
-
DPYD_000053
1 heterozygous, no homozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs72549304
Germline
-
1/2795 individuals
-
-
-
Mohammed Faruq
-/-, -/., ?/.
9
13
c.1601G>A
r.(?), r.1601g>a
p.(Ser534Asn), p.Ser534Asn
DPYD*4
-
benign, VUS
g.97981421C>T
g.97515865C>T
DPYD(NM_000110.3):c.1601G>A (p.S534N), G1601A
-
DPYD_000003
conflicting interpretations of pathogenicity; 51 heterozygous, no homozygous;
Clinindb (India)
,
2 more items
PubMed: McLeod 1998
,
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs1801158
CLASSIFICATION record, Germline
-
51/2795 individuals
-
-
-
Gerard C.P. Schaafsma
,
Johan den Dunnen
,
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
,
Mohammed Faruq
?/.
1
-
c.1615G>A
r.(?)
p.(Gly539Arg)
-
-
VUS
g.97981407C>T
-
DPYD(NM_000110.3):c.1615G>A (p.G539R)
-
DPYD_000067
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/-, -/.
3
13
c.1627A=
r.(=), r.1627a=
p.(Ile543=), p.Ile543=
DPYD*2A
-
benign
g.97981395T=
-
-
-
DPYD_000000
2 more items
PubMed: Johnson 2002
,
PubMed: McLeod 1998
-
-
Germline, Unknown
-, yes
-
-
-
-
Johan den Dunnen
-/., -?/-?, ?/.
30
13
c.1627A>G
r.(?), r.1627a>g
p.(Ile543Val), p.Ile543Val
DPYD*2B, DPYD*5
-
benign, likely benign, VUS
g.97981395T>C
g.97515839T>C
A1627G, DPYD(NM_000110.3):c.1627A>G (p.I543V)
-
DPYD_000001
mixed haplotype DPYD*5/*6; haplotype assignment requested, VKGL data sharing initiative Nederland,
2 more items
pers. comm.,
PubMed: McLeod 1998
-
rs1801159
CLASSIFICATION record, Germline, Unknown
-
-
-
-
-
Gerard C.P. Schaafsma
,
Johan den Dunnen
,
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
?/.
1
-
c.1675A>G
r.(?)
p.(Met559Val)
-
-
VUS
g.97981347T>C
g.97515791T>C
DPYD(NM_000110.3):c.1675A>G (p.M559V)
-
DPYD_000048
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+, +/., +?/.
8
13
c.1679T>G
r.(?)
p.(Ile560Ser)
DPYD*13
-
benign (!), likely pathogenic, pathogenic
g.97981343A>C
g.97515787A>C
DPYD(NM_000110.3):c.1679T>G (p.I560S), I560S
-
DPYD_000016
reference haplotype DPYD*13 [1679T>G]; no activity, VKGL data sharing initiative Nederland,
1 more item
PubMed: Henricks 2018
,
PubMed: Johnson 2002
-
rs55886062
CLASSIFICATION record, Germline, SUMMARY record
-, yes
1/1103 patients
-
-
-
Johan den Dunnen
,
VKGL-NL_Rotterdam
,
VKGL-NL_Groningen
,
VKGL-NL_VUmc
+?/.
2
13
c.1700G>A
r.(?)
p.(Gly567Glu)
-
-
likely pathogenic
g.97981322C>T
g.97515766C>T
-
-
DPYD_000031
no DPD activity in cultured fibroblasts at 37oC
PubMed: van Kuilenburg 2018
,
Journal: van Kuilenburg 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.1740+2T>C
r.spl?
p.?
-
-
pathogenic
g.97981280A>G
g.97515724A>G
DPYD(NM_000110.3):c.1740+2T>C
-
DPYD_000039
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.1774C>T
r.(?)
p.(Arg592Trp)
-
-
VUS
g.97915746G>A
-
DPYD(NM_000110.3):c.1774C>T (p.R592W)
-
DPYD_000062
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
2
-
c.1896T>C
r.(=)
p.(=)
-
-
likely benign
g.97915624A>G
g.97450068A>G
-
-
DPYD_000052
204 heterozygous;
Clinindb (India)
, 4 homozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs17376848
Germline
-
204/2795 individuals, 4/2795 individuals
-
-
-
Mohammed Faruq
+/+, +/.
3
14
c.1898del
r.1898del
p.Pro633Glnfs*5
DPYD*3
-
pathogenic
g.97915623del
g.97450067del
delC1897
-
DPYD_000008
other deleterious variant on maternal allele expected but not identified, reduced RNA stability (NMD),
1 more item
PubMed: McLeod 1998
,
PubMed: Vreken 1997
-
rs72549303
Germline, Unknown
-, ?
<0.008
-
-
-
Johan den Dunnen
-/-
2
14i
c.1905+1G=
r.=
p.=
DPYD*5
-
benign
g.97915614C=
-
-
-
DPYD_000000
2 more items
pers. comm.,
PubMed: McLeod 1998
-
-
Germline, Unknown
-
-
-
-
-
Johan den Dunnen
+/+, +/., ./., ?/.
23
14i
c.1905+1G>A
r.(1741_1905del), r.1741_1905del, r.spl, r.spl?
p.(Asp581_Asn635del), p.(D581_N635del), p.?, p.Asp581_Asn635del
DPYD*1/*2A, DPYD*2A, DPYD*2B
ACMG
benign (!), pathogenic, pathogenic (recessive), VUS
g.97915614C>T
g.97450058C>T
DPYD(NM_000110.3):c.1905+1G>A, IVS14 G1A, IVS14+1G>A
-
DPYD_000006
drug response; 19 heterozygous, no homozygous;
Clinindb (India)
,
5 more items
IP3 project, submitted,
PubMed: Henricks 2018
,
PubMed: Johnson 1999
,
PubMed: Johnson 2002
,
7 more items
-
rs3918290
CLASSIFICATION record, Germline, SUMMARY record, Unknown
-, ?, yes
16/1103 patients, 19/2795 individuals
MaeII-
-
-
Johan den Dunnen
,
Zdenek Kleibl
,
VKGL-NL_Rotterdam
,
Maja Tarailo-Graovac
,
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
,
Jesse Swen
,
Mohammed Faruq
?/.
2
-
c.1925T>C
r.(?)
p.(Met642Thr)
-
-
VUS
g.97847998A>G
g.97382442A>G
DPYD(NM_000110.3):c.1925T>C (p.M642T)
-
DPYD_000026
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_VUmc
?/.
1
-
c.2058+1G>T
r.spl?
p.?
-
-
VUS
g.97839116C>A
-
DPYD(NM_000110.3):c.2058+1G>T
-
DPYD_000058
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
?/.
1
-
c.2071G>T
r.(?)
p.(Val691Leu)
-
-
VUS
g.97771841C>A
-
DPYD(NM_000110.3):c.2071G>T (p.V691L)
-
DPYD_000061
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+?/.
1
-
c.2121dup
r.(?)
p.(Ala708Cysfs*9)
-
-
likely pathogenic
g.97771797dup
-
DPYD(NM_000110.3):c.2121dupT (p.A708Cfs*9)
-
DPYD_000066
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.2161G>A
r.(?)
p.(Ala721Thr)
-
-
VUS
g.97771751C>T
g.97306195C>T
DPYD(NM_000110.3):c.2161G>A (p.A721T)
-
DPYD_000038
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.2180-9C>T
r.(=)
p.(=)
-
-
likely benign
g.97770943G>A
-
DPYD(NM_000110.3):c.2180-9C>T
-
DPYD_000057
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.2189A>G
r.(?)
p.(Asn730Ser)
-
-
likely benign
g.97770925T>C
-
DPYD(NM_000110.3):c.2189A>G (p.N730S)
-
DPYD_000056
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/., -?/-?
3
18
c.2194G>A
r.(?), r.219g>a
p.(Val732Ile), p.Val732Ile
DPYD*6
-
benign, likely benign
g.97770920C>T
g.97305364C>T
2194C>T, DPYD(NM_000110.3):c.2194G>A (p.V732I), DPYD-AS1(NR_046590.1):n.129-825C>T
-
DPYD_000007
mixed haplotype DPYD*5/*6, haplotype assignment requested, reference haplotype DPYD*6 [2194G>A],
1 more item
pers. comm.,
PubMed: McLeod 1998
-
rs1801160
CLASSIFICATION record, Germline, Unknown
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Groningen
?/.
1
-
c.2195T>G
r.(?)
p.(Val732Gly)
-
-
VUS
g.97770919A>C
g.97305363A>C
DPYD(NM_000110.3):c.2195T>G (p.V732G)
-
DPYD_000037
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.2279C>T
r.(?)
p.(Thr760Ile)
-
-
likely benign
g.97770835G>A
g.97305279G>A
DPYD(NM_000110.3):c.2279C>T (p.T760I)
-
DPYD_000055
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.2303C>A
r.(?)
p.(Thr768Lys)
-
-
VUS
g.97700547G>T
g.97234991G>T
DPYD(NM_000110.3):c.2303C>A (p.T768K)
-
DPYD_000054
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.2405G>T
r.(?)
p.(Gly802Val)
-
-
VUS
g.97700445C>A
g.97234889C>A
DPYD(NM_000110.3):c.2405G>T (p.G802V)
-
DPYD_000036
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
?/.
1
-
c.2434G>A
r.(?)
p.(Val812Ile)
-
-
VUS
g.97700416C>T
g.97234860C>T
-
-
DPYD_000051
-
-
-
rs371313778
Germline
-
-
-
-
-
Nedal Bukhari
?/.
2
-
c.2494A>G
r.(?)
p.(Thr832Ala)
-
-
VUS
g.97658753T>C
g.97193197T>C
DPYD(NM_000110.3):c.2494A>G (p.T832A, p.(Thr832Ala))
-
DPYD_000024
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_Rotterdam
?/.
1
-
c.2551G>A
r.(?)
p.(Gly851Arg)
-
-
VUS
g.97658696C>T
-
DPYD(NM_000110.3):c.2551G>A (p.G851R)
-
DPYD_000065
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/., ?/.
2
-
c.2567C>T
r.(?)
p.(Thr856Ile)
-
-
likely benign, VUS
g.97658680G>A
g.97193124G>A
DPYD(NM_000110.3):c.2567C>T (p.T856I, p.(Thr856Ile))
-
DPYD_000023
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_Rotterdam
?/.
1
-
c.2590C>G
r.(?)
p.(Pro864Ala)
-
-
VUS
g.97658657G>C
g.97193101G>C
DPYD(NM_000110.3):c.2590C>G (p.(Pro864Ala))
-
DPYD_000022
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-?/.
1
-
c.2623A>C
r.(?)
p.(Lys875Gln)
-
-
likely benign
g.97564188T>G
g.97098632T>G
DPYD(NM_000110.3):c.2623A>C (p.K875Q)
-
DPYD_000035
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/-, -?/.
3
21
c.2657G=
r.(=), r.2657g=
p.Arg886=
DPYD*1, DPYD*9A
-
benign, likely benign
g.97564154C=
-
-
-
DPYD_000000
3 more items
PubMed: Johnson 2002
,
PubMed: McLeod 1998
-
-
Germline, Unknown
-
-
-
-
-
Johan den Dunnen
+/., +?/., ?/?
3
21
c.2657G>A
r.(?), r.2657g>a
p.Arg886His
DPYD*9B
-
likely pathogenic, NA, VUS
g.97564154C>T
g.97098598C>T
G2657A, G2758A (R886H)
-
DPYD_000000
expression cloning no detecable DPD activity,
1 more item
PubMed: McLeod 1998
,
PubMed: Vreken 1997
-
rs1801267
Germline, In vitro (cloned), Unknown
-, yes
-
-
-
-
Johan den Dunnen
?/.
1
-
c.2807G>A
r.(?)
p.(Gly936Asp)
-
-
VUS
g.97547986C>T
g.97082430C>T
-
-
DPYD_000047
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/+, +/., +?/., ?/.
13
22
c.2846A>T
r.(2846a>u), r.(?)
p.(Asp949Val)
DPYD 2846AT
-
benign (!), likely pathogenic, pathogenic, VUS
g.97547947T>A
g.97082391T>A
DPYD(NM_000110.3):c.2846A>T (p.D949V)
-
DPYD_000004
drug response; 2 heterozygous, no homozygous;
Clinindb (India)
, VKGL data sharing initiative Nederland,
3 more items
IP3 project, submitted,
PubMed: Henricks 2018
,
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs67376798
CLASSIFICATION record, Germline, SUMMARY record
-
17/1103 patients, 2/2789 individuals
-
-
-
Gerard C.P. Schaafsma
,
Johan den Dunnen
,
VKGL-NL_Rotterdam
,
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
Jesse Swen
,
Mohammed Faruq
-?/.
1
-
c.2931C>G
r.(?)
p.(Thr977=)
-
-
likely benign
g.97544679G>C
g.97079123G>C
DPYD(NM_000110.3):c.2931C>G (p.T977=)
-
DPYD_000034
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+?/+?
1
23
c.2983G>T
r.2983g>t
p.Val995Phe
DPYD*10
-
likely pathogenic
g.97544627C>A
g.97079071C>A
G2983T
-
DPYD_000012
reference haplotype DPYD*10 [2983G>T]
PubMed: McLeod 1998
-
rs1801268
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
-
c.2998G>A
r.(?)
p.(Asp1000Asn)
-
-
VUS
g.97544612C>T
g.97079056C>T
DPYD(NM_000110.3):c.2998G>A (p.D1000N)
-
DPYD_000021
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.3052C>G
r.(?)
p.(Pro1018Ala)
-
-
likely benign
g.97544558G>C
g.97079002G>C
DPYD(NM_000110.3):c.3052C>G (p.P1018A)
-
DPYD_000033
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+?/.
1
-
c.3067C>T
r.(?)
p.(Pro1023Ser)
-
-
likely pathogenic
g.97544543G>A
-
-
-
DPYD_000064
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.3074_3076dup
r.(?)
p.(Ter1026CysextTer1)
-
-
VUS
g.97544535_97544537dup
g.97078979_97078981dup
DPYD(NM_000110.3):c.3074_3076dupGTT (p.C1025dup)
-
DPYD_000032
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
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