Global Variome shared LOVD
CDH1 (cadherin 1, type 1, E-cadherin (epithelial))
LOVD v.3.0 Build 25c [
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Curator:
Carla Oliveira
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Unique variants in the CDH1 gene
CDH1 (cadherin 1, type 1, E-cadherin (epithelial))
EPCAM (epithelial cell adhesion molecule)
GALNT12 (UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalacto...)
MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli))
MLH3 (mutL homolog 3 (E. coli))
MSH2 (mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli))
MSH6 (mutS homolog 6 (E. coli))
PMS2 (PMS2 postmeiotic segregation increased 2 (S. cerevisiae))
The variants shown are described using the NM_004360.3 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
Classification method
: The method used for the clinical classification of this variant.
All options:
ACMG
ACGS
EAHAD-CFDB
ENIGMA
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, sex-linked and 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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372 entries on 4 pages. Showing entries 1 - 100.
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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
+/., -/.
2
_1
c.-472delA
r.(=)
p.(=)
-
benign, pathogenic
g.68770847del
g.68736944del
-347G>GA, -472G/GA
-
CDH1_000079
expression cloning normal activity in luciferase promoter construct,
1 more item
PubMed: Nakamura 2002
,
PubMed: Shin 2004
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
_1
c.-288delT
r.(=)
p.(=)
-
pathogenic
g.68771031del
g.68737128del
-
-
CDH1_000078
expression cloning 0.8 activity in luciferase promoter construct
PubMed: Nakamura 2002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
_1
c.-285C>A
r.(=)
p.(=)
-
pathogenic
g.68771034C>A
g.68737131C>A
-
-
CDH1_000077
expression cloning 0.66 activity in luciferase promoter construct
PubMed: Nakamura 2002
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
_1
c.-126_-125delinsAA
r.(=)
p.(=)
-
VUS
g.68771193_68771194delinsAA
g.68737290_68737291delinsAA
-124-5_6delinsAA
-
CDH1_000149
not in 609 Brazilian controls
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
Germline
-
1/196 cases
-
-
-
Maria Rita Passos-Bueno
?/.
1
1
c.-84G>A
r.(=)
p.(=)
-
VUS
g.68771235G>A
g.68737332G>A
-
-
CDH1_000132
-
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
Germline
-
-
-
-
-
Maria Rita Passos-Bueno
?/.
4
1
c.-71C>G
r.(=)
p.(=)
-
VUS
g.68771248C>G
g.68737345C>G
-
-
CDH1_000128
-
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
Germline
-
16/1218 chromosomes
-
-
-
Maria Rita Passos-Bueno
?/.
1
1
c.-64G>T
r.(=)
p.(=)
-
VUS
g.68771255G>T
g.68737352G>T
-
-
CDH1_000097
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
+/., -?/.
2
1
c.-54G>C
r.(=), r.(?)
p.(=)
-
likely benign, pathogenic
g.68771265G>C
g.68737362G>C
-
-
CDH1_000076
expression cloning 0.66 activity in luciferase promoter construct,
1 more item
PubMed: Nakamura 2002
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Nijmegen
+/.
1
1
c.3G>A
r.(?)
p.(Met1?)
-
pathogenic
g.68771321G>A
g.68737418G>A
-
-
CDH1_000197
-
PubMed: Pandalai 2011
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
1
c.3G>C
r.(?)
p.(Met1?)
-
pathogenic
g.68771321G>C
g.68737418G>C
M1I
-
CDH1_000060
-
PubMed: Suriano 2005
-
-
Unknown
-
-
-
-
-
Johan den Dunnen
?/.
1
1
c.22C>T
r.(?)
p.(Leu8Phe)
-
VUS
g.68771340C>T
g.68737437C>T
-
-
CDH1_000196
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
-?/.
2
-
c.27G>A
r.(?)
p.(Ser9=)
-
likely benign
g.68771345G>A
g.68737442G>A
CDH1(NM_004360.3):c.27G>A (p.S9=)
-
CDH1_000156
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_VUmc
+/.
1
1
c.41del
r.(?)
p.(Leu14Argfs*42)
-
pathogenic
g.68771359del
g.68737456del
-
-
CDH1_000061
-
PubMed: Bacani 2006
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
-?/.
1
-
c.41_46dup
r.(?)
p.(Leu14_Leu15dup)
-
likely benign
g.68771359_68771364dup
g.68737456_68737461dup
CDH1(NM_004360.3):c.41_46dupTGCTGC (p.L14_L15dup)
-
CDH1_000340
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
1
c.44dup
r.(?)
p.(Gln16Alafs*18)
-
pathogenic
g.68771362dup
g.68737459dup
-
-
CDH1_000062
-
PubMed: Oliveira 2002
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
-?/.
1
-
c.44_46del
r.(?)
p.(Leu15del)
-
likely benign
g.68771362_68771364del
g.68737459_68737461del
CDH1(NM_004360.3):c.44_46delTGC (p.L15del)
-
CDH1_000378
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+/., +?/.
3
1i
c.48+1G>A
r.spl, r.spl?
p.?
ACMG
pathogenic
g.68771367G>A
g.68737464G>A
IVS1+1G>A
-
CDH1_000195
ACMG grading: PVS1, PM2, PP5 (=class 5)
PubMed: Pandalai 2011
,
PubMed: Petridis 2014
-
-
Germline
?
-
-
-
-
Johan den Dunnen
,
Andreas Laner
-/., -?/.
3
-
c.48+5C>G
r.spl?
p.?
-
benign, likely benign
g.68771371C>G
g.68737468C>G
CDH1(NM_004360.3):c.48+5C>G
-
CDH1_000158
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
-/.
8
1i
c.48+6C>T
r.(=), r.(?)
p.(=)
-
benign
g.68771372C>T
g.68737469C>T
CDH1(NM_004360.3):c.48+6C>T
-
CDH1_000159
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
,
Maximiliano Zeballos
,
Carlos Vaccaro
-?/.
1
1i
c.48+7C>G
r.(=)
p.(=)
-
likely benign
g.68771373C>G
g.68737470C>G
-
-
CDH1_000133
conservation, in silico analysis: IARC-2 likely not pathogenic
-
-
-
Unknown
?
-
-
-
-
Pränatalmedizin & Genetik MVZ Nürnberg
?/.
1
1i
c.48+22G>A
r.(=)
p.(=)
-
VUS
g.68771388G>A
g.68737485G>A
-
-
CDH1_000129
not in 609 Brazilian controls
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
Germline
-
-
-
-
-
Maria Rita Passos-Bueno
+/.
1
2
c.54del
r.(?)
p.(Ser19Leufs*37)
-
pathogenic
g.68772205del
g.68738302del
-
-
CDH1_000065
-
PubMed: Humar 2002
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
+/.
1
2
c.59G>A
r.(?)
p.(Trp20*)
-
pathogenic
g.68772210G>A
g.68738307G>A
-
-
CDH1_000067
-
PubMed: Richards 1999
,
OMIM:var0009
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
+/.
2
-
c.60G>A
r.(?)
p.(Trp20*)
-
pathogenic
g.68772211G>A
g.68738308G>A
-
-
CDH1_000376
1 homozygous;
Clinindb (India)
, 2 heterozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs786203576
Germline
-
1/2748 individuals, 2/2748 individuals
-
-
-
Mohammed Faruq
?/.
1
-
c.61C>G
r.(?)
p.(Leu21Val)
-
VUS
g.68772212C>G
g.68738309C>G
-
-
CDH1_000199
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/12486 controls
-
-
-
Yukihide Momozawa
+/.
1
2
c.70G>T
r.(?)
p.(Glu24*)
-
pathogenic
g.68772221G>T
g.68738318G>T
-
-
CDH1_000069
-
PubMed: Guilford 1999
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
+/.
1
-
c.76G>T
r.(?)
p.(Glu26*)
-
pathogenic
g.68772227G>T
g.68738324G>T
-
-
CDH1_000377
8 heterozygous, no homozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs786201058
Germline
-
8/2746 individuals
-
-
-
Mohammed Faruq
?/.
1
-
c.80C>G
r.(?)
p.(Pro27Arg)
-
VUS
g.68772231C>G
g.68738328C>G
-
-
CDH1_000200
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/12486 controls
-
-
-
Yukihide Momozawa
-?/., ./., ?/.
6
2
c.88C>A
r.(?)
p.(Pro30Thr)
-
likely benign, VUS
g.68772239C>A
g.68738336C>A
CDH1(NM_004360.3):c.88C>A (p.P30T)
-
CDH1_000135
VKGL data sharing initiative Nederland
Thibodeau lab (Mayo Clinic)
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Melissa DeRycke
,
VKGL-NL_Rotterdam
,
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
?/.
1
2
c.130C>A
r.(?)
p.(Arg44Ser)
-
VUS
g.68772281C>A
g.68738378C>A
-
-
CDH1_000198
not in 7051 cases breast cancer
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
2/11241 controls
-
-
-
Yukihide Momozawa
?/.
2
2
c.154C>T
r.(?)
p.(=)
-
VUS
g.68772305C>T
g.68738402C>T
-
-
CDH1_000201
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs374569322
Germline
-
1/12486 controls, 1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
+/.
1
-
c.163+2T>A
r.spl?
p.?
-
pathogenic
g.68772316T>A
g.68738413T>A
-
-
CDH1_000175
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
2i
c.163+43G>T
r.(=)
p.(=)
-
benign
g.68772357G>T
g.68738454G>T
-
-
CDH1_000093
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
-/.
2
2i
c.164-14627G>A
r.(?)
p.(=)
-
benign
g.68820946G>A
g.68787043G>A
-
-
CDH1_000369
-
-
-
-
Germline
-
-
-
-
-
Maximiliano Zeballos
?/.
1
-
c.164-32A>G
r.spl?
p.(=)
-
VUS
g.68835541A>G
g.68801638A>G
-
-
CDH1_000382
-
-
-
rs762799038
Germline
-
-
-
-
-
CEGH-CEL
./.
1
3
c.164T>G
r.spl?
p?
-
VUS
g.68835573T>G
g.68801670T>G
-
-
CDH1_000136
-
Thibodeau lab (Mayo Clinic)
-
-
Germline
-
-
-
-
-
Melissa DeRycke
+/., -/., ?/.
5
3
c.185G>T
r.(?)
p.(Gly62Val)
-
benign, pathogenic, VUS
g.68835594G>T
g.68801691G>T
-
-
CDH1_000033
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
,
PubMed: Shinmura 1999
-
rs786203727
Germline
-
1/11241 controls, 14/7051 cases breast cancer, 43/12490 controls, 47/11241 controls
-
-
-
Global Variome, with Curator vacancy
,
Yukihide Momozawa
+/.
2
3
c.187C>T
r.(?)
p.(Arg63*)
-
pathogenic
g.68835596C>T
g.68801693C>T
-
-
CDH1_000035
1 heterozygous, no homozygous;
Clinindb (India)
PubMed: Gayther 1998
,
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs587783047
Germline
-
1/2795 individuals
-
-
-
Global Variome, with Curator vacancy
,
Mohammed Faruq
-/.
1
3
c.188G>A
r.(?)
p.(Arg63Gln)
-
benign
g.68835597G>A
g.68801694G>A
-
-
CDH1_000370
-
-
-
-
Germline
-
-
-
-
-
Maximiliano Zeballos
+/.
1
3
c.190C>T
r.(?)
p.(Gln64*)
-
pathogenic
g.68835599C>T
g.68801696C>T
-
-
CDH1_000037
-
PubMed: Guilford 1999
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
./., ?/.
2
3
c.214G>A
r.(?)
p.(Asp72Asn)
-
VUS
g.68835623G>A
g.68801720G>A
-
-
CDH1_000137
not in 7051 cases breast cancer
Thibodeau lab (Mayo Clinic),
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs35606263
Germline
-
1/11241 controls
-
-
-
Yukihide Momozawa
,
Melissa DeRycke
+/.
1
3
c.220C>T
r.(?)
p.(Arg74*)
-
pathogenic
g.68835629C>T
g.68801726C>T
-
-
CDH1_000202
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
?/.
1
3
c.226A>G
r.(?)
p.(Lys76Glu)
-
VUS
g.68835635A>G
g.68801732A>G
-
-
CDH1_000203
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
?/.
1
-
c.233G>A
r.(?)
p.(Gly78Asp)
-
VUS
g.68835642G>A
g.68801739G>A
-
-
CDH1_000205
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs587781404
Germline
-
1/12490 controls
-
-
-
Yukihide Momozawa
?/.
1
3
c.235A>G
r.(?)
p.(Thr79Ala)
-
VUS
g.68835644A>G
g.68801741A>G
-
-
CDH1_000204
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs745327620
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
+/.
1
3
c.241_244dup
r.(?)
p.(Val82Glyfs*13)
-
pathogenic
g.68835650_68835653dup
g.68801747_68801750dup
241_244dupGGTG
-
CDH1_000053
-
PubMed: Christgen 2008
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
?/.
1
-
c.242_244del
r.(?)
p.(Gly81del)
-
VUS
g.68835651_68835653del
g.68801748_68801750del
242_244delGTG
-
CDH1_000336
-
-
-
-
Unknown
-
-
-
-
-
IMGAG
?/.
1
-
c.244G>T
r.(?)
p.(Val82Leu)
-
VUS
g.68835653G>T
g.68801750G>T
-
-
CDH1_000207
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/12490 controls
-
-
-
Yukihide Momozawa
?/.
1
-
c.269G>A
r.(?)
p.(Arg90Gln)
-
VUS
g.68835678G>A
g.68801775G>A
-
-
CDH1_000208
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs587782647
Germline
-
1/12490 controls
-
-
-
Yukihide Momozawa
+/.
2
3
c.283C>T
r.(?)
p.(Gln95*)
-
pathogenic
g.68835692C>T
g.68801789C>T
-
-
CDH1_000055
-
PubMed: Dassaulx-Garin 2001
-
-
Germline, Unknown
-
-
-
-
-
Global Variome, with Curator vacancy
,
Nancy Uhrhammer
?/.
1
-
c.294C>T
r.(?)
p.(=)
-
VUS
g.68835703C>T
g.68801800C>T
-
-
CDH1_000209
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/12490 controls
-
-
-
Yukihide Momozawa
?/.
1
3
c.298G>A
r.(?)
p.(Val100Ile)
-
VUS
g.68835707G>A
g.68801804G>A
-
-
CDH1_000206
not in 7051 cases breast cancer
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/11241 controls
-
-
-
Yukihide Momozawa
-?/.
1
-
c.303C>T
r.(?)
p.(Tyr101=)
-
likely benign
g.68835712C>T
g.68801809C>T
CDH1(NM_004360.3):c.303C>T (p.Y101=)
-
CDH1_000379
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-?/., ?/.
3
3
c.324A>G
r.(=), r.(?)
p.(=), p.(Arg108=)
-
likely benign, VUS
g.68835733A>G
g.68801830A>G
-
-
CDH1_000130
VKGL data sharing initiative Nederland
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
CLASSIFICATION record, Germline
-
6/1218 chromosomes
-
-
-
Maria Rita Passos-Bueno
,
VKGL-NL_Nijmegen
?/.
1
3
c.326A>T
r.(?)
p.(Lys109Met)
-
VUS
g.68835735A>T
g.68801832A>T
-
-
CDH1_000210
not in 7051 cases breast cancer
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/11241 controls
-
-
-
Yukihide Momozawa
+/.
1
-
c.326del
r.(?)
p.(Lys109Serfs*8)
-
pathogenic
g.68835735del
g.68801832del
-
-
CDH1_000371
-
-
-
-
Germline
-
-
-
-
-
Carlos Vaccaro
-?/.
1
-
c.337A>G
r.(?)
p.(Lys113Glu)
-
likely benign
g.68835746A>G
g.68801843A>G
-
-
CDH1_000341
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.344C>T
r.(?)
p.(Thr115Met)
-
VUS
g.68835753C>T
g.68801850C>T
-
-
CDH1_000212
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs370973869
Germline
-
1/12490 controls
-
-
-
Yukihide Momozawa
-/., ?/.
5
3
c.345G>A
r.(=), r.(?)
p.(=), p.(Thr115=)
-
benign, VUS
g.68835754G>A
g.68801851G>A
CDH1(NM_004360.3):c.345G>A (p.T115=)
-
CDH1_000131
VKGL data sharing initiative Nederland
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
CLASSIFICATION record, Germline
-
6/1218 chromosomes
-
-
-
Maria Rita Passos-Bueno
,
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
+/.
1
3
c.353C>G
r.(?)
p.(Thr118Arg)
-
pathogenic
g.68835762C>G
g.68801859C>G
-
-
CDH1_000056
-
PubMed: Suriano 2006
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
?/.
1
3
c.353C>T
r.(?)
p.(Thr118Ile)
-
VUS
g.68835762C>T
g.68801859C>T
-
-
CDH1_000211
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
+?/.
1
3
c.360del
r.(?)
p.(His121Thrfs*94)
ACMG
likely pathogenic (dominant)
g.68835769del
g.68801866del
360delG
-
CDH1_000375
-
-
-
-
Germline
-
-
-
-
-
Valli De Re
?/.
2
3
c.363C>G
r.(?)
p.(His121Gln)
-
VUS
g.68835772C>G
g.68801869C>G
-
-
CDH1_000213
not in 7051 cases breast cancer
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/11241 controls, 2/12490 controls
-
-
-
Yukihide Momozawa
?/.
4
3
c.370C>T
r.(?)
p.(Arg124Cys)
-
VUS
g.68835779C>T
g.68801876C>T
-
-
CDH1_000214
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs748086082
Germline
-
1/11241 controls, 2/7051 cases breast cancer, 4/12490 controls, 7/11241 controls
-
-
-
Yukihide Momozawa
+/.
1
3
c.372_377del
r.(?)
p.(Pro126_Pro127del)
-
pathogenic
g.68835781_68835786del
g.68801878_68801883del
372_377delCCCCCC
-
CDH1_000057
-
PubMed: Keller 1999
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
?/.
1
3
c.374C>T
r.(?)
p.(Pro125Leu)
-
VUS
g.68835783C>T
g.68801880C>T
-
-
CDH1_000215
not in 7051 cases breast cancer
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/11241 controls
-
-
-
Yukihide Momozawa
-/., ?/.
3
3
c.377C>A
r.(?)
p.(Pro126Gln)
-
benign, VUS
g.68835786C>A
g.68801883C>A
-
-
CDH1_000216
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs746703615
Germline
-
2/11241 controls, 4/7051 cases breast cancer, 5/12490 controls
-
-
-
Yukihide Momozawa
+/.
1
3
c.377del
r.(?)
p.(Pro126Argfs*89)
-
pathogenic
g.68835786del
g.68801883del
377delC
-
CDH1_000058
-
PubMed: Keller 1999
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
+/.
1
3
c.377dup
r.(?)
p.(Pro127Alafs*41)
-
pathogenic
g.68835786dup
g.68801883dup
-
-
CDH1_000094
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
-/.
1
3
c.378G>A
r.(?)
p.(=)
-
benign
g.68835787G>A
g.68801884G>A
-
-
CDH1_000217
not in 7051 cases breast cancer
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs786201504
Germline
-
1/11241 controls
-
-
-
Yukihide Momozawa
+/.
1
3
c.382del
r.(?)
p.(His128Ilefs*87)
-
pathogenic
g.68835791del
g.68801888del
-
-
CDH1_000059
-
PubMed: Brooks-Wilson 2004
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
+?/.
1
3i
c.387+5G>A
r.spl?
p.?
-
likely pathogenic
g.68835801G>A
g.68801898G>A
-
-
CDH1_000080
-
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
Germline
-
-
-
-
-
Maria Rita Passos-Bueno
-?/.
1
-
c.387+18T>C
r.(=)
p.(=)
-
likely benign
g.68835814T>C
g.68801911T>C
CDH1(NM_004360.3):c.387+18T>C
-
CDH1_000342
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
?/.
2
3i
c.387+27C>T
r.(=)
p.(=)
-
VUS
g.68835823C>T
g.68801920C>T
-
-
CDH1_000117
-
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
Germline
-
5/1218 chromosomes
-
-
-
Maria Rita Passos-Bueno
-?/.
1
-
c.387+28G>A
r.(=)
p.(=)
-
likely benign
g.68835824G>A
g.68801921G>A
-
-
CDH1_000343
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
-
c.387+76C>A
r.(=)
p.(=)
-
benign
g.68835872C>A
g.68801969C>A
-
-
CDH1_000373
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
4
c.400G>A
r.(?)
p.(Gly134Arg)
-
VUS
g.68842339G>A
g.68808436G>A
-
-
CDH1_000218
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
?/.
1
4
c.431A>G
r.(?)
p.(Asn144Ser)
-
VUS
g.68842370A>G
g.68808467A>G
-
-
CDH1_000219
not in 7051 cases breast cancer
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/11241 controls
-
-
-
Yukihide Momozawa
?/.
1
4
c.438T>C
r.(?)
p.(=)
-
VUS
g.68842377T>C
g.68808474T>C
-
-
CDH1_000220
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
?/.
2
4
c.456G>C
r.(?)
p.(Gln152His)
-
VUS
g.68842395G>C
g.68808492G>C
-
-
CDH1_000221
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs745589555
Germline
-
1/12490 controls, 3/7051 cases breast cancer
-
-
-
Yukihide Momozawa
-/.
1
-
c.480C>T
r.(?)
p.(=)
-
benign
g.68842419C>T
g.68808516C>T
-
-
CDH1_000223
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs769371658
Germline
-
2/12490 controls
-
-
-
Yukihide Momozawa
?/.
1
-
c.499G>A
r.(?)
p.(Glu167Lys)
-
VUS
g.68842438G>A
g.68808535G>A
CDH1(NM_004360.3):c.499G>A (p.E167K)
-
CDH1_000160
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+/.
1
4
c.515C>G
r.(?)
p.(Pro172Arg)
-
pathogenic
g.68842454C>G
g.68808551C>G
-
-
CDH1_000063
-
PubMed: Avizienyte 2001
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
+/.
1
4
c.521dup
r.(?)
p.(Asn174Lysfs*25)
-
pathogenic
g.68842460dup
g.68808557dup
-
-
CDH1_000064
-
PubMed: Masciari 2007
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
-?/.
1
-
c.531+3A>G
r.spl?
p.?
-
likely benign
g.68842473A>G
g.68808570A>G
-
-
CDH1_000344
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/., ?/.
5
4i
c.531+10G>C
r.(=)
p.(=)
-
benign, VUS
g.68842480G>C
g.68808577G>C
CDH1(NM_004360.3):c.531+10G>C
-
CDH1_000118
VKGL data sharing initiative Nederland
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
CLASSIFICATION record, Germline
-
35/1218 chromosomes
-
-
-
Maria Rita Passos-Bueno
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
?/.
1
4i
c.532-27dup
r.(=)
p.(=)
-
VUS
g.68842569dup
g.68808666dup
532-27_-26insA
-
CDH1_000119
not in 609 Brazilian controls
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
Germline
-
1/219 cases
-
-
-
Maria Rita Passos-Bueno
-/., -?/., ?/.
7
4i
c.532-18C>T
r.(=)
p.(=)
-
benign, likely benign, VUS
g.68842578C>T
g.68808675C>T
CDH1(NM_004360.3):c.532-18C>T
-
CDH1_000095
VKGL data sharing initiative Nederland
PubMed: Brito 2015
,
Journal: Brito 2015
-
-
CLASSIFICATION record, Germline
?
4/1218 chromosomes
-
-
-
Maria Rita Passos-Bueno
,
Andreas Laner
,
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
+?/.
1
-
c.532-1G>T
r.(?)
p.(?)
ACMG
likely pathogenic
g.68842595G>T
g.68808692G>T
-
-
CDH1_000372
ACMG: PVS1,PM2
-
-
-
Germline
-
-
-
-
-
Andreas Laner
+?/.
1
-
c.535A>G
r.(?)
p.(Lys179Glu)
-
likely pathogenic
g.68842599A>G
g.68808696A>G
-
-
CDH1_000177
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
3
5
c.546A>C
r.(?)
p.(Lys182Asn)
-
benign
g.68842610A>C
g.68808707A>C
-
-
CDH1_000222
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs201141645
Germline
-
10/7051 cases breast cancer, 16/12489 controls, 19/11241 controls
-
-
-
Yukihide Momozawa
?/.
1
5
c.576C>A
r.(?)
p.(=)
-
VUS
g.68842640C>A
g.68808737C>A
-
-
CDH1_000224
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
+/.
1
-
c.583C>T
r.(?)
p.(Gln195*)
-
pathogenic
g.68842647C>T
g.68808744C>T
-
-
CDH1_000194
-
-
-
-
Unknown
-
-
-
-
-
IMGAG
+/.
1
5
c.586G>T
r.(?)
p.(Gly196*)
-
pathogenic
g.68842650G>T
g.68808747G>T
-
-
CDH1_000066
-
PubMed: Guilford 1999
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
?/.
1
-
c.600C>T
r.(?)
p.(=)
-
VUS
g.68842664C>T
g.68808761C>T
-
-
CDH1_000226
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/12489 controls
-
-
-
Yukihide Momozawa
-/.
5
5
c.604G>A
r.(?)
p.(Val202Ile)
-
benign
g.68842668G>A
g.68808765G>A
CDH1(NM_004360.3):c.604G>A (p.V202I)
-
CDH1_000225
VKGL data sharing initiative Nederland
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs546716073
CLASSIFICATION record, Germline
-
4/7051 cases breast cancer, 5/11241 controls, 6/12489 controls
-
-
-
Yukihide Momozawa
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
?/.
1
-
c.614T>C
r.(?)
p.(Phe205Ser)
-
VUS
g.68842678T>C
g.68808775T>C
-
-
CDH1_000178
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
3
5
c.636A>G
r.(?)
p.(=)
-
benign
g.68842700A>G
g.68808797A>G
-
-
CDH1_000227
-
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
rs758991562
Germline
-
2/12489 controls, 2/7051 cases breast cancer, 3/11241 controls
-
-
-
Yukihide Momozawa
+/.
1
5
c.641T>C
r.(?)
p.(Leu214Pro)
-
pathogenic
g.68842705T>C
g.68808802T>C
-
-
CDH1_000068
-
PubMed: Suriano 2006
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
?/.
1
5
c.652G>A
r.(?)
p.(Glu218Lys)
-
VUS
g.68842716G>A
g.68808813G>A
-
-
CDH1_000228
not in 11241 controls
PubMed: Momozawa 2018
,
Journal: Momozawa 2018
-
-
Germline
-
1/7051 cases breast cancer
-
-
-
Yukihide Momozawa
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This database is one of the
InSiGHT
gene variant databases
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