Global Variome shared LOVD
TCF4 (transcription factor 4)
LOVD v.3.0 Build 25c [
Current LOVD status
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Curators:
Irina Giurgea
and
Johan den Dunnen
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Unique variants in the TCF4 gene
The variants shown are described using the NM_001083962.1 transcript reference sequence.
Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect
: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
Reported
: The number of times this variant has been reported in the database.
Exon
: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
DNA change (cDNA)
: description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.
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
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'
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.
171 entries on 2 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
-
c.?
-
r.?
p.?
-
pathogenic
g.?
-
t(14;18)(q13.1;q21.2)
-
TCF4_000000
translocation chromosomes 14;20
PubMed: Marangi 2011
-
-
De novo
-
-
-
-
-
Irina Giurgea
./.
1
_1_20_
c.-24759932_*4532602del
-
r.0?
p.0?
-
pathogenic
g.48362664_78015180del
-
-
-
ATP8B1_000025
mosaicism, hemizygous in 0.46 cells
PubMed: DDDS 2015
,
Journal: DDDS 2015
-
-
Somatic
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.-47853G>C
-
r.(?)
p.(=)
-
benign
g.53303101C>G
g.55635870=
TCF4(NM_001243226.2):c.28G>C (p.A10P)
-
TCF4_000166
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-/.
1
-
c.-47597G>A
-
r.(?)
p.(=)
-
benign
g.53302845C>T
g.55635614C>T
TCF4(NM_001243226.3):c.195+89G>A
-
TCF4_000177
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/.
1
-
c.-43559del
-
r.(?)
p.(=)
-
benign
g.53298807del
g.55631576del
TCF4(NM_001243226.2):c.196-188delA
-
TCF4_000164
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
?/.
1
-
c.-43295C>T
-
r.(?)
p.(=)
-
VUS
g.53298543G>A
g.55631312G>A
TCF4(NM_001243226.3):c.272C>T (p.T91I)
-
TCF4_000163
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+/.
1
_1_10i
c.(?_-612)_789+?del
-
r.0?
p.0?
-
pathogenic
g.?
-
del ex1-10
-
TCF4_000008
0.5 Mb deletion
PubMed: Brockschmidt 2007
-
-
De novo
-
-
-
-
-
Johan den Dunnen
-/., -?/.
2
-
c.-387del
-
r.(?)
p.(=)
-
benign, likely benign
g.53255646del
g.55588415del
TCF4(NM_001083962.1):c.-387delT
-
TCF4_000132
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_AMC
+/.
21
_1_20_
c.(?_-1)_(*1_?)del
-
r.0?, r.0
p.0?, p.0
-
pathogenic
g.?, g.(38100000_38400000)_(50200000_57600000)del, g.(51000000_51994667)_(58706460_59000000)del,
2 more items
-
del RP11-397A16, g.50552638_517423685, del 18q21.1-q22.3, hg18? g.50248665_56248665, large del,
3 more items
18q21.1-q22.1del, 18q21.2-q22.1del
TCF4_000000, TCF4_000009, TCF4_000015, TCF4_000016
1.8 Mb deletion, 1.2 Mb deletion, 6.2 Mb deletion, >13 Mb deletion, >10 Mb deletion, del 11 Mb,
8 more items
PubMed: Amiel 2007
,
PubMed: Zweier 2007
;
PubMed: Peippo 2006
,
PubMed: Andrieux 2008
, Gustavsson,
5 more items
-
-
De novo, Somatic
-
-
-
-
-
Johan den Dunnen
,
Irina Giurgea
+/.
1
3i
c.145+1_146-1::NM_032221.4:c.(-24+1_-23-1)
-
r.?
p.?
-
pathogenic
g.(53131369_53252510)_qterdelins[NC_000020.10:g.(40180000_40246978)_qter]
-
TCF4-CHD6 fusion
t(18;20)(q21.1;q11.2)
TCF4_000000
fusion transcript TCF4::CHD6 ?
PubMed: Kalscheuer 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
6
2i
c.72+804_73-747[ins(51_?)]
GCT[>40]
r.(?)
p.(?)
-
pathogenic (dominant), pathogenic (!), pathogenic
g.53253330_5325347[ins(51_?)]
-
expanded >40 units
-
TCF4_000150
incomplete penetrance
PubMed: Mootha 2014
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/.
1
1i
c.72+804_73-747[ins(81_?)]
GCT[>50]
r.(?)
p.(?)
-
pathogenic (!)
g.53253330_5325347[ins(81_?)]
-
-
-
TCF4_000000
18/344 cases are homozygous; >76-fold increased risk
PubMed: Zarouchlioti 2018
-
-
Germline
yes
344/450 cases FECD
-
-
-
Johan den Dunnen
-/.
1
2i
c.72+817_73-802GCT[12]
-
r.(?)
p.(=)
-
benign
g.53253385_53253459AGC[12]
-
-
-
TCF4_000154
-
PubMed: Mootha 2014
-
-
Germline
no
-
-
-
-
Johan den Dunnen
-/.
1
2i
c.72+817_73-802GCT[12_26]
-
r.(?)
p.(=)
-
benign
g.53253385_53253459AGC[12_26]
-
-
-
TCF4_000152
-
PubMed: Mootha 2014
-
-
Germline
no
-
-
-
-
Johan den Dunnen
-/.
2
3i
c.72+817_73-802GCT[12_35]
-
r.(?)
p.(=)
-
benign
g.53253385_53253459AGC[12_35]
-
-
-
TCF4_000153, TCF4_000000
-
PubMed: Mootha 2014
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
2i
c.72+817_73-802GCT[21]
-
r.(?)
p.(=)
-
benign
g.53253385_53253459AGC[21]
-
-
-
TCF4_000000
-
PubMed: Mootha 2014
-
-
Germline
no
-
-
-
-
Johan den Dunnen
-/.
1
3i
c72+817_73-802GCT[12_35]
-
r.(?)
p.(=)
-
benign
g.53253385_53253459AGC[12_35]
-
-
-
TCF4_000000
-
PubMed: Mootha 2014
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3i
NM_032221.4:c.(-24+1_-23-1)::c.(145+1_146-1)
-
NM_032221.4:r.-178_-24::r.146_*5704
p.?
-
pathogenic
g.[NC_000020.10:(40180000_40246978)_qter]delinsg.(53131369_53252510)_qter
-
CHD6-TCF4 fusion
t(18;20)(q21.1;q11.2)
TCF4_000107
fusion transcript CHD6 exon 1 spliced to TCF4 exon 4
PubMed: Kalscheuer 2008
-
-
DUPLICATE record
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.72+37A>G
-
r.(=)
p.(=)
-
benign
g.53254239T>C
g.55587008T>C
TCF4(NM_001083962.1):c.72+37A>G
-
TCF4_000162
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-?/.
1
-
c.73-3T>C
-
r.spl?
p.?
-
likely benign
g.53252586A>G
g.55585355A>G
TCF4(NM_001083962.1):c.73-3T>C
-
TCF4_000131
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.145+12C>A
-
r.(=)
p.(=)
-
likely benign
g.53252499G>T
g.55585268G>T
TCF4(NM_001083962.1):c.145+12C>A
-
TCF4_000130
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
6
3i
c.145+42209=
-
r.(=), r.(?)
p.(=)
-
benign
g.53210302=
g.55543071=
rs613872 G
-
TCF4_000151
-
PubMed: Mootha 2014
-
rs613872
Germline
-
-
-
-
-
Johan den Dunnen
-/.
1
-
c.146-46406C>G
-
r.(=)
p.(=)
-
benign
g.53177774G>C
g.55510543G>C
TCF4(NM_001243228.2):c.146-46406C>G
-
TCF4_000176
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/.
1
-
c.146-46374T>C
-
r.(=)
p.(=)
-
benign
g.53177742A>G
g.55510511A>G
TCF4(NM_001083962.1):c.146-46374T>C
-
TCF4_000129
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
1
-
c.146-46372T>A
-
r.(=)
p.(=)
-
benign
g.53177740A>T
g.55510509A>T
TCF4(NM_001243228.2):c.146-46372T>A
-
TCF4_000175
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
?/.
1
-
c.146-120G>T
-
r.(=)
p.(=)
-
VUS
g.53131488C>A
g.55464257C>A
-
-
TCF4_000081
-
PubMed: Almomani 2011
dbSNP
-
-
Germline
-
-
-
-
-
Gerard C.P. Schaafsma
-?/.
1
-
c.146-8G>A
-
r.(=)
p.(=)
-
likely benign
g.53131376C>T
g.55464145C>T
TCF4(NM_001083962.1):c.146-8G>A (p.(=))
-
TCF4_000161
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
1
3i_6i
c.146-?_369+?del
-
r.del
p.del
-
pathogenic
g.53070685_53131368del
g.55403454_55464137del
del ex4-6
-
TCF4_000068
1 more item
-
-
-
De novo
-
-
-
-
-
Irina Giurgea
?/.
1
-
c.176G>A
-
r.(?)
p.(Trp59Ter)
-
VUS
g.53131338C>T
g.55464107C>T
TCF4(NM_001083962.1):c.176G>A (p.(Trp59Ter))
-
TCF4_000128
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-/.
1
-
c.207+94C>G
-
r.(=)
p.(=)
-
benign
g.53131213G>C
g.55463982G>C
-
-
TCF4_000090
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
-/.
2
-
c.207+97T>A
-
r.(=)
p.(=)
-
benign
g.53131210A>T
g.55463979A>T
TCF4(NM_001083962.1):c.207+97T>A, TCF4(NM_001243228.2):c.207+97T>A
-
TCF4_000127
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_AMC
-/.
1
-
c.207+99A>T
-
r.(=)
p.(=)
-
benign
g.53131208T>A
g.55463977T>A
TCF4(NM_001083962.1):c.207+99A>T
-
TCF4_000126
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
1
-
c.208-122C>A
-
r.(=)
p.(=)
-
benign
g.53128468G>T
g.55461237G>T
TCF4(NM_001083962.1):c.208-122C>A
-
TCF4_000160
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-?/.
1
-
c.208-8A>G
-
r.(=)
p.(=)
-
likely benign
g.53128354T>C
g.55461123T>C
TCF4(NM_001083962.1):c.208-8A>G
-
TCF4_000125
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
?/.
1
-
c.224C>G
-
r.(?)
p.(Thr75Ser)
-
VUS
g.53128330G>C
g.55461099G>C
TCF4(NM_001243228.2):c.224C>G (p.T75S)
-
TCF4_000174
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/.
1
-
c.304+203G>T
-
r.(=)
p.(=)
-
benign
g.53128047C>A
g.55460816C>A
TCF4(NM_001083962.1):c.304+203G>T
-
TCF4_000124
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
1
-
c.305-165C>T
-
r.(=)
p.(=)
-
benign
g.53070914G>A
g.55403683G>A
TCF4(NM_001243232.1):c.32C>T (p.A11V)
-
TCF4_000123
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/.
3
5i_8i
c.305-?_549+?del
-
r.del
p.del
-
pathogenic
g.53017590_53070749del
g.55350359_55403518del
del ex6-8
-
TCF4_000069
2 more items
PubMed: Rosenfeld 2009
-
-
De novo
-
-
-
-
-
Irina Giurgea
?/.
1
-
c.369+35G>A
-
r.(=)
p.(=)
-
VUS
g.53070650C>T
g.55403419C>T
-
-
TCF4_000089
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
+/.
1
-
c.415del
-
r.(?)
p.(Leu139PhefsTer95)
-
pathogenic
g.53018191del
g.55350960del
TCF4(NM_001083962.1):c.415delC (p.L139Ffs*95)
-
TCF4_000159
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/.
2
7
c.469C>T
-
r.(?)
p.(Arg157*), p.(Arg157Ter)
-
pathogenic
g.53018135G>A
g.55350904G>A
-
-
TCF4_000022
VKGL data sharing initiative Nederland
PubMed: Zweier 2008
-
-
De novo, CLASSIFICATION record
-
-
-
-
-
Irina Giurgea
,
VKGL-NL_Nijmegen
+/.
1
-
c.499+1G>A
-
r.spl?
p.?
-
pathogenic
g.53018104C>T
g.55350873C>T
TCF4(NM_001083962.1):c.499+1G>A
-
TCF4_000158
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
?/.
1
-
c.500-56A>G
-
r.(=)
p.(=)
-
VUS
g.53017695T>C
g.55350464T>C
-
-
TCF4_000091
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
+?/., +?/+?
2
8
c.505C>T
-
r.(?)
p.(Gln169*)
-
likely pathogenic (dominant), likely pathogenic
g.53017634G>A
g.55350403G>A
-
-
TCF4_000104
-
PubMed: Grozeva 2015
,
Journal: Grozeva 2015
,
PubMed: Grozeva 2015
-
-
Germline/De novo (untested), De novo
-
-
-
-
-
Johan den Dunnen
,
Irina Giurgea
+?/+?, +/.
2
8
c.514_517del
-
r.(?)
p.(Lys172Phefs*61)
-
likely pathogenic, pathogenic
g.53017626_53017629del
g.55350395_55350398del
-
-
TCF4_000047
ClinVar-ClinVar ID (RCV000079461.4)
PubMed: Redin 2014
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/., +?/+?
3
8
c.520C>T
-
r.(?)
p.(Arg174Ter), p.(Arg174*)
-
pathogenic, likely pathogenic
g.53017619G>A
g.55350388G>A
-
-
TCF4_000023
VKGL data sharing initiative Nederland,
ClinVar-ClinVar ID (RCV000224478.1)
PubMed: Redin 2014
-
-
CLASSIFICATION record, De novo
-
-
-
-
-
VKGL-NL_Nijmegen
,
Irina Giurgea
-/.
1
-
c.549+28833A>G
-
r.(=)
p.(=)
-
benign
g.52988757T>C
g.55321526T>C
TCF4(NM_001083962.1):c.549+28833A>G
-
TCF4_000122
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
1
-
c.549+28879del
-
r.(=)
p.(=)
-
benign
g.52988717del
g.55321486del
TCF4(NM_001083962.1):c.549+28879delT
-
TCF4_000121
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
?/.
1
-
c.550-22846A>G
-
r.(=)
p.(=)
-
VUS
g.52969733T>C
g.55302502T>C
TCF4(NM_001243236.1):c.-18A>G
-
TCF4_000120
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+?/., +?/+?
2
8i
c.550-1G>A
-
r.spl, r.spl?
p.?
-
likely pathogenic (dominant), likely pathogenic
g.52946888C>T
g.55279657C>T
-
-
TCF4_000105
-
PubMed: Grozeva 2015
,
Journal: Grozeva 2015
,
PubMed: Grozeva 2015
-
-
Germline/De novo (untested), Unknown
-
-
-
-
-
Johan den Dunnen
,
Irina Giurgea
+/.
1
8i
c.550-1G>C
-
r.spl
p.(Val184Metfs*15)
-
pathogenic
g.52946888C>G
g.55279657C>G
-
-
TCF4_000077
-
PubMed: Marangi 2011
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
9
c.550-?_655+?del
-
r.del
p.del
-
pathogenic
g.52946782_52946887del
g.55279551_55279656del
del ex9
-
TCF4_000070
1 more item
-
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
8i_15i
c.550-?_1350+?del
-
r.del
p.del
-
pathogenic
g.52921728_52946887del
g.55254497_55279656del
del ex9-15
-
TCF4_000071
1 more item
PubMed: Rosenfeld 2009
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
8i_17i
c.550-?_1649+?del
-
r.del
p.del
-
pathogenic
g.52899740_52946887del
g.55232509_55279656del
del ex9-17
-
TCF4_000072
1 more item
PubMed: Rosenfeld 2009
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
8i_20_
c.550-?_*5704+?del
-
r.del
p.del
-
pathogenic
g.52889562_52946887del
g.55222331_55279656del
del ex9-20
-
TCF4_000073
1 more item
PubMed: Rosenfeld 2009
-
-
De novo
-
-
-
-
-
Irina Giurgea
+?/.
1
-
c.654A>G
-
r.(?)
p.(Gln218=)
-
likely pathogenic
g.52946783T>C
g.55279552T>C
TCF4(NM_001083962.1):c.654A>G (p.(=))
-
TCF4_000157
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
1
-
c.655+1G>A
-
r.spl?
p.?
-
pathogenic
g.52946781C>T
g.55279550C>T
-
-
TCF4_000146
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
9i
c.655+1_655+2dup
-
r.spl?
p.(Val184Metfs*15)
-
pathogenic
g.52946780_52946781dup
g.55279549_55279550dup
IVS9+2insGT
-
TCF4_000078
-
PubMed: Zweier 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
-/.
1
-
c.656-182T>A
-
r.(=)
p.(=)
-
benign
g.52943165A>T
g.55275934A>T
TCF4(NM_001083962.1):c.656-182T>A
-
TCF4_000156
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
1
9i
c.656-1G>C
-
r.spl?
p.(?)
-
pathogenic
g.52942984C>G
g.55275753C>G
IVS9-1G>C
-
TCF4_000004
not in 360 control chromosomes
PubMed: Zweier 2007
;
PubMed: Peippo 2006
;
OMIM:var00004
-
-
De novo
-
-
-
-
-
Johan den Dunnen
+/.
1
9i_18i
c.656-?_1879+?del
-
r.spl
p.?
-
pathogenic
g.52896078_52942983del
g.55228847_55275752del
del ex10-18
-
TCF4_000067
1 more item
PubMed: Lehalle 2011
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
-
c.680G>T
-
r.(?)
p.(Trp227Leu)
-
pathogenic
g.52942959C>A
g.55275728C>A
-
-
TCF4_000171
2 heterozygous, no homozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs796053425
Germline
-
2/2795 individuals
-
-
-
Mohammed Faruq
+/.
1
10
c.687del
-
r.(?)
p.(Ser230Profs*4)
-
pathogenic
g.52942953del
g.55275722del
-
-
TCF4_000013
-
PubMed: Giurgea 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
10
c.693dup
-
r.(?)
p.(Gly232Trpfs*25)
-
pathogenic
g.52942946dup
g.55275715dup
692-694insT
-
TCF4_000006
-
PubMed: Zweier 2007
;
PubMed: Peippo 2006
-
-
De novo
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.696_699dup
-
r.(?)
p.(Asn234AspfsTer24)
-
pathogenic
g.52942941_52942944dup
g.55275710_55275713dup
-
-
TCF4_000144
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
-
c.759C>G
-
r.(?)
p.(Ser253Arg)
-
pathogenic (dominant)
g.52942880G>C
g.55275649G>C
-
-
TCF4_000182
-
PubMed: Srivastava 2018
-
-
De novo
-
-
-
-
-
Johan den Dunnen
+/.
1
10
c.788del
-
r.(?)
p.(Leu263*)
-
pathogenic
g.52942853del
g.55275622del
-
-
TCF4_000014
-
PubMed: Giurgea 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
-?/.
1
-
c.790-9T>C
-
r.(=)
p.(=)
-
likely benign
g.52937203A>G
g.55269972A>G
TCF4(NM_001083962.1):c.790-9T>C
-
TCF4_000119
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
1
11
c.791del
-
r.(?)
p.(Ser264Thrfs*43)
-
pathogenic
g.52937193del
g.55269962del
-
-
TCF4_000049
-
PubMed: Zweier 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+?/+?
1
12
c.873C>A
-
r.(?)
p.(Tyr291*)
-
likely pathogenic
g.52937111G>T
g.55269880G>T
-
-
TCF4_000100
-
-
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
11
c.908del
-
r.(?)
p.(Thr303Lysfs*4)
-
pathogenic
g.52937076del
g.55269845del
-
-
TCF4_000063
-
PubMed: Zweier 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
-
c.922+5G>A
-
r.790_922del
p.Cys296_Ala308delinsSer
-
pathogenic (dominant)
g.52937057C>T
g.55269826C>T
-
-
TCF4_000178
Splicing change confirmed by RT-PCR - skipping of exon 11
-
-
-
De novo
yes
-
-
-
-
Peter Sparber
+/.
1
-
c.922+6T>G
-
r.(=)
p.(=)
-
pathogenic
g.52937056A>C
g.55269825A>C
-
-
TCF4_000143
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
2
-
c.923-43G>A
-
r.(=)
p.(=)
-
benign
g.52928807C>T
g.55261576C>T
TCF4(NM_001083962.1):c.923-43G>A
-
TCF4_000088
VKGL data sharing initiative Nederland
-
-
rs35918540
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Utrecht
,
Andreas Laner
+/.
1
11i
c.923-2A>G
-
r.spl
p.?
-
pathogenic
g.52928766T>C
g.55261535T>C
923-2A>G
-
TCF4_000074
-
PubMed: De Pontual 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
12
c.928dup
-
r.(?)
p.(Arg310Lysfs*29)
-
pathogenic
g.52928759dup
g.55261528dup
-
-
TCF4_000024
-
-
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
12
c.940del
-
r.(?)
p.(Ala314Glnfs*77)
-
pathogenic
g.52928750del
g.55261519del
937-940delG
-
TCF4_000018
-
PubMed: Zweier 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
-?/.
2
-
c.944C>T
-
r.(?)
p.(Ala315Val)
-
likely benign
g.52928743G>A
g.55261512G>A
-
-
TCF4_000142
2 heterozygous, no homozygous;
Clinindb (India)
, VKGL data sharing initiative Nederland
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs147445499
Germline, CLASSIFICATION record
-
2/2775 individuals
-
-
-
Mohammed Faruq
,
VKGL-NL_Nijmegen
+/.
1
12
c.949del
-
r.(?)
p.(Ser317Alafs*74)
-
pathogenic
g.52928738del
g.55261507del
-
-
TCF4_000050
-
PubMed: Zweier 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
12
c.965_969del
-
r.(?)
p.(Asp322Alafs*15 )
-
pathogenic
g.52928718_52928722del
g.55261487_55261491del
965-969delATGCT
-
TCF4_000007
-
PubMed: Zweier 2007
;
PubMed: Peippo 2006
-
-
De novo
-
-
-
-
-
Johan den Dunnen
+/.
1
12
c.988_989del
-
r.(?)
p.(Ser330Aspfs*8)
-
pathogenic
g.52928698_52928699del
g.55261467_55261468del
-
-
TCF4_000051
-
-
-
-
De novo
-
-
-
-
-
Irina Giurgea
./., +/., +?/+?
4
12
c.990G>A
-
r.(=), r.(?), r.spl?
p.(=), p.(Ser330=)
ACMG
likely pathogenic, pathogenic
g.52928697C>T
g.55261466C>T
-
-
TCF4_000098
VKGL data sharing initiative Nederland,
ClinVar-ClinVar ID (RCV000147730.1)
PubMed: Tan 2015
-
-
De novo, CLASSIFICATION record
yes
-
-
-
-
Irina Giurgea
,
VKGL-NL_Nijmegen
,
Bernt Popp
+/.
1
-
c.990+1G>A
-
r.spl?
p.?
-
pathogenic
g.52928696C>T
g.55261465C>T
-
-
TCF4_000141
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
1
-
c.990+38_990+40del
-
r.(=)
p.(=)
-
VUS
g.52928658_52928660del
g.55261427_55261429del
-
-
TCF4_000087
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
?/.
1
-
c.990+42A>T
-
r.(=)
p.(=)
-
VUS
g.52928655T>A
g.55261424T>A
-
-
TCF4_000086
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
-/.
1
-
c.991-18del
-
r.(=)
p.(=)
-
benign
g.52927285del
g.55260054del
TCF4(NM_001083962.1):c.991-18delT
-
TCF4_000118
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+?/+?
1
13i
c.991-2A>G
-
r.spl?
p.?
-
likely pathogenic
g.52927260T>C
g.55260029T>C
-
-
TCF4_000106
ClinVar-ClinVar ID (RCV000147731.1)
PubMed: Tan 2015
-
-
Unknown
-
-
-
-
-
Irina Giurgea
+/.
1
13
c.1018del
-
r.(?)
p.(Ser340AlafsTer51)
-
pathogenic
g.52927231del
g.55260000del
-
-
TCF4_000010
-
PubMed: Giurgea 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
-
c.1028C>G
-
r.(?)
p.(Ser343Ter)
-
pathogenic
g.52927221G>C
g.55259990G>C
-
-
TCF4_000169
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
13i
c.1069+2T>G
-
r.spl
p.?
-
pathogenic
g.52927178A>C
g.55259947A>C
-
-
TCF4_000099
-
-
-
-
De novo
yes
-
-
-
-
Wenjuan Qiu
?/.
1
-
c.1070-2A>G
-
r.spl
p.?
ACMG
VUS
g.52924624T>C
g.55257393T>C
-
-
TCF4_000179
1 more item
-
-
-
Germline
no
-
-
-
-
Andreas Laner
+/.
1
14
c.1073G>T
-
r.(?)
p.(Gly358Val)
-
pathogenic
g.52924619C>A
g.55257388C>A
-
-
TCF4_000043
site d'epissage GT
PubMed: Zweier 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
14
c.1077del
-
r.(?)
p.(Ala360Leufs*31)
-
pathogenic
g.52924615del
g.55257384del
-
-
TCF4_000019
-
-
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
14
c.1113del
-
r.(?)
p.(Ser372Leufs*19)
-
pathogenic
g.52924579del
g.55257348del
1113delG (Ser372Leu)
-
TCF4_000052
-
-
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
-
c.1134del
-
r.(?)
p.(Leu379TyrfsTer12)
-
pathogenic
g.52924560del
g.55257329del
-
-
TCF4_000139
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
14
c.1142del
-
r.(?)
p.(Ser381Phefs*10)
-
pathogenic
g.52924550del
g.55257319del
-
-
TCF4_000011
-
PubMed: Giurgea 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
14i
c.1146+1G>A
-
r.spl
p.?
-
pathogenic
g.52924545C>T
g.55257314C>T
-
-
TCF4_000075
-
PubMed: De Pontual 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
+/.
1
14i
c.1146+3A>G
-
r.spl?
p.(Gly358Lysfs*4)
-
pathogenic
g.52924543T>C
g.55257312T>C
IVS14+3A>G
-
TCF4_000066
-
PubMed: Zweier 2008
-
-
De novo
-
-
-
-
-
Irina Giurgea
-/.
1
-
c.1147-76G>A
-
r.(=)
p.(=)
-
benign
g.52922007C>T
g.55254776C>T
TCF4(NM_001083962.1):c.1147-76G>A
-
TCF4_000117
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
1
15
c.1151del
-
r.(?)
p.(Ser384Thrfs*7)
-
pathogenic
g.52921927del
g.55254696del
-
-
TCF4_000053
-
PubMed: Takano 2010
-
-
De novo
-
-
-
-
-
Irina Giurgea
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