Global Variome shared LOVD
SMAD4 (SMAD family member 4)
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Curators:
Karl Heinimann
,
Robert Blatter
, and
Benjamin Tschupp
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Unique variants in the SMAD4 gene
The variants shown are described using the NM_005359.5 transcript reference sequence.
Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect
: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
Reported
: The number of times this variant has been reported in the database.
Exon
: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
DNA change (cDNA)
: description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.
RNA change
: description of variant at RNA level (following HGVS recommendations).
r.123c>u
r.? = unknown
r.(?) = RNA not analysed but probably transcribed copy of DNA variant
r.spl? = RNA not analysed but variant probably affects splicing
r.(spl?) = RNA not analysed but variant may affect splicing
r.0? = change expected to abolish transcription
Protein
: description of variant at protein level (following HGVS recommendations).
p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced
Classification method
: The method used for the clinical classification of this variant.
All options:
ACMG
ACGS
EAHAD-CFDB
ENIGMA
IARC
InSiGHT
kConFab
other
Clinical classification
: Clinical classification of variant, preferably based on standardised criteria (e.g. ACMG), directed on the clinical consequences as published/submitted, indicated using an enriched system including inheritance: e.g. pathogenic, pathogenic (dominant), pathogenic (recessive), pathogenic (!), pathogenic (maternal), pathogenic (paternal). Standard inheritance is covered by dominant/recessive, imprinting by maternal/paternal. A '!' warns for exceptional circumstances to be explained in the 'Remarks' field (low penetrance, variants pathogenic in heterozygous state only, hypomorphic/hypermorphic variants, protective variants, etc.). Non-disease consequences (e.g. drug metabolism (pharmacogenetics), risk factor, blood group, tasting bitter) are indicated using additions to the benign classification; benign (dominant), benign (recessive), benign (!), etc. The value 'association' is used for variants associated with a phenotype and 'NA' for variants from in vitro/in silico records. NOTE: classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional.
All options:
pathogenic
pathogenic (dominant)
pathogenic (recessive)
pathogenic (!)
pathogenic (maternal)
pathogenic (paternal)
likely pathogenic
likely pathogenic (dominant)
likely pathogenic (recessive)
likely pathogenic (!)
likely pathogenic (maternal)
likely pathogenic (paternal)
VUS
VUS (!)
likely benign
likely benign (dominant)
likely benign (recessive)
likely benign (!)
likely benign (maternal)
likely benign (paternal)
benign
benign (dominant)
benign (recessive)
benign (!)
benign (maternal)
benign (paternal)
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%)
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Operator
Column type
Example
Matches
Text
Arg
all entries containing 'Arg'
space
Text
Arg Ser
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|
Text
Arg|Ser
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!
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'
!=""
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!=""
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
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>
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'
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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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230 entries on 3 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
+/+, ?/?
5
-
c.?
r.(?)
p.(?), p.?
ACMG
pathogenic (dominant), VUS
g.?
-
IVS10+109A>G, IVS11+118A>G, t(1;18)(p36.1;q21.1),
1 more item
-
SMAD4_000000, SMCHD1_000000
ACMG PM2
Hao et al 2017, IJCEM, IJCEM0043096,
Journal: Brusgaard 2017
,
PubMed: Tram 2011
,
Journal: Tram 2011
-
-
Germline
-
-
-
-
-
Karl Heinimann
,
Benjamin Tschupp
./.
1
-
c.-194457_*29410343del
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
+/.
4
_1_13_
c.(?_-17093)_(*6575_?)del
r.0
p.0
-
pathogenic (dominant)
g.(?_48540028)_(48611412 _?)del
-
‐17093‐?_1659+?del
-
SMAD4_000133
-
PubMed: Aretz 2007
-
-
De novo, Germline
-
-
-
-
-
Johan den Dunnen
?/+
1
_1
c.(?_-1382)_(-128+2238_-127-1)del
r.0?
p.0?
ACMG
VUS
g.(?_48555739)_(48559231_48573289)del
-
heterozygous deletion of a probe upstream of NC exon 4 and all probes located within NC exon 4
-
SMAD4_000136
ACMG PVS1, PM2
Journal: Calva 2011
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/?
1
_1_1i
c.(?_-538)_(-128+1_-127-1)del
r.0?
p.0?
ACMG
pathogenic
g.(?_48556583)_(48556994_48573289)del
-
del promotor, 2 non-coding exons
-
SMAD4_000137
ACMG PVS1
PubMed: Calva-Cerqueira 2009
,
Journal: Calva-Cerqueira 2009
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/?, ?/+
2
_1_9i
c.(?_-538)_(1139+1_1140-1)del
r.0?
p.0?
ACMG
pathogenic, VUS
g.(?_48556583)_(48591977_48593388)del
-
del ex1-8,
1 more item
-
SMAD4_000138
ACMG PVS1, ACMG PVS1, PM2
Journal: Calva 2011
,
PubMed: Calva-Cerqueira 2009
,
Journal: Calva-Cerqueira 2009
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/+, ?/+, ?/?
6
_1_12_
c.(?_-538)_(*6575_?)del
r.0
p.0, p.0?
ACMG
pathogenic, VUS
g.(?_48556583)_(48611412_?)del
-
complete gene deletion, del ex1-11, hemizygous deletion
-
SMAD4_000139
ACMG PVS1, ACMG PVS1, PM2, ACMG PVS1, PM2, PP3
Journal: Langeveld 2010
,
Journal: Soer 2015
,
Journal: Wain 2014
,
1 more item
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/.
4
_1_12_
c.-358_*6575del
r.0
p.0
-
VUS
g.(?_48556763)_(48611412_?)del, g.48556763_48611412del
g.51030393_51085042del
-17093-?_1659+?del, del. SMAD4 gene+promotor
-
SMAD4_000201
-
-
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
-?/.
1
-
c.-127-11_-127-10del
r.(=)
p.(=)
-
likely benign
g.48573279_48573280del
g.51046909_51046910del
SMAD4(NM_005359.5):c.-127-11_-127-10delTT
-
SMAD4_000089
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-?/.
1
-
c.-127-9C>T
r.(=)
p.(=)
-
likely benign
g.48573281C>T
g.51046911C>T
SMAD4(NM_005359.5):c.-127-9C>T
-
SMAD4_000090
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-?/., ?/.
2
-
c.-127-2A>T
r.spl?
p.?
-
likely benign, VUS
g.48573288A>T
g.51046918A>T
SMAD4(NM_005359.5):c.-127-2A>T (, p.(=))
-
SMAD4_000091
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_Rotterdam
-?/.
1
-
c.-127-2_-127del
r.spl?
p.?
-
likely benign
g.48573288_48573290del
g.51046918_51046920del
SMAD4(NM_005359.5):c.-127-2_-127del (p.(=))
-
SMAD4_000183
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-?/.
1
-
c.-127-1G>T
r.spl?
p.?
-
likely benign
g.48573289G>T
g.51046919G>T
SMAD4(NM_005359.5):c.-127-1G>T (p.(=))
-
SMAD4_000184
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
?/?
1
_2_9i
c.(?_-127-1)_(1139+1_1140-1)del
r.0?
p.0?
ACMG
VUS
g.(?_48573289)_(48591977_48593388)del
-
deletion exons 1-8
-
SMAD4_000140
ACMG PVS1
Journal: Soer 2015
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/.
1
_2_3i
c.(?_-1)_(424+1_425-1)del
r.?
p.?
-
VUS
g.(?_48573416)_(48575231_48575664)del
-
del exon 1+2
-
SMAD4_000202
-
-
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
+/.
2
_2_9i
c.(?_-1)_(1139+1_1140-1)del
r.?
p.?
-
VUS
g.(?_48573416)_(48591977_48593388)del
-
del exon 1-8
-
SMAD4_000203
-
-
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
?/?
3
2
c.20C>T
r.(?)
p.(Thr7Met)
-
VUS
g.48573436C>T
g.51047066C>T
1244_1247delACAG + 20C>T, 20C>T / 1244_1247delACAG
-
SMAD4_000204
-
-
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
-?/.
3
-
c.21G>A
r.(?)
p.(Thr7=)
-
likely benign
g.48573437G>A
g.51047067G>A
SMAD4(NM_005359.5):c.21G>A (p.T7=)
-
SMAD4_000092
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
,
VKGL-NL_NKI
+/?, ?/?
2
1, 2
c.38A>G
r.(?)
p.(Asn13Ser)
ACMG
pathogenic, VUS
g.48573454A>G
g.51047084A>G
-
-
SMAD4_000004
rare variant found in a patient with pulmonary arterial hypertension; ACMG PM2, PP3
Journal: Nasim 2011
,
PubMed: Nasim 2011
,
ExPASy_066870
,
Journal: Nasim 2011
-
-
Germline
-
-
-
-
-
SIB - Livia Famiglietti
,
Benjamin Tschupp
-?/.
1
-
c.150A>G
r.(?)
p.(Lys50=)
-
likely benign
g.48573566A>G
g.51047196A>G
SMAD4(NM_005359.5):c.150A>G (p.K50=)
-
SMAD4_000185
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+
1
2
c.153del
r.(?)
p.(Asp52Metfs*6)
-
pathogenic (dominant)
g.48573569del
g.51047199del
153delA
-
SMAD4_000205
-
Journal: Stoffel 2018
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
+?/.
1
-
c.153dup
r.(?)
p.Asp52Argfs*2
ACMG
likely pathogenic
g.48573569dup
g.51047199dup
-
-
SMAD4_000200
ACMG grading: PVS1,PM2
-
-
rs786203560
Germline
-
-
-
-
-
Andreas Laner
?/?
2
2
c.189_197del
r.(?)
p.(Asn64_Ala66del)
ACMG
VUS
g.48573605_48573613del
g.51047235_51047243del
189_197delAAATGGAGC
-
SMAD4_000141
ACMG PM2, PM4
PubMed: Woodford-Richens 2000
,
Journal: Woodford-Richens et a 2000
-
-
Germline
-
-
-
-
-
Karl Heinimann
-?/.
3
-
c.228A>G
r.(?)
p.(Arg76=)
-
likely benign
g.48573644A>G
g.51047274A>G
SMAD4(NM_005359.5):c.228A>G (p.R76=)
-
SMAD4_000093
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
-?/.
1
-
c.249+14G>A
r.(=)
p.(=)
-
likely benign
g.48573679G>A
g.51047309G>A
SMAD4(NM_005359.5):c.249+14G>A
-
SMAD4_000094
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/.
2
2i
c.249+24A>G
r.(=)
p.(=)
-
benign
g.48573689A>G
g.51047319A>G
-
-
SMAD4_000010
VKGL data sharing initiative Nederland
-
-
rs77389132
CLASSIFICATION record, Germline
-
up to 0.025
-
-
-
Andreas Laner
,
VKGL-NL_Nijmegen
-?/.
1
-
c.249+71A>G
r.(=)
p.(=)
-
likely benign
g.48573736A>G
-
-
-
SMAD4_000235
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
2
-
c.250-10A>G
r.(=)
p.(=)
-
likely benign
g.48575046A>G
g.51048676A>G
SMAD4(NM_005359.5):c.250-10A>G
-
SMAD4_000095
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_VUmc
+/+
4
3
c.260_261del
r.(?)
p.(Arg87Glnfs*16)
-
pathogenic (dominant)
g.48575066_48575067del
g.51048696_51048697del
260_261delGG
-
SMAD4_000206
-
-
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
+/+
6
3
c.263_267del
r.(?)
p.(Lys88Ilefs*14)
ACMG
pathogenic
g.48575069_48575073del
g.51048699_51048703del
263-267delAAGGA
-
SMAD4_000142
ACMG PVS1, PM4, PM2, PP3
Journal: Wain 2014
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/.
1
-
c.285T>A
r.(?)
p.(Tyr95*)
-
pathogenic
g.48575091T>A
g.51048721T>A
-
-
SMAD4_000239
-
-
-
-
Germline
yes
-
-
-
-
Yi-Qing Yang
-?/.
1
-
c.294C>T
r.(?)
p.(Leu98=)
-
likely benign
g.48575100C>T
g.51048730C>T
SMAD4(NM_005359.5):c.294C>T (p.L98=)
-
SMAD4_000225
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/?
1
3
c.302G>A
r.(?)
p.(Trp101*)
ACMG
pathogenic
g.48575108G>A
g.51048738G>A
302G>A | W101X
-
SMAD4_000077
ACMG PM2, PM4, PP3
PubMed: Gallione 2010
,
Journal: Gallione 2010
-
rs377767323
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
-/., -?/.
5
-
c.354G>A
r.(?)
p.(Ala118=)
-
benign, likely benign
g.48575160G>A
g.51048790G>A
SMAD4(NM_005359.5):c.354G>A (p.A118=)
-
SMAD4_000096
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
,
VKGL-NL_AMC
+/+
1
3
c.373_374insAT
r.(?)
p.(Ser125Asnfs*5)
ACMG
pathogenic
g.48575179_48575180insAT
g.51048809_51048810insAT
373_4insAT
-
SMAD4_000062
ACMG PVS1, PM2, PM4, PP3
PubMed: Calva-Cerqueira 2009
,
Journal: Calva-Cerqueira 2009
-
rs377767324
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
+/+, ?/+
2
3
c.375_381dup
r.(?)
p.(Val128Cysfs*17)
ACMG
pathogenic, VUS
g.48575181_48575187dup
g.51048811_51048817dup
375dup7, 375_381dupTGTCTGT
-
SMAD4_000037
ACMG PVS1, PM2, PM4, PP3
PubMed: Handra-Luca 2005
,
Journal: Handra-Luca 2005
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Karl Heinimann
?/., ?/?
2
3, 4
c.380G>T
r.(?)
p.(Cys127Phe)
-
VUS
g.48575186G>T
g.51048816G>T
-
-
SMAD4_000009
-
-
-
-
Germline
-
-
-
-
-
Christopher Watson
,
Benjamin Tschupp
?/.
1
-
c.400G>A
r.(?)
p.(Glu134Lys)
-
VUS
g.48575206G>A
g.51048836G>A
SMAD4(NM_005359.5):c.400G>A (p.E134K)
-
SMAD4_000186
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+, +/.
6
2, 3
c.403C>T
r.(?)
p.(Arg135*), p.(Arg135Ter)
ACMG
pathogenic, pathogenic (dominant)
g.48575209C>T
g.51048839C>T
403C>T | R135X, SMAD4(NM_005359.5):c.403C>T (p.R135*)
-
SMAD4_000038
ACMG PVS1, PM2, PM4, PP3, VKGL data sharing initiative Nederland
PubMed: Aretz 2007
,
PubMed: Pyatt 2006
,
Journal: Pyatt 2006
-
rs377767326
CLASSIFICATION record, Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Johan den Dunnen
,
Benjamin Tschupp
,
VKGL-NL_Rotterdam
+/+, ?/+
2
2i, 3i
c.424+1G>A
r.spl
p.?
ACMG
pathogenic, VUS
g.48575231G>A
g.51048861G>A
-
-
SMAD4_000129
ACMG PVS1, PM2, PP3, PP5
Journal: Alberici 2008
,
PubMed: Woodford-Richens 2001
,
Journal: Woodford-Richens 2001
-
rs377767386
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Karl Heinimann
-/?, -?/., ?/.
5
3i
c.424+5G>A
r.(?), r.spl?
p.?
ACMG
benign, likely benign, VUS
g.48575235G>A
g.51048865G>A
SMAD4(NM_005359.5):c.424+5G>A
-
SMAD4_000127
;ACMG PP3, BP6, VKGL data sharing initiative Nederland,
1 more item
Journal: Jelsig 2016
-
rs200772603
CLASSIFICATION record, Germline
-
-
-
-
-
Karl Heinimann
,
InSiGHT - John-Paul Plazzer
,
Andreas Laner
,
VKGL-NL_Rotterdam
,
VKGL-NL_Nijmegen
-/.
1
-
c.424+19C>A
r.(=)
p.(=)
-
benign
g.48575249C>A
g.51048879C>A
-
-
SMAD4_000116
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/+, ?/.
2
3i
c.425-6A>G
r.spl?
p.(=)
ACMG
pathogenic, VUS
g.48575659A>G
g.51049289A>G
-
-
SMAD4_000128, SMAD4_000131
1 more item
PubMed: Aretz 2007
-
rs377767327
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Andreas Laner
+/+, ?/+
5
4
c.430_431del
r.(?)
p.(Ser144Argfs*7)
ACMG
pathogenic, VUS
g.48575670_48575671del
g.51049300_51049301del
320-431delTC, 426_427delTC, 430-431delTC
-
SMAD4_000039
ACMG PVS1, PM2, PM4, PP3
Journal: Ngeow 2013
,
Journal: O'Malley 2011
,
Journal: Pearlman 2016
,
1 more item
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Karl Heinimann
+/+
2
2, 4
c.437T>A
r.(?)
p.(Leu146*)
-
pathogenic, pathogenic (dominant)
g.48575677T>A
g.51049307T>A
-
-
SMAD4_000040
-
PubMed: Aretz 2007
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Benjamin Tschupp
+/.
1
-
c.452dup
r.(?)
p.(Asn151LysfsTer11)
-
pathogenic
g.48575692dup
g.51049322dup
SMAD4(NM_005359.5):c.452dupA (p.N151Kfs*11)
-
SMAD4_000097
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/.
1
-
c.454+54T>G
r.(=)
p.(=)
-
benign
g.48575748T>G
g.51049378T>G
-
-
SMAD4_000187
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
-
c.454+2088G>C
r.(=)
p.(=)
-
benign
g.48577782G>C
g.51051412G>C
SMAD4(NM_005359.5):c.454+2088G>C
-
SMAD4_000188
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
1
-
c.455-8C>T
r.(=)
p.(=)
-
likely benign
g.48581143C>T
g.51054773C>T
SMAD4(NM_005359.5):c.455-8C>T (p.(=))
-
SMAD4_000189
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-/.
1
-
c.455-6A>G
r.(=)
p.(=)
-
benign
g.48581145A>G
g.51054775A>G
SMAD4(NM_005359.5):c.455-6A>G
-
SMAD4_000190
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/.
1
4i_12_
c.(454+1_455-1)_*6575del
r.(?)
p.(?)
-
VUS
g.(48575695_48581150)_(48611412_?)del
-
del exon 5-12
-
SMAD4_000207
-
-
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
./.
1
-
c.457C>T
r.(?)
p.(Pro153Ser)
-
VUS
g.48581153C>T
g.51054783C>T
-
-
SMAD4_000087
-
Thibodeau lab (Mayo Clinic)
-
-
Germline
-
-
-
-
-
Melissa DeRycke
./.
1
-
c.466A>T
r.(?)
p.(Met156Leu)
-
VUS
g.48581162A>T
g.51054792A>T
-
-
SMAD4_000088
-
Thibodeau lab (Mayo Clinic)
-
-
Germline
-
-
-
-
-
Melissa DeRycke
+/+, ?/+
8
2, 5
c.517_527del
r.(?)
p.(Ser173Thrfs*12)
ACMG
pathogenic (dominant), VUS
g.48581213_48581223del
g.51054843_51054853del
517_527del11, 517_527delTCCACTGAAGG
-
SMAD4_000041
ACMG PVS1, PM2, PM4, PP3
PubMed: Woodford-Richens 2000
,
Journal: Woodford-Richens et a 2000
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Benjamin Tschupp
-?/.
1
-
c.520A>G
r.(?)
p.(Thr174Ala)
-
likely benign
g.48581216A>G
-
SMAD4(NM_005359.5):c.520A>G (p.T174A)
-
SMAD4_000237
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/+, +/?
4
5
c.533C>G
r.(?)
p.(Ser178*)
ACMG
pathogenic, pathogenic (dominant)
g.48581229C>G
g.51054859C>G
661C>G
-
SMAD4_000042
ACMG PM2, PP3
PubMed: Roth 1999
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Benjamin Tschupp
+/+
1
2
c.538C>T
r.(?)
p.(Gln180*)
-
pathogenic
g.48581234C>T
g.51054864C>T
538C>T | Q180X
-
SMAD4_000043
-
PubMed: Woodford-Richens 2001
,
Journal: Woodford-Richens 2001
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
?/?
1
5
c.543C>G
r.(?)
p.(=)
-
VUS
g.48581239C>G
g.51054869C>G
-
-
SMAD4_000208
-
-
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
?/?
1
5
c.543C>T
r.(?)
p.Thr181=
-
VUS
g.48581239C>T
g.51054869C>T
1081C>T
-
SMAD4_000209
-
PubMed: Szigeti 2012
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
+/+, ?/+
11
5
c.543del
r.(?)
p.(Ile182Serfs*20)
ACMG
pathogenic (dominant), VUS
g.48581239del
g.51054869del
543delC, 543_543delC
-
SMAD4_000143
ACMG PVS1, PM2, PP3
Journal: Schwetz 2012
-
-
Germline
-
-
-
-
-
Karl Heinimann
,
Benjamin Tschupp
?/?
1
5
c.554C>A
r.(?)
p.(Pro185Gln)
ACMG
VUS
g.48581250C>A
g.51054880C>A
554C>A
-
SMAD4_000144
ACMG PM2, PP3
Journal: Pearlman 2016
-
-
Germline
-
-
-
-
-
Karl Heinimann
-?/., ./.
3
-
c.565C>T
r.(?)
p.(Arg189Cys)
-
likely benign, VUS
g.48581261C>T
g.51054891C>T
SMAD4(NM_005359.5):c.565C>T (p.R189C)
-
SMAD4_000083
VKGL data sharing initiative Nederland
Thibodeau lab (Mayo Clinic)
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Melissa DeRycke
,
VKGL-NL_Nijmegen
,
VKGL-NL_AMC
-?/.
1
-
c.566G>A
r.(?)
p.(Arg189His)
-
likely benign
g.48581262G>A
g.51054892G>A
SMAD4(NM_005359.5):c.566G>A (p.R189H)
-
SMAD4_000098
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+/+
1
5
c.576dup
r.(?)
p.(Glu193Argfs*13)
-
pathogenic (dominant)
g.48581272dup
g.51054902dup
576_577insA
-
SMAD4_000210
-
-
-
-
Germline
-
-
-
-
-
Benjamin Tschupp
+/+, ?/+
6
5
c.608del
r.(?)
p.(Pro203Hisfs*38)
ACMG
pathogenic, VUS
g.48581304del
g.51054934del
608delC, 608delC (P203HfsX)
-
SMAD4_000044
ACMG PM2, PM4, PP3, PVS1, ACMG PVS1, PM2, PM4, PP3
Journal: Carr 2012
,
Journal: Howe 2004
,
Journal: Howe 2004
,
PubMed: Sayed 2002
,
Journal: Sayed 2002
,
1 more item
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Karl Heinimann
+/.
1
-
c.609del
r.(?)
p.(Ser204Leufs*37)
-
pathogenic
g.48581305del
-
SMAD4(NM_005359.5):c.609delA (p.S204Lfs*37)
-
SMAD4_000240
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
1
-
c.651T>A
r.(?)
p.(Ile217=)
-
likely benign
g.48581347T>A
-
-
-
SMAD4_000236
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.667+12A>T
r.(=)
p.(=)
-
likely benign
g.48581375A>T
g.51055005A>T
SMAD4(NM_005359.5):c.667+12A>T
-
SMAD4_000191
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/.
1
5i_12_
c.(667+1_668-1)_(*6575_?)del
r.?
p.?
-
pathogenic (dominant)
g.(48581364_48584494)_(48611412 _?)del
-
668‐?_1659+?del
-
SMAD4_000134
-
PubMed: Aretz 2007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/., ?/?
2
6
c.677C>T
r.(?)
p.(Ala226Val)
ACMG
likely benign, VUS
g.48584504C>T
g.51058134C>T
-
-
SMAD4_000145
ACMG PP3, VKGL data sharing initiative Nederland
Journal: Pearlman 2016
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Karl Heinimann
,
VKGL-NL_Nijmegen
+/+, +/., +/?
6
6
c.692dup
r.(?)
p.(Ser232Glnfs*3)
ACMG
pathogenic, pathogenic (dominant)
g.48584519dup
g.51058149dup
691-692insG, 692dupG, 692insG, 815-820(687insG), 820dupG
-
SMAD4_000015
ACMG PM2, PM4, PP3, ACMG PS1, PM2, PM6, ACMG PVS1, PM2, PM4, PP3, not in 214 control chromosomes
Journal: Jelsig 2015
,
PubMed: Gallione 2010
,
Journal: Gallione 2010
,
2 more items
-
-
De novo, Germline, Unknown
-
-
-
-
-
Johan den Dunnen
,
Karl Heinimann
,
Benjamin Tschupp
?/+
2
6
c.728_735del
r.(?)
p.(Gly243Alafs*18)
ACMG
VUS
g.48584555_48584562del
g.51058185_51058192del
724_731delTCAGGGCC
-
SMAD4_000146
ACMG PM2, PS1, PP1, PP3
Journal: Schwenter 2012
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/+
1
6
c.731_732insGCCC
r.(?)
p.(Gln245Profs*20)
ACMG
pathogenic
g.48584558_48584559insGCCC
g.51058188_51058189insGCCC
729-730insCCGC
-
SMAD4_000045
ACMG PVS1, PM2, PM4, PP3
PubMed: Pyatt 2006
,
Journal: Pyatt 2006
-
rs377767335
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
+/+, ?/+
2
6
c.745C>T
r.(?)
p.(Gln249*)
ACMG
pathogenic (dominant), VUS
g.48584572C>T
g.51058202C>T
-
-
SMAD4_000147
ACMG PVS1, PM2, PM4, PP3
Journal: Pantelis 2016
-
-
Germline
-
-
-
-
-
Karl Heinimann
,
Benjamin Tschupp
?/+
1
6
c.746_747delinsCC
r.(?)
p.(Gln249Pro)
ACMG
VUS
g.48584573_48584574delinsCC
g.51058203_51058204delinsCC
746_747AG>CC
-
SMAD4_000148
ACMG PM2, PS1, PP5, PP3
Journal: Schwenter 2012
-
rs587782209
Germline
-
-
-
-
-
Karl Heinimann
+/+
1
6
c.759del
r.(?)
p.(Phe253Leufs*83)
ACMG
pathogenic
g.48584586del
g.51058216del
759delT
-
SMAD4_000149
ACMG PVS1, PM4, PM2, PP3
Journal: Wain 2014
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/.
1
6i_12_
c.(787+1_788-1)_(*6575_?)del
r.?
p.?
-
pathogenic (dominant)
g.(48584615_48584709)_(48611412 _?)del
-
788‐?_1659+?del
-
SMAD4_000135
-
PubMed: Aretz 2007
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/+
1
7
c.798del
r.(?)
p.(Thr267Profs*69)
ACMG
VUS
g.48584720del
g.51058350del
798delC
-
SMAD4_000150
ACMG PVS1, PM2, PM4, PP3
Journal: Ngeow 2013
-
-
Germline
-
-
-
-
-
Karl Heinimann
?/+
1
6i_9i
c.(787+1_830)_(1139+1_1140-1)del
r.?
p.?
ACMG
VUS
g.(48584615_48584752)_(48591977_48593388)del
-
830-?_1139+?del
-
SMAD4_000151
ACMG PVS1, PM2
Journal: Ngeow 2013
-
-
Germline
-
-
-
-
-
Karl Heinimann
+/+, +/.
2
3, 6
c.831_832del
r.(?)
p.(Pro278*)
-
pathogenic (dominant)
g.48584753_48584754del
g.51058383_51058384del
831_832delAC, 959–960delAC
-
SMAD4_000046
-
PubMed: Aretz 2007
,
PubMed: Friedl 1999
,
PubMed: Friedl 2002
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
,
Johan den Dunnen
?/.
1
-
c.872A>C
r.(?)
p.(His291Pro)
-
VUS
g.48584794A>C
g.51058424A>C
SMAD4(NM_005359.5):c.872A>C (p.H291P)
-
SMAD4_000099
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
1
-
c.880A>G
r.(?)
p.(Met294Val)
-
likely benign
g.48584802A>G
g.51058432A>G
SMAD4(NM_005359.5):c.880A>G (p.M294V)
-
SMAD4_000100
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
?/+
1
7
c.902dup
r.(?)
p.(Tyr301*)
ACMG
VUS
g.48584824dup
g.51058454dup
902_903insA
-
SMAD4_000152
ACMG PVS1, PM2, PM4, PP3
Journal: Ngeow 2013
-
-
Germline
-
-
-
-
-
Karl Heinimann
-?/.
2
-
c.904+11G>A
r.(=)
p.(=)
-
likely benign
g.48584837G>A
g.51058467G>A
SMAD4(NM_005359.5):c.904+11G>A
-
SMAD4_000101
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_VUmc
?/.
1
-
c.904+14T>C
r.(=)
p.(=)
-
VUS
g.48584840T>C
g.51058470T>C
SMAD4(NM_005359.5):c.904+14T>C
-
SMAD4_000102
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-?/.
1
-
c.904+216C>T
r.(=)
p.(=)
-
likely benign
g.48585042C>T
g.51058672C>T
SMAD4(NM_005359.5):c.904+216C>T
-
SMAD4_000232
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-/.
1
7i
c.905-199_905-196del
r.(=)
p.(=)
-
benign
g.48586037_48586040del
g.51059667_51059670del
-
-
SMAD4_000011
-
-
-
rs71880423
Germline
-
-
-
-
-
Andreas Laner
-?/.
1
-
c.905-91A>G
r.(=)
p.(=)
-
likely benign
g.48586145A>G
g.51059775A>G
-
-
SMAD4_000226
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.905-75T>C
r.(=)
p.(=)
-
likely benign
g.48586161T>C
g.51059791T>C
-
-
SMAD4_000192
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
-
c.905-52A>G
r.(=)
p.(=)
-
benign
g.48586184A>G
g.51059814A>G
-
-
SMAD4_000118
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.905-3T>C
r.spl?
p.?
-
likely benign
g.48586233T>C
g.51059863T>C
SMAD4(NM_005359.5):c.905-3T>C
-
SMAD4_000103
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-?/.
1
-
c.909T>G
r.(?)
p.(Pro303=)
-
likely benign
g.48586240T>G
g.51059870T>G
SMAD4(NM_005359.5):c.909T>G (p.P303=)
-
SMAD4_000233
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+
1
8
c.925_928dup
r.(?)
p.(Phe310Cysfs*13)
ACMG
pathogenic
g.48586256_48586259dup
g.51059886_51059889dup
925-928dupGCAT
-
SMAD4_000047
ACMG PVS1, PM2, PM4, PP3
PubMed: Pyatt 2006
,
Journal: Pyatt 2006
-
-
Germline
-
-
-
-
-
Global Variome, with Curator vacancy
?/.
1
-
c.926C>T
r.(?)
p.(Ala309Val)
-
VUS
g.48586257C>T
g.51059887C>T
SMAD4(NM_005359.5):c.926C>T (p.A309V)
-
SMAD4_000104
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
?/+
1
8
c.939del
r.(?)
p.(Ile314Phefs*22)
ACMG
VUS
g.48586270del
g.51059900del
939delC
-
SMAD4_000153
ACMG PVS1, PM2, PM4, PP3
Journal: Torring 2013
-
-
Germline
-
-
-
-
-
Karl Heinimann
?/.
1
-
c.947A>G
r.(?)
p.(Asn316Ser)
-
VUS
g.48586278A>G
g.51059908A>G
SMAD4(NM_005359.5):c.947A>G (p.N316S)
-
SMAD4_000234
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.955+18T>C
r.(=)
p.(=)
-
likely benign
g.48586304T>C
g.51059934T>C
SMAD4(NM_005359.5):c.955+18T>C
-
SMAD4_000105
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/.
1
-
c.955+58C>T
r.(=)
p.(=)
-
benign
g.48586344C>T
g.51059974C>T
-
-
SMAD4_000119
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.956-16C>T
r.(=)
p.(=)
-
likely benign
g.48591777C>T
g.51065407C>T
SMAD4(NM_005359.5):c.956-16C>T
-
SMAD4_000106
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
?/?
2
8i_9i
c.(955+1_956-1)_(1139+1_1140-1)dup
r.?
p.?
ACMG
VUS
g.(48586287_48591792)_(48591977_48593388)dup
-
dup ex8
-
SMAD4_000154
ACMG PVS1
Journal: O'Malley 2011
-
-
Germline
-
-
-
-
-
Karl Heinimann
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