Zhejiang University Center for Genetic and Genomic Medicine (ZJU-CGGM)
MSH2 (mutS homolog 2, colon cancer, nonpolyposis ty...)
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Unique variants in the MSH2 gene
The variants shown are described using the NM_000251.1 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 = exons 3 to 7, 8i_9 = border intron 8/exon 9.
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.
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
Type
: Type of variant at DNA level; note that the variant type can also be derived from the variant description (for all levels).
All options:
Substitution
Deletion
Duplication
Insertion
Inversion
Insertion/Deletion
Translocation
Other/Complex
DNA change (genomic) (hg19)
: Description of variant at DNA level, based on the genomic DNA reference sequence (following HGVS recommendations).
g.12345678C>T
g.12345678_12345890del
g.12345678_12345890dup
Reference
: Reference to publication describing the variant, including links to OMIM (when available), PubMed or or other source, e.g. "den Dunnen ASHG2003 P2346".
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.
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).
Variant remarks
: Remarks regarding the variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.
ClassClinical
: ClassClinical
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.
77 entries on 1 page. Showing entries 1 - 77.
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Legend
How to query
Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
Type
DNA change (genomic) (hg19)
Reference
DB-ID
Frequency
Variant remarks
ClassClinical
Owner
./.
1
00
c.-78_-79delGT
-
-
c.-78_-79delGT
-
GenBank
MSH2_00056
0.027
5' UTR
-
Qi Ming
./.
1
00
c.(?_-68)-1276+?del
-
-
exon1-7del
-
GenBank
MSH2_00138
0.0714
Exon
-
Qi Ming
./.
2
00
c.(?_-68)_1076+?del
-
-
del ex1_6, EX1_6del
-
GenBank
MSH2_00128
0.0238, 0.0154
Exon
-
Qi Ming
./.
1
00
c.(?_-68)_1661+?del
-
-
EX1_10del
-
GenBank
MSH2_00129
0.0154
Exon
-
Qi Ming
./.
1
00
c.(?_-68)_792+?del
-
-
exon1-4 del
-
GenBank
MSH2_00085
0.006
Exon
-
Qi Ming
./.
2
01
c.14C>A
-
p.Pro5Gln
hMSH2 at 14 codon 5: CCG->CAG, code 5 CCG>CAG;Pro>Gln
-
GenBank
MSH2_00119, MSH2_00093
0.0833, 0.25
Exon
-
Qi Ming
./.
1
01
c.21G>C
-
p.Glu7Asp
21G-C; nonsense
-
GenBank
MSH2_00028
0.0833
Exon
-
Qi Ming
./.
2
01
c.23C>T
-
p.Thr8Met
g.23C>T
-
GenBank
MSH2_00010
0.0645, 0.0263
Exon
-
Qi Ming
./.
1
01
c.54C>G
-
p.Gly18Gly
g.54C>G
-
GenBank
MSH2_00002
0.0323
Exon
-
Qi Ming
./.
1
01
c.187dupG
-
p.Val63GlyfsX19
missense changes starting from codon 63 and hits a stop codon at 81
-
GenBank
MSH2_00146
-
Exon
-
Qi Ming
./.
2
01
c.211+9C>G
-
-
g.211+9C>G, +9,intron1
-
GenBank
MSH2_00007
0.0968, 0.0238
Intron
-
Qi Ming
./.
1
02
c.212-?_1076+?del
-
-
Del exons 2-6
-
GenBank
MSH2_00133
0.0154
Exon
-
Qi Ming
./.
1
02
c.295A>C
-
p.Arg99Arg
c.295A>C;p.Arg99Arg
-
GenBank
MSH2_00060
0.0833
Exon
-
Qi Ming
./.
1
02
c.295_296delinsC
-
p.Arg99GlnfsX75
at 295 and 296 codon 99 exon 2: 295: A->C, 296:del. G
-
GenBank
MSH2_00123
0.0833
Exon
-
Qi Ming
./.
1
03
c.505A>G
-
p.Ile169Val
c.505A>G;p.Ile169Val
-
GenBank
MSH2_00019
0.0122
Exon
-
Qi Ming
./.
1
03
c.513delG
-
p.Arg171ArgfsX3
c.513delG
-
GenBank
MSH2_00100
0.0161
Exon
-
Qi Ming
./.
1
03
c.518T>G
-
p.Leu173Arg
c.518T>G;p.Leu173Arg
-
GenBank
MSH2_00018
0.0122
Exon
-
Qi Ming
./.
1
03
c.529G>A
-
p.Glu177Lys
c.529G>A
-
GenBank
MSH2_00038
0.0359
Exon
-
Qi Ming
./.
1
03
c.597T>C
-
p.Cys199Arg
c.597T>C(C199R)
-
GenBank
MSH2_00098
0.0081
Exon
-
Qi Ming
./.
4
03
c.610G>T
-
p.Gly204X
c.610G>T;G204stop, g.610G>T, G240X
-
GenBank
MSH2_00027
0.04, 0.0357, 0.0417
Exon
-
Qi Ming
./.
1
03
c.616_617insA
-
p.Thr206AsnfsX26
-
-
GenBank
MSH2_00094
0.25
Exon
-
Qi Ming
./.
2
04
c.646-?_942+?del
-
-
exon 4-5 del, exon 4-5 c.206-?_792+?del
-
GenBank
MSH2_00039
0.006, 0.0132
Exon
-
Qi Ming
./.
1
04
c.736A>T
-
p.Lys246X
c.736A>T;p.K346X
-
GenBank
MSH2_00032
0.0359
Exon
-
Qi Ming
./.
1
05
c.795T>C
-
p.Val265Val
c.795C>T
-
GenBank
MSH2_00014
0.0323
Exon
-
Qi Ming
./.
1
05
c.899_890insAT
-
p.Ile484IlefsX12
c.899_890insAT
-
GenBank
MSH2_00026
0.04
Exon
-
Qi Ming
./.
1
05
c.942+3A>T
-
-
-
-
GenBank
MSH2_00109
0.0132
Intron
-
Qi Ming
./.
2
07
c.1077-?_1276+?del
-
-
Del exon 7
-
GenBank
MSH2_00134
0.0154, 0.0132
Exon
-
Qi Ming
./.
1
07
c.1145G>A
-
p.Arg382His
c.1145G>A;p.382Arg>His
-
GenBank
MSH2_00059
0.0068
Exon
-
Qi Ming
./.
7
07
c.1168C>T
-
p.Leu390Phe
c.1168C>T;p.Leu390Phe, 1168,C>T;390,Arg-Phe, p.Phe390Leu, c.1168C>T;p.L390F, 1168C>T;L390F,
1 more item
-
GenBank
MSH2_00015
0.0488, 0.0238, 0.0495, 0.0068, 0.0118, 0.0263
Exon
-
Qi Ming
./.
3
07
c.1216_1219dupCGAC
-
p.Leu407ProfsX11
c.1215_1218dupCCGA; p.L407fsX417, p.L407fsX417
-
GenBank
MSH2_00021
-
Exon
-
Qi Ming
./.
3
07
c.1221C>G
-
p.Leu407Leu
g.1221C>G, c.1221C>G;p.Leu407Leu
-
GenBank
MSH2_00008
0.0323, 0.0122, 0.0714
Exon
-
Qi Ming
./.
2
07
c.1223A>G
-
p.Tyr408Cys
c.1223A>G;p.Tyr408Cys
-
GenBank
MSH2_00020
0.0095, 0.0099
Exon
-
Qi Ming
./.
1
07
c.1225C>A
-
p.Gln409Lys
c.1225C>A;p.409Gln>Lys
-
GenBank
MSH2_00058
0.0068
Exon
-
Qi Ming
./.
4
07
c.1255C>A
-
p.Gln419Lys
c.1255C>A;p.Gln419Lys, c.1255C>A;p.Q419K, 1255C>A;Q419K
-
GenBank
MSH2_00016
0.019, 0.0198, 0.0353, 0.0789
Exon
-
Qi Ming
./.
1
07
c.1261C>A
-
p.Leu421Met
c.1261C>A;p.Leu421Met
-
GenBank
MSH2_00017
0.0112
Exon
-
Qi Ming
./.
1
07
c.1276+47T>A
-
-
g.1276+47T>A
-
GenBank
MSH2_00003
0.0323
Intron
-
Qi Ming
./.
1
08
c.1277-1G>A
-
-
IVS7-1G>A
-
GenBank
MSH2_00086
0.04
Intron
-
Qi Ming
./.
1
09
c.1387-?_1510+?del
-
-
-
-
GenBank
MSH2_00142
0.0132
Exon
-
Qi Ming
./.
3
09
c.1452_1455delAATG
-
p.Ile484IlefsX12
c.1452_1455delAATG
-
GenBank
MSH2_00097, MSH2_00083
0.0161, 0.04, 0.0145
Exon
-
Qi Ming
./.
1
10
c.1552_1553delCA
-
p.Gln518ValfsX10
c.1550-1551delCA;p.Q518Valfs10
-
GenBank
MSH2_00033
0.0299
Exon
-
Qi Ming
./.
1
10
c.1571G>T
-
p.Arg524Leu
-
-
GenBank
MSH2_00110
0.0132
Exon
-
Qi Ming
./.
3
10
c.1661+12G>A
-
-
g.1661+12G>A, g.1661+12A>G
-
GenBank
MSH2_00006, MSH2_00087
0.0323, 0.1786, 0.179
Intron
-
Qi Ming
./.
1
11
c.1662-2A>G
-
-
g.1662-2A>G
-
GenBank
MSH2_00012
0.0323
Intron
-
Qi Ming
./.
1
11
c.1662-?_1759+?del
-
-
Del exon 11
-
GenBank
MSH2_00131
0.0154
Exon
-
Qi Ming
./.
1
11
c.1665delA
-
p.Lys555AsnfsX2
g.1664delA
-
GenBank
MSH2_00011
0.0323
Exon
-
Qi Ming
./.
2
11
c.1688A>C
-
p.Tyr563Ser
1688 A-C, 1688A-C;condon563Try-Ser
-
GenBank
MSH2_00043
0.0833
Exon
-
Qi Ming
./.
2
11
c.1690A>G
-
p.Thr564Ala
c.1690A>G;p.T564A, 1690A>G;T564A
-
GenBank
MSH2_00061
0.0118, 0.0263
Exon
-
Qi Ming
./.
1
11
c.1717delG
-
p.Ala573ProfsX17
c.1717delG;p.Ala573ProfsX17
-
GenBank
MSH2_00034
0.006
Exon
-
Qi Ming
./.
1
11
c.1738G>T
-
p.Glu580X
c.1738G>T(E580X)
-
GenBank
MSH2_00101
0.0081
Exon
-
Qi Ming
./.
2
11
c.1759_1760insT
-
p.Gly587ValfsX11
1760insT
-
GenBank
MSH2_00029
0.0833
Exon
-
Qi Ming
./.
1
12
c.1760delG
-
p.Gly587AlafsX3
c.1760delG
-
GenBank
MSH2_00095
0.0081
Exon
-
Qi Ming
./.
1
12
c.1760-?_2005+?del
-
-
exon 12 del
-
GenBank
MSH2_00037
0.006
Exon
-
Qi Ming
./.
1
12
c.1808A>G
-
p.Asp603Gly
c.1808A>G;p.Asp603Gly
-
GenBank
MSH2_00022
0.2
Exon
-
Qi Ming
./.
6
12
c.1886A>G
-
p.Gln629Arg
g.1886A>G, c.1886A>G;p.Q629R, 1886A>G;Q629R
-
GenBank
MSH2_00004
0.0323, 0.0714, 0.0198, 0.0353, 0.0526
Exon
-
Qi Ming
./.
1
12
c.1917T>A
-
p.His639Gln
-
-
GenBank
MSH2_00111
0.0132
Exon
-
Qi Ming
./.
1
12
c.1955C>A
-
p.Pro652His
-
-
GenBank
MSH2_00112
0.0132
Exon
-
Qi Ming
./.
3
13
c.2006-6T>C
-
-
g.2006-6T>C, -6, upstream of exon13, c.gIVS12-6T>C
-
GenBank
MSH2_00009
0.0323, 0.0238, 0.1957
Intron
-
Qi Ming
./.
1
13
c.2021_2022delGT
-
p.Gly674GlufsX23
c.2012-22delGT;p.Gly674Glufs23
-
GenBank
MSH2_00036
0.012
Exon
-
Qi Ming
./.
1
13
c.2038C>T
-
p.Arg680X
code680 CGA>TGA
-
GenBank
MSH2_00092
0.25
Exon
-
Qi Ming
./.
1
13
c.2047G>A
-
p.Gly683Arg
-
-
GenBank
MSH2_00113
0.0132
Exon
-
Qi Ming
./.
1
13
c.2064G>A
-
p.Met688Ile
Codon 688, Missense, ATG(Met)->ATA(Ile)
-
GenBank
MSH2_00126
0.0294
Exon
-
Qi Ming
./.
1
13
c.2091T>A
-
p.Cys697X
2091 T-A
-
GenBank
MSH2_00044
0.0833
Exon
-
Qi Ming
./.
1
13
c.2108C>A
-
p.Ser703Tyr
c.2108C>A;p.Ser703Tyr
-
GenBank
MSH2_00041
0.006
Exon
-
Qi Ming
./.
2
13
c.2210+1G>A
-
-
c.2210+1G>A;r.2006-2210del
-
GenBank
MSH2_00035
0.006, 0.027
Intron
-
Qi Ming
./.
2
14
c.2211-2A>C
-
-
g.2211-2A>C
-
GenBank
MSH2_00073
0.0357, 0.0417
Intron
-
Qi Ming
./.
1
14
c.2211-2A>G
-
-
-
-
GenBank
MSH2_00145
0.0357
Intron
-
Qi Ming
./.
1
14
c.2211-?_2458+?del
-
-
-
-
GenBank
MSH2_00143
0.0132
Exon
-
Qi Ming
./.
1
14
c.2228C>A
-
p.Ser743X
-
-
GenBank
MSH2_00050
0.0313
Exon
-
Qi Ming
./.
1
14
c.2253_2254delAA
-
p.Gly751GlyfsX35
exon19 751 AAdel
-
GenBank
MSH2_00127
-
Exon
-
Qi Ming
./.
1
14
c.2292G>A
-
p.Trp764X
g.2292G>A
-
GenBank
MSH2_00013
0.0323
Exon
-
Qi Ming
./.
2
15
c.2468_2469insC
-
p.Asp823AspfsX13
2469insC, 2469insG
-
GenBank
MSH2_00063, MSH2_00106
0.0833
Exon
-
Qi Ming
./.
2
15
c.2470_2471insG
-
p.Gln824ArgfsX12
2471insG
-
GenBank
MSH2_00062
0.0833
Exon
-
Qi Ming
./.
2
15
c.2516A>G
-
p.His839Arg
g.2516A>G
-
GenBank
MSH2_00005
0.0323, 0.0714
Exon
-
Qi Ming
./.
1
15
c.2577_2578insT
-
p.Ser860PhefsX5
2578insT
-
GenBank
MSH2_00107
-
Exon
-
Qi Ming
./.
1
15
c.2583A>G
-
p.Gln861Gln
c.2583A>G;Q861Q
-
GenBank
MSH2_00024
0.04
Exon
-
Qi Ming
./.
1
15
c.2632_2633delGA
-
p.Glu878AlafsX3
Codon 878, Frameshift, 2 bp (GA) deletion
-
GenBank
MSH2_00125
0.0294
Exon
-
Qi Ming
./.
1
16
c.2635-?_*3084del
-
-
-
-
GenBank
MSH2_00144
0.0132
Exon
-
Qi Ming
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