Zhejiang University Center for Genetic and Genomic Medicine (ZJU-CGGM)
PTEN (phosphatase and tensin homolog)
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Unique variants in the PTEN gene
The variants shown are described using the NM_000314.4 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
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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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238 entries on 3 pages. Showing entries 1 - 100.
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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.-1238A>G
-
-
Substitution
-
GenBank
PTEN_00110
-
peripheral blood (PB)
-
Qi Ming
./.
1
00
c.-1110A>G
-
-
Substitution
-
GenBank
PTEN_00111
-
peripheral blood (PB)
-
Qi Ming
./.
1
00
c.-1088C>T
-
-
Substitution
-
GenBank
PTEN_00165
-
unkonw
-
Qi Ming
./.
2
00
c.-1084C>T
-
-
Substitution
-
GenBank
PTEN_00112
-
peripheral blood (PB), unkonw
-
Qi Ming
./.
2
01
c.-1026C>A
-
-
Substitution
-
GenBank
PTEN_00113
-
peripheral blood (PB), unkonw
-
Qi Ming
./.
1
01
c.-1000T>C
-
-
Substitution
-
GenBank
PTEN_00114
-
peripheral blood (PB)
-
Qi Ming
./.
1
01
c.-930G>A
-
-
Substitution
-
GenBank
PTEN_00115
-
peripheral blood (PB)
-
Qi Ming
./.
1
01
c.-920G>T
-
-
Substitution
-
GenBank
PTEN_00116
-
peripheral blood (PB)
-
Qi Ming
./.
2
01
c.-903G>A
-
-
Substitution
-
GenBank
PTEN_00117
-
peripheral blood (PB), unkonw
-
Qi Ming
./.
1
01
c.-895A>C
-
-
Substitution
-
GenBank
PTEN_00118
-
peripheral blood (PB)
-
Qi Ming
./.
1
01
c.-861G>T
-
-
Substitution
-
GenBank
PTEN_00104
-
peripheral blood (PB)
-
Qi Ming
./.
1
01
c.-834C>T
-
-
Substitution
-
GenBank
PTEN_00106
-
peripheral blood (PB)
-
Qi Ming
./.
1
01
c.-764G>A
-
-
Substitution
-
GenBank
PTEN_00108
-
peripheral blood (PB)
-
Qi Ming
./.
1
01
c.-9C>G
-
-
Substitution
-
GenBank
PTEN_00069
-
blood
-
Qi Ming
./.
1
7
c. 649 G>A
-
val Ile
Substitution
-
GenBank
PTEN_00263
-
peripheral blood (pb)
-
Qi Ming
./.
1
9
c.1153 T>A
-
Ser-Thr
Substitution
-
GenBank
PTEN_00264
-
peripheral blood (pb)
-
Qi Ming
./.
2
02
c.144C>?
-
p.Asn48Lys
Substitution
-
GenBank
PTEN_00254, PTEN_00255
-
blood & tumor, lymphocytes
-
Qi Ming
./.
1
05
c.384C>?
-
p.Lys128Asn
Substitution
-
GenBank
PTEN_00257
-
unkonw
-
Qi Ming
./.
1
06
c.540C>?
-
p.Tyr180X
Substitution
-
GenBank
PTEN_00258
-
muscles, epidermal naevus,vessels
-
Qi Ming
./.
1
08
c.945T>?
-
p.Tyr315X
Substitution
-
GenBank
PTEN_00063
-
blood
-
Qi Ming
./.
9
04, 02, 01, 09, 07
c.?
-
p.Thr78Thr, p.Tyr46_Arg47insAsn, p.?
Substitution, Insertion, Deletion, Duplication
-
GenBank
PTEN_00031, PTEN_00020, PTEN_00024
0.6%, 37%
lymphocytes, peripheral blood , unkonw, peripheral blood lymphocytes, lymphocyte, Unknown
-
Qi Ming
./.
1
-
IVS2+65 G>A
-
-
Substitution
-
GenBank
PTEN_00265
-
peripheral blood (pb)
-
Qi Ming
./.
1
01
c.17_18delAA
-
p.Lys6ArgfsX4
Deletion
-
GenBank
PTEN_00123
-
cerebellar tissue
-
Qi Ming
./.
2
01
c.40dup
-
p.Arg14LysfsX30
Duplication
-
GenBank
PTEN_00234
-
skin, blood
-
Qi Ming
./.
1
01
c.47_48insA
-
p.Tyr16X
Insertion
-
GenBank
PTEN_00109
-
urine,neck,thorax,abdomen
-
Qi Ming
./.
1
01
c.48T>A
-
p.Tyr16X
Substitution
-
GenBank
PTEN_00132
-
cerebellar tissue
-
Qi Ming
./.
1
01
c.53delA
-
p.Glu18GlyfsX6
Deletion
-
GenBank
PTEN_00222
-
cerebellar tissue
-
Qi Ming
./.
1
01
c.66C>G
-
p.Asp22Glu
Substitution
-
GenBank
PTEN_00172
-
unkonw
-
Qi Ming
./.
1
01
c.68T>A
-
p.Leu23X
Substitution
-
GenBank
PTEN_00021
-
blood
-
Qi Ming
./.
1
01
c.69_74del
-
p.Asp24_Leu25del
Deletion
-
GenBank
PTEN_00093
-
lymphocytes
-
Qi Ming
./.
1
01
c.74dupA
-
p.Leu25PhefsX19
Duplication
-
GenBank
PTEN_00101
-
lymphocytes
-
Qi Ming
./.
2
02
c.97_99delATT
-
p.Ile33del
Deletion
-
GenBank
PTEN_00042
-
blood
-
Qi Ming
./.
1
02
c.99delT
-
p.Ile33MetfsX21
Deletion
-
GenBank
PTEN_00128
-
cerebellar tissue
-
Qi Ming
./.
2
02
c.101C>A
-
p.Ala34Asp
Substitution
-
GenBank
PTEN_00069
-
muscles, epidermal naevus,vessels, Blood
-
Qi Ming
./.
1
02
c.103A>G
-
p.Met35Val
Substitution
-
GenBank
PTEN_00080
-
connective tissue
-
Qi Ming
./.
1
02
c.104T>C
-
p.Met35Thr
Substitution
-
GenBank
PTEN_00070
-
muscles, epidermal naevus,vessels
-
Qi Ming
./.
1
02
c.104T>G
-
p.Met35Arg
Substitution
-
GenBank
PTEN_00039
-
unknown
-
Qi Ming
./.
1
02
c.106G>A
-
p.Gly36Arg
Substitution
-
GenBank
PTEN_00040
-
blood
-
Qi Ming
./.
1
02
c.106G>C
-
p.Gly36Arg
Substitution
-
GenBank
PTEN_00134
-
cerebellar tissue
-
Qi Ming
./.
1
02
c.111T>C
-
p.Phe37Phe
Substitution
-
GenBank
PTEN_00211
-
unkonw
-
Qi Ming
./.
2
02
c.115G>C
-
p.Ala39Pro
Substitution
-
GenBank
PTEN_00119
-
blood, unkonw
-
Qi Ming
./.
1
02
c.141delG
-
p.Asn48ThrfsX6
Deletion
-
GenBank
PTEN_00193
-
unkonw
-
Qi Ming
./.
1
02
c.144C>A
-
p.Asn48Lys
Substitution
-
GenBank
PTEN_00178
-
unkonw
-
Qi Ming
./.
1
02
c.151_157del
-
p.Asp51X
Deletion
-
GenBank
PTEN_00208
-
DNA sample
-
Qi Ming
./.
1
02
c.155_157delATG
-
p.Asp52del
Deletion
-
GenBank
PTEN_00210
-
unkonw
-
Qi Ming
./.
1
02
c.157_158insATAC
-
p.Val53AspfsX11
Insertion
-
GenBank
PTEN_00216
-
blood
-
Qi Ming
./.
1
02
c.158_159delTA
-
p.Val53GlyfsX9
Deletion
-
GenBank
PTEN_00042
-
blood
-
Qi Ming
./.
2
02
c.164+1G>A
-
-
Substitution
-
GenBank
PTEN_00097, PTEN_00201
-
peripheral blood, unkonw
-
Qi Ming
./.
1
02
c.164+1_164+5delGTAAG
-
-
Deletion
-
GenBank
PTEN_00226
-
lymphocytes
-
Qi Ming
./.
1
03
c.165-2A>G
-
-
Substitution
-
GenBank
PTEN_00148
-
blood
-
Qi Ming
./.
1
03
c.170_171insTTAC
-
p.Leu57PhefsX7
Insertion
-
GenBank
PTEN_00232
-
lymphocyte
-
Qi Ming
./.
1
03
c.175T>C
-
p.Ser59Pro
Substitution
-
GenBank
PTEN_00164
-
blood
-
Qi Ming
./.
1
03
c.176C>A
-
p.Ser59X
Substitution
-
GenBank
PTEN_00098
-
lymphocytes
-
Qi Ming
./.
2
03
c.179del
-
p.Lys60SerfsX39
Deletion
-
GenBank
PTEN_00095
-
blood, peripheral blood leucocytes
-
Qi Ming
./.
1
03
c.181C>A
-
p.His61Asn
Substitution
-
GenBank
PTEN_00088
-
embryonic and fetal
-
Qi Ming
./.
1
03
c.186_187insCA
-
p.Asn63GlnfsX37
Insertion
-
GenBank
PTEN_00073
-
Unknown
-
Qi Ming
./.
1
03
c.200T>G
-
p.Ile67Arg
Substitution
-
GenBank
PTEN_00221
-
blood
-
Qi Ming
./.
2
03
c.202T>C
-
p.Tyr68His
Substitution
-
GenBank
PTEN_00121
-
blood
-
Qi Ming
./.
1
03
c.202T>G
-
p.Tyr68Asp
Substitution
-
GenBank
PTEN_00120
-
blood and the epidermal naevus
-
Qi Ming
./.
1
03
c.203A>G
-
p.Tyr68Cys
Substitution
-
GenBank
PTEN_00044
-
pulverized tissue
-
Qi Ming
./.
1
03
c.209T>C
-
p.Leu70Pro
Substitution
-
GenBank
PTEN_00005
2%
unkonwn
-
Qi Ming
./.
3
03
c.209+1G>A
-
-
Substitution
-
GenBank
PTEN_00099
-
muscles, epidermal naevus,vessels, lymphocytes, Blood
-
Qi Ming
./.
1
03
c.209+1G>C
-
-
Substitution
-
GenBank
PTEN_00043
-
blood
-
Qi Ming
./.
1
03
c.209+1_209+2delGT
-
-
Deletion
-
GenBank
PTEN_00141
-
blood
-
Qi Ming
./.
1
03
c.209+4_209+7delAGTA
-
-
Deletion
-
GenBank
PTEN_00245
-
blood
-
Qi Ming
./.
1
03
c.209+5G>A
-
-
Substitution
-
GenBank
PTEN_00036
-
unknown
-
Qi Ming
./.
1
04
c.210-39A>G
-
-
Substitution
-
GenBank
PTEN_00037
-
unknown
-
Qi Ming
./.
1
04
c.210-9T>C
-
-
Substitution
-
GenBank
PTEN_00209
-
unkonw
-
Qi Ming
./.
1
04
c.210-7_210-3del
-
-
Deletion
-
GenBank
PTEN_00140
-
blood
-
Qi Ming
./.
1
04
c.210-7_210-3delCTTTT
-
-
Deletion
-
GenBank
PTEN_00253
-
Blood
-
Qi Ming
./.
1
04
c.210-1G>A
-
-
Substitution
-
GenBank
PTEN_00149
-
blood
-
Qi Ming
./.
1
04
c.219_222delAAGA
-
p.Glu73AspfsX25
Deletion
-
GenBank
PTEN_00247
-
blood
-
Qi Ming
./.
1
04
c.220delA
-
p.Arg74AspfsX25
Deletion
-
GenBank
PTEN_00072
-
muscles, epidermal naevus,vessels
-
Qi Ming
./.
1
04
c.232A>G
-
p.Thr78Ala
Substitution
-
GenBank
PTEN_00076
-
DNA sample
-
Qi Ming
./.
1
04
c.235G>A
-
p.Ala79Thr
Substitution
-
GenBank
PTEN_00248
-
Unknown
-
Qi Ming
./.
1
04
c.238A>G
-
p.Lys80Glu
Substitution
-
GenBank
PTEN_00135
-
cerebellar tissue
-
Qi Ming
./.
1
04
c.242T>C
-
p.Phe81Ser
Substitution
-
GenBank
PTEN_00045
-
pulverized tissue
-
Qi Ming
./.
2
04
c.245A>C
-
p.Asp82Thr, p.Asn82Thr
Substitution
-
GenBank
PTEN_00075
-
DNA sample, Unknown
-
Qi Ming
./.
1
04
c.248G>A
-
p.Cys83Tyr
Substitution
-
GenBank
PTEN_00046
-
pulverized tissue
-
Qi Ming
./.
1
04
c.253+1G>T
-
-
Substitution
-
GenBank
PTEN_00044
-
blood
-
Qi Ming
./.
1
04
c.253+2T>C
-
-
Substitution
-
GenBank
PTEN_00150
-
blood
-
Qi Ming
./.
1
04
c.253+108_253+109insTCTTA
-
-
Insertion
-
GenBank
PTEN_00241
-
unknown
-
Qi Ming
./.
1
05
c.254-27dup
-
-
Duplication
-
GenBank
PTEN_00242
-
unknown
-
Qi Ming
./.
1
05
c.254-11T>G
-
-
Substitution
-
GenBank
PTEN_00070
-
blood
-
Qi Ming
./.
1
05
c.258A>G
-
p.Ala86Ala
Substitution
-
GenBank
PTEN_00047
-
pulverized tissue
-
Qi Ming
./.
2
05
c.259C>T
-
p.Gln87X
Substitution
-
GenBank
PTEN_00050
-
unkonw, blood
-
Qi Ming
./.
1
05
c.262T>C
-
p.Tyr88His
Substitution
-
GenBank
PTEN_00133
-
cerebellar tissue
-
Qi Ming
./.
1
05
c.265_266insTT
-
p.Pro89LeufsX11
Insertion
-
GenBank
PTEN_00159
-
unkonw
-
Qi Ming
./.
1
05
c.275A>G
-
p.Asp92Gly
Substitution
-
GenBank
PTEN_00166
-
blood
-
Qi Ming
./.
1
05
c.276C>A
-
p.Asp92Glu
Substitution
-
GenBank
PTEN_00143
-
blood
-
Qi Ming
./.
1
05
c.277C>T
-
p.His93Tyr
Substitution
-
GenBank
PTEN_00167
-
blood
-
Qi Ming
./.
1
05
c.286C>T
-
p.Pro96Ser
Substitution
-
GenBank
PTEN_00251
-
blood
-
Qi Ming
./.
1
05
c.287C>A
-
p.Pro96Gln
Substitution
-
GenBank
PTEN_00009
-
blood
-
Qi Ming
./.
1
05
c.289C>T
-
p.Gln97fsX
Substitution
-
GenBank
PTEN_00045
-
blood
-
Qi Ming
./.
2
05
c.302_304delinsCC
-
p.Ile101ThrfsX12
Insertion/Deletion
-
GenBank
PTEN_00228, PTEN_00217
-
muscles, epidermal naevus,vessels, blood
-
Qi Ming
./.
1
05
c.303_304insT
-
p.Lys102X
Insertion
-
GenBank
PTEN_00218
-
blood
-
Qi Ming
./.
1
05
c.307C>A
-
p.Pro103Thr
Substitution
-
GenBank
PTEN_00092
-
embryonic and fetal
-
Qi Ming
./.
1
05
c.314G>A
-
p.Cys105Tyr
Substitution
-
GenBank
PTEN_00122
-
Blood
-
Qi Ming
./.
1
05
c.323T>C
-
p.Leu108Pro
Substitution
-
GenBank
PTEN_00074
-
muscles, epidermal naevus,vessels
-
Qi Ming
./.
1
05
c.324del
-
p.Asp109ThrfsX4
Deletion
-
GenBank
PTEN_00256
-
Blood
-
Qi Ming
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