Unique variants in the PTEN gene

The variants shown are described using the NM_000314.6 transcript reference sequence.

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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.

Published as: Variant as originally reported (e.g. 521delT); listed only when different from "DNA change". Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G).

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

GVS function: The functional annotation of this position from the Genome Variation Server.
All options:

intergenic
near-gene-5
utr-5
start-lost
coding
non-coding-exon
coding-near-splice
non-coding-exon-near-splice
coding-synonymous
coding-synonymous-near-splice
codingComplex
codingComplex-near-splice
frameshift
frameshift-near-splice
missense
missense-near-splice
splice-5
splice
non-coding-intron-near-splice
intron
splice-3
stop-gained
stop-gained-near-splice
stop-lost
stop-lost-near-splice
utr-3
near-gene-3

Clinical classification: Clinical classification of variant

DNA change (genomic) (hg38): 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

Published as: Variant as originally reported (e.g. 521delT); listed only when different from "DNA change". Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G).

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.

dbSNP ID: The dbSNP ID.

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.

How to query this table

All list views have search fields which can be used to search data. You can search for a complete word or you can search for a part of a search term. If you enclose two or more words in double quotes, LOVD will search for the combination of those words only exactly in the order you specify. Note that search terms are case-insensitive and that wildcards such as * are treated as normal text! For all options, like "and", "or", and "not" searches, or searching for prefixes or suffixes, see the table below.

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.

6 entries on 1 page. Showing entries 1 - 6.

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How to query

Effect	Reported	Exon	DNA change (cDNA)	Published as	RNA change	Protein	GVS function	Clinical classification	DNA change (genomic) (hg38)	Published as	Reference	DB-ID	dbSNP ID	Frequency	Variant remarks	Owner
+/., -?/.	2	5	c.314G>C	-	r.(?)	p.(Cys105Ser)	-	ClinVar, ClinVar	g.87933073G>C	-	Jafri Malin Abdullah et al. (2006), dbSNP, ClinVar, N Zainuddin et al. (2004), dbSNP, ClinVar	PTEN_000003	rs780083983	1/14, 1/37	-	Nuur Athirah Binti Mohd Daud
+/., +?/.	2	5	c.370T>A	-	r.(?)	p.(Cys124Ser)	-	ClinVar	g.87933129T>A	-	Jafri Malin Abdullah et al. (2006), dbSNP, ClinVar, N Zainuddin et al. (2004), dbSNP, ClinVar	PTEN_000005	rs121909223	1/14, 1/37	-	Nuur Athirah Binti Mohd Daud
+/.	2	5	c.388C>T	-	r.(?)	p.(Arg130*)	-	ClinVar	g.87933147C>T	-	Jafri Malin Abdullah et al. (2006), dbSNP, ClinVar, N Zainuddin et al. (2004), dbSNP, ClinVar	PTEN_000002	rs121909224	2/14, 2/37	-	Nuur Athirah Binti Mohd Daud
+/.	2	6	c.511C>T	-	r.(?)	p.(Gln171*)	-	ClinVar	g.87952136C>T	-	Jafri Malin Abdullah et al. (2006), dbSNP, ClinVar, N Zainuddin et al. (2004), dbSNP, ClinVar	PTEN_000006	rs786204864	1/37, 1/9	-	Nuur Athirah Binti Mohd Daud
+/.	2	6	c.517C>T	-	r.(?)	p.(Arg173Cys)	-	ClinVar	g.87952142C>T	-	Jafri Malin Abdullah et al. (2006), dbSNP, ClinVar, N Zainuddin et al. (2004), dbSNP, ClinVar	PTEN_000004	rs121913293	2/14, 2/37	-	Nuur Athirah Binti Mohd Daud
+/., +?/.	2	6	c.518G>A	-	r.(?)	p.(Arg173His)	-	ClinVar, ClinVar	g.87952143G>A	-	Jafri Malin Abdullah et al. (2006), dbSNP, ClinVar, N Zainuddin et al. (2004), dbSNP, ClinVar	PTEN_000001	rs121913294	2/14, 2/37	-	Nuur Athirah Binti Mohd Daud

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How to query

Malaysian Node of the Human Variome Project Database

PTEN (phosphatase and tensin homolog)