Global Variome shared LOVD
PAX2 (paired box 2)
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Curator:
Matthew Bower
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Unique variants in the PAX2 gene
The variants shown are described using the NM_003990.3 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%)
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.
154 entries on 2 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
-/.
1
-
c.-10538G>T
r.(?)
p.(=)
-
benign
g.102495480G>T
g.100735723G>T
PAX2(NM_001304569.2):c.15G>T (p.A5=)
-
PAX2_000134
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/.
1
-
c.-10522A>T
r.(?)
p.(=)
-
likely benign
g.102495496A>T
-
PAX2(NM_001304569.2):c.25+6A>T
-
PAX2_000186
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
1
-
c.-203A>G
r.(?)
p.(=)
-
benign
g.102505815A>G
g.100746058A>G
-
-
PAX2_000127
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-?/.
1
-
c.-160G>T
r.(?)
p.(=)
-
likely benign
g.102505858G>T
g.100746101G>T
-
-
PAX2_000128
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/+
1
_1_3i
c.(?_-30)_(410+1_411-1)del
r.0?
p.0?
-
pathogenic
g.(?_102505988)_(102510649_102539254)del
-
(?_-30)_(410+?)del
-
PAX2_000100
-
PubMed: Heidet 2017
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+
1
_1_11_
c.(?_-30)_(*220_?)del
r.0?
p.0?
-
pathogenic
g.(?_102505988)_(102587660_?)del
-
-
-
PAX2_000096
-
PubMed: Heidet 2017
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+
5
_1_11_
c.-550_*2258{0}
r.0
p.0
-
pathogenic
g.(99928954_99948269)_(103741327_103757755)del, g.(?_102020722)_(102825352 _?)del,
3 more items
g.(98169197_98188512)_(101981570_101997998)del, g.(?_100260965)_(101065595_?)del,
3 more items
hg18:g.(99918944_99938259)_(103731317_103747745)del, hg18:g.(?_102438000)_(102678000_?)del,
3 more items
46,XX,del(10)(q23.2q24.3)
PAX2_000069, PAX2_000070, PAX2_000071, PAX2_000102
19 total genes in deleted segment, 240kb deletion, includes PAX2 and portion FAM178A gene,
3 more items
PubMed: Benetti 2007
,
PubMed: Hoefele 2012
,
PubMed: Peltekova 2014
,
PubMed: Pfundt 2017
,
1 more item
-
-
De novo, Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+
1
?
c.?
r.?
p.?
-
pathogenic
g.?
-
46,XY,t(10;13)(q24.3q12.3)
46,XY,t(10;13)(q24.3q12.3)
PAX2_000043
translocation breakpoint believed to localize to intron 3 or 4 by Southern blot RFLP analysis
PubMed: Narahara 1997
-
-
De novo
-
-
-
-
-
Matthew Bower
+?/+?
1
1
c.5A>G
r.(?)
p.(Asp2Gly)
-
likely pathogenic
g.102506022A>G
g.100746265A>G
-
-
PAX2_000086
-
PubMed: Barua 2014
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+?/.
1
1
c.8T>C
r.(?)
p.(Met3Thr)
ACMG
VUS
g.102506025T>C
g.100746268T>C
-
-
PAX2_000172
Mother is heterozygous, Father (variant not found).
-
-
rs754968736
Germline
?
-
BciVI+, MslI-
-
-
Miriam Erandi Reyna-Fabián
+/+
1
1i
c.43+1G>C
r.spl
p.?
-
pathogenic
g.102506061G>C
g.100746304G>C
-
-
PAX2_000044
-
PubMed: Bower 2012
-
-
De novo
-
-
-
-
-
Matthew Bower
-?/.
1
-
c.43+3G>A
r.spl?
p.?
-
likely benign
g.102506063G>A
-
PAX2(NM_003988.4):c.43+3G>A
-
PAX2_000175
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/.
3
-
c.43+10G>C
r.(=)
p.(=)
-
benign
g.102506070G>C
g.100746313G>C
PAX2(NM_003988.5):c.43+10G>C
-
PAX2_000156
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
+/+
1
2
c.58_64dup
r.(?)
p.(Gln22Argfs*34)
-
pathogenic
g.102509517_102509523dup
g.100749760_100749766dup
57_58insGTGAACC
-
PAX2_000094
-
PubMed: Okumura et al.,2015
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+
1
2
c.59del
r.(?)
p.(Val20Glyfs*9)
-
pathogenic
g.102509518del
g.100749761del
-
-
PAX2_000002
somatic mosaicism
PubMed: Chung 2001
-
-
Somatic
-
-
-
-
-
Matthew Bower
+/+
1
2
c.68del
r.(?)
p.(Leu23Profs*6)
-
pathogenic
g.102509527del
g.100749770del
-
-
PAX2_000003
-
PubMed: Cunliffe 1998
-
-
Germline
-
-
-
-
-
Matthew Bower
+/+, +/.
2
2
c.69del
r.(?)
p.(Val26Cysfs*3)
-
pathogenic, pathogenic (dominant)
g.102509528del
g.100749771del
69delC
-
PAX2_000004
-
Journal: Negrisolo 2023
,
PubMed: Negrisolo 2010
-
-
De novo
-
-
-
-
-
Susanna Negrisolo
,
Matthew Bower
?/.
1
-
c.70G>C
r.(?)
p.(Gly24Arg)
-
VUS
g.102509529G>C
g.100749772G>C
-
-
PAX2_000135
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+?/+?
1
2
c.71G>A
r.(?)
p.(Gly24Glu)
-
likely pathogenic
g.102509530G>A
g.100749773G>A
-
-
PAX2_000005
-
PubMed: Thomas 2011
-
-
Germline
-
-
-
-
-
Matthew Bower
?/.
1
-
c.73G>C
r.(?)
p.(Gly25Arg)
-
VUS
g.102509532G>C
g.100749775G>C
-
-
PAX2_000129
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+?/+?
2
2
c.74G>T
r.(?)
p.(Gly25Val)
-
likely pathogenic
g.102509533G>T
-
-
-
PAX2_000045
de novo in mother
PubMed: Bower 2012
-
-
De novo, Germline
-
-
-
-
-
Matthew Bower
+/+
1
2
c.75_76dup
r.(?)
p.(Val26Glyfs*4)
-
pathogenic
g.102509534_102509535dup
g.100749777_100749778dup
-
-
PAX2_000007
-
PubMed: Amiel 2000
-
-
De novo
-
-
-
-
-
Matthew Bower
+/+
3
2
c.76del
r.(?)
p.(Val26Cysfs*3)
-
pathogenic
g.102509535del
g.100749778del
-
-
PAX2_000006
de novo in mother
PubMed: Heidet 2017
, {PMID:Schimmenti 1999},
PubMed: Schimmenti 1999
, {PMID:Schimmenti 1999}
-
-
De novo, Germline
-
-
-
-
-
Matthew Bower
+/+, +/.
59
2
c.76dup
r.(?)
p.(Val26GlyFS*28), p.(Val26GlyfsTer28)
-
pathogenic
g.102509535dup
g.100749778dup
NM_003987.3:69_70insG,
1 more item
-
PAX2_000001
germline and somatic mosaicism, germline mosaicism, presumed de novo- no prior family history,
1 more item
PubMed: Amiel 2000
,
PubMed: Amiel 2000
,
PubMed: Beby 2010
,
PubMed: Bower 2012
,
PubMed: Cheong 2007
,
18 more items
-
-
CLASSIFICATION record, De novo, Germline, Somatic
-
-
-
-
-
VKGL-NL_Leiden
,
VKGL-NL_Groningen
,
Matthew Bower
+?/+?
1
2
c.92_97del
r.(?)
p.(Arg31_Pro32del)
-
likely pathogenic
g.102509551_102509556del
g.100749794_100749799del
-
-
PAX2_000008
-
PubMed: Weber 2006
-
-
Germline
-
-
-
-
-
Matthew Bower
+?/.
1
-
c.95C>G
r.(?)
p.(Pro32Arg)
ACMG
VUS
g.102509554C>G
-
-
-
PAX2_000165
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Jinu Han
-?/.
1
-
c.96C>G
r.(?)
p.(Pro32=)
-
likely benign
g.102509555C>G
-
PAX2(NM_003988.4):c.96C>G (p.P32=)
-
PAX2_000176
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.97C>T
r.(?)
p.(Leu33=)
-
likely benign
g.102509556C>T
-
PAX2(NM_003988.4):c.97C>T (p.L33=)
-
PAX2_000167
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+?/+?
1
2
c.98T>G
r.(?)
p.(Leu33Arg)
-
likely pathogenic
g.102509557T>G
g.100749800T>G
-
-
PAX2_000046
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
?/.
1
-
c.103G>C
r.(?)
p.(Asp35His)
-
VUS
g.102509562G>C
g.100749805G>C
PAX2(NM_000278.3):c.103G>C (p.(Asp35His))
-
PAX2_000137
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+?/+?
1
2
c.115_120del
r.(?)
p.(Gln39_Arg40del)
-
likely pathogenic
g.102509574_102509579del
g.100749817_100749822del
-
-
PAX2_000009
-
PubMed: Salomon 2001
-
-
Germline
-
-
-
-
-
Matthew Bower
+/+
5
2
c.119_120del
r.(?)
p.(Arg40Hisfs*13)
-
pathogenic
g.102509578_102509579del
g.100749821_100749822del
-
-
PAX2_000092
-
PubMed: Okumura 2015
-
-
Germline, Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+
1
2
c.129_150del
r.(?)
p.(Glu43Aspfs*33)
-
pathogenic
g.102509588_102509609del
g.100749831_100749852del
-
-
PAX2_000010
-
PubMed: Schimmenti 1997
-
-
De novo
-
-
-
-
-
Matthew Bower
?/.
1
-
c.131T>C
r.(?)
p.(Leu44Pro)
-
VUS
g.102509590T>C
-
-
-
PAX2_000177
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/+
6
2
c.139_148del
r.(?)
p.(Gln47Glyfs*33)
-
pathogenic
g.102509598_102509607del
g.100749841_100749850del
-
-
PAX2_000011
de novo in mother
PubMed: Fletcher 2005
-
-
De novo, Germline
-
-
-
-
-
Matthew Bower
+?/.
1
2
c.153_155delinsTT
r.(?)
p.(Cys52Leufs*31)
-
likely pathogenic (dominant)
g.102509612_102509614delinsTT
g.100749855_100749857delinsTT
153_155delCTGinsTT
-
PAX2_000174
-
Journal: Negrisolo 2023
-
-
De novo
-
-
-
-
-
Susanna Negrisolo
+?/+?
2
2
c.155G>A
r.(?)
p.(Cys52Tyr)
-
likely pathogenic
g.102509614G>A
g.100749857G>A
-
-
PAX2_000068
-
PubMed: Iatropoulos 2012
-
-
De novo
-
-
-
-
-
Matthew Bower
+?/+?
1
2
c.167G>A
r.(?)
p.(Arg56Gln)
-
likely pathogenic
g.102509626G>A
g.100749869G>A
-
-
PAX2_000081
-
PubMed: Barua 2014
-
-
Germline
-
-
-
-
-
Matthew Bower
+?/+?
2
2
c.182G>A
r.(?)
p.(Ser61Asn)
-
likely pathogenic
g.102509641G>A
g.100749884G>A
-
-
PAX2_000064
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
+?/+?
1
2
c.182G>T
r.(?)
p.(Ser61Ile)
-
likely pathogenic
g.102509641G>T
g.100749884G>T
-
-
PAX2_000047
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
+?/+?
1
2
c.183C>A
r.(?)
p.(Ser61Arg)
-
likely pathogenic
g.102509642C>A
g.100749885C>A
-
-
PAX2_000097
-
PubMed: Heidet 2017
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+
1
2
c.184_198del
r.(?)
p.(His62_Ser66del)
-
pathogenic
g.102509643_102509657del
g.100749886_100749900del
-
-
PAX2_000048
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
+/., +?/+?
2
2
c.187G>A
r.(?)
p.(Gly63Ser)
-
likely pathogenic, pathogenic
g.102509646G>A
g.100749889G>A
-
-
PAX2_000093
-
PubMed: Okumura 2015
,
PubMed: Sanna-Cherchi 2017
,
Journal: Sanna-Cherchi 2017
-
-
De novo, Germline/De novo (untested)
-
-
-
-
-
Johan den Dunnen
,
Matthew Bower
+?/+?
3
2
c.206T>C
r.(?)
p.(Leu69Pro)
-
likely pathogenic
g.102509665T>C
g.100749908T>C
-
-
PAX2_000031
-
PubMed: Bower 2012
-
-
De novo, Germline
-
-
-
-
-
Matthew Bower
+?/+?
1
2
c.211A>G
r.(?)
p.(Arg71Gly)
-
likely pathogenic
g.102509670A>G
g.100749913A>G
-
-
PAX2_000075
-
PubMed: Hwang 2013
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+?/+?
1
2
c.212G>A
r.(?)
p.(Arg71Lys)
-
likely pathogenic
g.102509671G>A
g.100749914G>A
-
-
PAX2_000099
-
PubMed: Heidet 2017
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+?/+?
4
2
c.212G>C
r.(?)
p.(Arg71Thr)
-
likely pathogenic
g.102509671G>C
g.100749914G>C
-
-
PAX2_000056
de novo in mother
PubMed: Higashide 2005
,
PubMed: Okumura 2015
-
-
De novo, Germline
-
-
-
-
-
Matthew Bower
+?/.
1
2
c.212G>T
r.(?)
p.(Arg71Met)
-
likely pathogenic (dominant)
g.102509671G>T
g.100749914G>T
-
-
PAX2_000173
-
Journal: Negrisolo 2023
-
-
De novo
-
-
-
-
-
Susanna Negrisolo
+/+?
1
2i
c.213-2A>G
r.(?)
p.?
-
pathogenic
g.102510449A>G
g.100750692A>G
-
-
PAX2_000103
-
PubMed: Galvez-Ruiz 2018
-
-
Germline
-
-
-
-
-
Matthew Bower
+/.
1
-
c.213-1G>A
r.spl?
p.?
-
pathogenic
g.102510450G>A
-
-
-
PAX2_000184
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/+
3
3
c.219C>G
r.(?)
p.(Tyr73*)
-
pathogenic
g.102510457C>G
g.100750700C>G
-
-
PAX2_000057
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
+/?, +?/+?
2
3
c.221_226dup
r.(?)
p.(Glu74_Thr75dup)
-
likely pathogenic, pathogenic
g.102510459_102510464dup
g.100750702_100750707dup
220_225dup
-
PAX2_000013
-
PubMed: DeVriendt 1998
,
PubMed: DeVriendt 1998
,
PubMed: Liu 2018
-
-
De novo
-
-
-
-
-
Matthew Bower
+/+
1
3
c.223_224dup
r.(?)
p.(Gly76Profs*8)
-
pathogenic
g.102510461_102510462dup
g.100750704_100750705dup
-
-
PAX2_000095
-
PubMed: Okumura 2015
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+, +/+?
12
3
c.223_225dup
r.(?)
p.(Thr75dup)
-
pathogenic
g.102510461_102510463dup
g.100750704_100750706dup
-
-
PAX2_000054
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
+/., +?/+?
7
3
c.226G>A
r.(?)
p.(Gly76Ser)
-
likely pathogenic, pathogenic
g.102510464G>A
-
PAX2(NM_003988.5):c.226G>A (p.G76S)
-
PAX2_000014
VKGL data sharing initiative Nederland
PubMed: Devriendt 1998
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Utrecht
,
Matthew Bower
?/.
1
-
c.226G>C
r.(?)
p.(Gly76Arg)
-
VUS
g.102510464G>C
-
PAX2(NM_003988.4):c.226G>C (p.G76R)
-
PAX2_000178
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+
3
3
c.228_251dup
r.(?)
p.(Ser77_Gly84dup)
-
pathogenic
g.102510466_102510489dup
g.100750709_100750732dup
-
-
PAX2_000052
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
+?/+?
1
3
c.239C>T
r.(?)
p.(Pro80Leu)
-
likely pathogenic
g.102510477C>T
g.100750720C>T
-
-
PAX2_000078
Maternal half sister and maternal grandmother reported to have renal disease, but not tested.
PubMed: Barua 2014
-
-
Germline
-
-
-
-
-
Matthew Bower
+?/+?
6
3
c.250G>A
r.(?)
p.(Gly84Ser)
-
likely pathogenic
g.102510488G>A
g.100750731G>A
-
-
PAX2_000034
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
-/.
1
-
c.255C>T
r.(?)
p.(Gly85=)
-
benign
g.102510493C>T
g.100750736C>T
PAX2(NM_003988.5):c.255C>T (p.G85=)
-
PAX2_000158
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+?/.
1
-
c.263C>T
r.(?)
p.(Pro88Leu)
-
likely pathogenic
g.102510501C>T
g.100750744C>T
PAX2(NM_003988.5):c.263C>T (p.P88L)
-
PAX2_000159
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/+
2
3
c.289del
r.(?)
p.(Asp97Thrfs*62)
-
pathogenic
g.102510527del
g.100750770del
-
-
PAX2_000015
de novo in father
PubMed: Amiel 2000
-
-
Germline
-
-
-
-
-
Matthew Bower
+/+
5
3
c.310C>T
r.(?)
p.(Arg104*)
-
pathogenic
g.102510548C>T
g.100750791C>T
-
-
PAX2_000016
-
PubMed: Cheong 2007
,
PubMed: Cheong 2007
,
PubMed: Samimi 2008
-
-
De novo
-
-
-
-
-
Matthew Bower
+?/+?
1
3
c.320C>T
r.(?)
p.(Pro107Leu)
-
likely pathogenic
g.102510558C>T
g.100750801C>T
-
-
PAX2_000076
-
PubMed: Hwang 2013
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+, +?/+?
10
3
c.331G>A
r.(?)
p.(Ala111Thr)
-
likely pathogenic, pathogenic
g.102510569G>A
g.100750812G>A
-
-
PAX2_000058
-
PubMed: Sellick 2004
,
PubMed: Bower 2012
-
-
De novo, Germline
-
-
-
-
-
Matthew Bower
+/.
1
-
c.337del
r.(?)
p.(Glu113ArgfsTer46)
-
pathogenic
g.102510575del
g.100750818del
PAX2(NM_003988.4):c.337delG (p.E113Rfs*46)
-
PAX2_000138
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+, +/.
8
3
c.343C>T
r.(?)
p.(Arg115*), p.(Arg115Ter)
-
pathogenic
g.102510581C>T
g.100750824C>T
PAX2(NM_003988.5):c.343C>T (p.R115*)
-
PAX2_000059
VKGL data sharing initiative Nederland
PubMed: Bower 2012
,
PubMed: Schimmenti 2003
,
PubMed: Schimmenti 2003
,
PubMed: Bower 2012
-
-
CLASSIFICATION record, De novo, Germline
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
,
Matthew Bower
+?/+?
2
3
c.350G>C
r.(?)
p.(Arg117Pro)
-
likely pathogenic
g.102510588G>C
g.100750831G>C
-
-
PAX2_000050
de novo in father
PubMed: Bower 2012
,
PubMed: Madariaga 2013
,
PubMed: Madariaga 2013
-
-
Germline
-
-
-
-
-
Matthew Bower
-/., -?/.
3
-
c.360C>T
r.(?)
p.(Ala120=)
-
benign, likely benign
g.102510598C>T
g.100750841C>T
PAX2(NM_003988.4):c.360C>T (p.A120=), PAX2(NM_003988.5):c.360C>T (p.A120=)
-
PAX2_000111
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
,
VKGL-NL_AMC
+/.
1
-
c.383_384del
r.(?)
p.(Thr128Serfs*52)
-
pathogenic
g.102510621_102510622del
-
PAX2(NM_003988.5):c.383_384delCA (p.T128Sfs*52)
-
PAX2_000168
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+?/+?
3
3
c.388C>T
r.(?)
p.(Pro130Ser)
-
likely pathogenic
g.102510626C>T
g.100750869C>T
-
-
PAX2_000060
de novo in mother (grandpaternal allele)
PubMed: Bower 2012
-
-
De novo, Germline
-
-
-
-
-
Matthew Bower
+?/+?
1
3
c.389C>A
r.(?)
p.(Pro130His)
-
likely pathogenic
g.102510627C>A
g.100750870C>A
-
-
PAX2_000018
-
PubMed: Miyazawa 2009
-
-
Germline
-
-
-
-
-
Matthew Bower
+?/+?
1
3
c.389C>G
r.(?)
p.(Pro130Arg)
-
likely pathogenic
g.102510627C>G
g.100750870C>G
-
-
PAX2_000104
-
PubMed: Galvez-Ruiz 2018
-
-
Germline
-
-
-
-
-
Matthew Bower
+/+
1
3
c.392del
r.(?)
p.(Ser131Thrfs*28)
-
pathogenic
g.102510630del
g.100750873del
-
-
PAX2_000019
-
PubMed: Martinovic-Bouriel 2010
-
-
De novo
-
-
-
-
-
Matthew Bower
+?/+?
1
3
c.398C>T
r.(?)
p.(Ser133Phe)
-
likely pathogenic
g.102510636C>T
g.100750879C>T
-
-
PAX2_000080
-
PubMed: Barua 2014
-
-
Germline
-
-
-
-
-
Matthew Bower
+/+
2
3
c.408del
r.(?)
p.(Asn136Lysfs*23)
-
pathogenic
g.102510646del
g.100750889del
-
-
PAX2_000077
-
PubMed: Hwang 2013
-
-
Germline
-
-
-
-
-
Matthew Bower
?/.
1
-
c.410G>A
r.(?)
p.(Arg137Lys)
-
VUS
g.102510648G>A
g.100750891G>A
-
-
PAX2_000139
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+?/+?, ?/?
2
3i
c.410+5G>A
r.spl
p.?
-
likely pathogenic, VUS
g.102510653G>A
g.100750896G>A
-
-
PAX2_000023
-
PubMed: Bower 2012
,
PubMed: Negrisolo 2011
,
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
-?/.
1
-
c.410+16G>A
r.(=)
p.(=)
-
likely benign
g.102510664G>A
-
PAX2(NM_003988.5):c.410+16G>A
-
PAX2_000183
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/.
1
-
c.410+68A>C
r.(=)
p.(=)
-
benign
g.102510716A>C
g.100750959A>C
PAX2(NM_003988.5):c.410+68A>C
-
PAX2_000112
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/+, +/.
3
3i
c.411-2A>G
r.spl, r.spl?
p.?
-
pathogenic
g.102539253A>G
g.100779496A>G
PAX2(NM_003988.5):c.411-2A>G
-
PAX2_000061
VKGL data sharing initiative Nederland
PubMed: Weber 2006
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Utrecht
,
Matthew Bower
?/?
1
4
c.415A>G
r.(?)
p.(Ile139Val)
-
VUS
g.102539259A>G
g.100779502A>G
-
-
PAX2_000084
Patient has two variants, both predicted benign by Polyphen2
PubMed: Barua 2014
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+?/.
3
4
c.418C>T
r.(?)
p.(Arg140Trp)
-
likely pathogenic
g.102539262C>T
g.100779505C>T
PAX2(NM_003988.5):c.418C>T (p.R140W), PAX2(NM_003990.3):c.418C>T( p.R140W )
-
PAX2_000090
variant inherited from mother with bilateral renal hypodysplasia and chronic kidney disease,
1 more item
PubMed: Negrisolo 2018
,
PubMed: Sun 2018
-
-
CLASSIFICATION record, Germline, Germline/De novo (untested)
?
229
-
-
-
VKGL-NL_Utrecht
,
Susanna Negrisolo
+?/+?
1
4
c.419G>A
r.(?)
p.(Arg140Gln)
-
likely pathogenic
g.102539263G>A
g.100779506G>A
-
-
PAX2_000055
-
PubMed: Weber 2006
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/.
1
-
c.433C>T
r.(?)
p.(Gln145Ter)
-
pathogenic
g.102539277C>T
g.100779520C>T
PAX2(NM_003988.5):c.433C>T (p.Q145*)
-
PAX2_000115
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/+
1
4
c.(?_442)_(496_?)del
r.?
p.?
-
pathogenic
g.(?_102539286)_(102539340_?)del
-
(?_442)_(496_?)del
-
PAX2_000101
-
PubMed: Heidet 2017
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+/+
1
4
c.446del
r.(?)
p.(Pro149Glnfs*10)
-
pathogenic
g.102539290del
g.100779533del
-
-
PAX2_000098
-
PubMed: Heidet 2017
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
+?/?
1
4
c.448A>G
r.(?)
p.(Thr150Ala)
-
likely pathogenic
g.102539292A>G
g.100779535A>G
-
-
PAX2_000082
1 more item
PubMed: Barua 2014
-
-
Germline
-
-
-
-
-
Matthew Bower
+/+
1
4
c.448del
r.(?)
p.(Thr150Argfs*9)
-
pathogenic
g.102539292del
g.100779535del
-
-
PAX2_000032
-
PubMed: Bower 2012
-
-
Germline
-
-
-
-
-
Matthew Bower
-?/-?, -?/.
2
4
c.453G>A
r.(?)
p.(=), p.(Pro151=)
-
likely benign
g.102539297G>A
g.100779540G>A
PAX2(NM_003988.4):c.453G>A (p.P151=)
-
PAX2_000065
VKGL data sharing initiative Nederland
PubMed: Bower 2012
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Rotterdam
,
Matthew Bower
-?/.
1
-
c.453G>C
r.(?)
p.(Pro151=)
-
likely benign
g.102539297G>C
-
PAX2(NM_003988.4):c.453G>C (p.P151=)
-
PAX2_000179
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
2
-
c.477C>T
r.(?)
p.(Thr159=)
-
likely benign
g.102539321C>T
-
PAX2(NM_003988.4):c.477C>T (p.T159=), PAX2(NM_003988.5):c.477C>T (p.T159=)
-
PAX2_000148
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_AMC
-?/-?, -?/.
3
4
c.478G>A
r.(?)
p.(Ala160Thr)
-
likely benign
g.102539322G>A
g.100779565G>A
PAX2(NM_003988.4):c.478G>A (p.A160T), PAX2(NM_003988.5):c.478G>A (p.A160T)
-
PAX2_000067
VKGL data sharing initiative Nederland
PubMed: Bower 2012
-
-
CLASSIFICATION record, Germline/De novo (untested)
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
,
Matthew Bower
-?/-?, -?/., ?/-?, ?/., ?/?
10
4
c.491C>A
r.(?)
p.(Thr164Asn)
-
likely benign, VUS
g.102539335C>A
g.100779578C>A
PAX2(NM_003988.4):c.491C>A (p.T164N), PAX2(NM_003988.5):c.491C>A (p.T164N)
-
PAX2_000036
present in asymptomatic family members, VKGL data sharing initiative Nederland,
3 more items
PubMed: Bower 2012
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_AMC
,
Matthew Bower
-?/.
1
-
c.492C>T
r.(?)
p.(Thr164=)
-
likely benign
g.102539336C>T
-
PAX2(NM_003988.4):c.492C>T (p.T164=)
-
PAX2_000169
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+?/+?
1
4i
c.497-1G>T
r.spl
p.?
-
likely pathogenic
g.102541002G>T
g.100781245G>T
-
-
PAX2_000024
-
PubMed: Thomas 2011
-
-
Germline
-
-
-
-
-
Matthew Bower
-?/-?
1
5
c.527G>C
r.(?)
p.(Ser176Thr)
-
likely benign
g.102541033G>C
g.100781276G>C
-
-
PAX2_000066
-
PubMed: Bower 2012
-
-
Germline/De novo (untested)
-
-
-
-
-
Matthew Bower
-?/., ?/.
2
-
c.529G>A
r.(?)
p.(Ala177Thr)
-
likely benign, VUS
g.102541035G>A
g.100781278G>A
PAX2(NM_003987.5):c.529G>A (p.A177T)
-
PAX2_000131
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_Nijmegen
+?/., ?/.
2
5
c.545T>G
r.(?)
p.(Val182Gly)
-
likely pathogenic, VUS
g.102541051T>G
g.100781294T>G
c.545T>G
-
PAX2_000160
-
PubMed: Zhou 2018
,
PubMed: Zhou-2011
-
-
Germline, Unknown
-
-
-
-
-
LOVD
+/+
4
5
c.561del
r.(?)
p.(Asn188Metfs*40)
-
pathogenic
g.102541067del
g.100781310del
-
-
PAX2_000025
de novo in father
PubMed: Sanyanusin 1995
-
-
De novo, Germline
-
-
-
-
-
Matthew Bower
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