Global Variome shared LOVD
APTX (aprataxin)
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Curator:
Rick van Minkelen
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Unique variants in the APTX gene
The variants shown are described using the
NM_175073.2
NM_001195248.1
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 = 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.
76 entries on 1 page. Showing entries 1 - 76.
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Legend
How to query
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.-111+16G>T
r.(=)
p.(=)
-
benign
g.33001549C>A
g.33001551C>A
APTX(NR_160931.1):n.78G>T
-
APTX_000068
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-?/.
1
-
c.-4-15T>C
r.(=)
p.(=)
-
likely benign
g.32989908A>G
g.32989910A>G
APTX(NM_001195249.1):c.-4-15T>C
-
APTX_000098
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+
2
_1_9_
c.0
r.0, r.0?
p.0, p.0?
-
pathogenic (recessive)
g.(?_32973495)_(32989890_?)del, g.32858130_33025183del
g.32858132_33025185del
-23729_*115366del155489, complete APTX deletion
-
APTX_000030, APTX_000042
-
PubMed: Amouri 2004
,
PubMed: Yoon 2009
,
PubMed: van Minkelen 2015
-
-
Germline
yes
-
-
-
-
Rick van Minkelen
?/.
1
-
c.1A>G
r.(?)
p.(Met1?)
-
VUS
g.32989889T>C
g.32989891T>C
APTX(NM_001195249.2):c.1A>G (p.M1?)
-
APTX_000097
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/+
1
2i_9_
c.5+1225_(*892_?)del
r.?
p.0?
-
pathogenic (recessive)
g.32928505_32988660del
g.32928507_32988662del
5+1225_*44991del67512
-
APTX_000041
-
PubMed: van Minkelen 2015
-
-
Germline
yes
-
-
-
-
Rick van Minkelen
-?/-?, ?/.
2
3
c.18G>T
r.(?)
p.(Trp6Cys)
-
likely benign, VUS
g.32989872C>A
g.32989874C>A
APTX(NM_001195249.1):c.18G>T (p.W6C)
-
APTX_000045, APTX_000067
VKGL data sharing initiative Nederland
PubMed: van Minkelen 2015
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
-?/.
1
-
c.38G>A
r.(?)
p.(Arg13Gln)
-
likely benign
g.32989852C>T
g.32989854C>T
APTX(NM_001195249.1):c.38G>A (p.R13Q)
-
APTX_000066
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
-
c.124C>T
r.(?)
p.(Arg42Ter)
-
pathogenic
g.32989766G>A
-
-
-
APTX_000103
-
-
-
-
Unknown
-
-
-
-
-
IMGAG
?/.
1
-
c.125G>T
r.(?)
p.(Arg42Leu)
-
VUS
g.32989765C>A
g.32989767C>A
APTX(NM_175073.2):c.125G>T (p.R42L)
-
APTX_000084
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
3i
c.134-61A>G
r.(=)
p.(=)
-
VUS
g.32988188T>C
g.32988190T>C
-
-
APTX_000051
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
?/., ?/?
2
5
c.203T>C
r.(?)
p.(Ile68Thr)
-
VUS
g.32987822A>G
g.32987824A>G
APTX(NM_175073.2):c.203T>C (p.I68T)
-
APTX_000046, APTX_000083
VKGL data sharing initiative Nederland
PubMed: van Minkelen 2015
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
-?/-?, -?/.
2
5
c.211G>T
r.(?)
p.(Val71Phe)
-
likely benign
g.32987814C>A
g.32987816C>A
APTX(NM_001195249.1):c.211G>T (p.V71F)
-
APTX_000036, APTX_000082
VKGL data sharing initiative Nederland
PubMed: van Minkelen 2015
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
-?/.
1
-
c.234G>A
r.(?)
p.(Glu78=)
-
likely benign
g.32987791C>T
g.32987793C>T
APTX(NM_001195249.1):c.234G>A (p.E78=)
-
APTX_000081
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/., -?/-?, -?/.
3
5
c.318C>T
r.(?)
p.(=), p.(Asn106=)
-
benign, likely benign
g.32987707G>A
g.32987709G>A
APTX(NM_001195249.1):c.318C>T (p.N106=), APTX(NM_175073.2):c.318C>T (p.N106=)
-
APTX_000044, APTX_000080
VKGL data sharing initiative Nederland
PubMed: van Minkelen 2015
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
,
VKGL-NL_AMC
-?/.
1
-
c.347A>G
r.(?)
p.(Lys116Arg)
-
likely benign
g.32987678T>C
g.32987680T>C
APTX(NM_001195249.1):c.347A>G (p.K116R)
-
APTX_000096
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-/.
1
-
c.378G>A
r.(?)
p.(Arg126=)
-
benign
g.32987647C>T
g.32987649C>T
APTX(NM_001195249.1):c.378G>A (p.R126=)
-
APTX_000095
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/., -?/-?
5
5
c.431C>A
r.(?)
p.(Ser144Tyr)
-
benign, likely benign
g.32987594G>T
g.32987596G>T
APTX(NM_001195249.1):c.431C>A (p.S144Y)
-
APTX_000035, APTX_000079
probably not pathogenic, VKGL data sharing initiative Nederland
van Minkelen et al. In preparation
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Utrecht
,
VKGL-NL_AMC
-/., -?/-?
2
5
c.457A>G
r.(?)
p.(Lys153Glu)
-
benign, likely benign
g.32987568T>C
g.32987570T>C
APTX(NM_001195249.1):c.457A>G (p.K153E)
-
APTX_000001, APTX_000078
VKGL data sharing initiative Nederland
PubMed: Baba 2007
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sergio Piñeiro
,
VKGL-NL_Rotterdam
+/+
1
5
c.477del
r.(?)
p.(Lys161Argfs*11)
-
pathogenic (recessive)
g.32987548del
g.32987550del
477delC
-
APTX_000025
-
PubMed: Castellotti 2011
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
-/.
1
-
c.484-25G>T
r.(=)
p.(=)
-
benign
g.32986053C>A
g.32986055C>A
APTX(NM_001195249.1):c.484-25G>T
-
APTX_000077
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-/-, ?/.
2
5i
c.484-25_484-6del
r.(=), r.(?)
p.(=)
-
benign, VUS
g.32986041_32986060del
g.32986043_32986062del
484-31_484-12del20, APTX(NM_001195248.1):c.526-25_526-6del (p.(=))
-
APTX_000027
VKGL data sharing initiative Nederland
PubMed: Moreira 2001
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Leiden
,
Rick van Minkelen
-/-, -/., -?/.
3
5i
c.484-25_484-5del
r.(?), r.spl?
p.?
-
benign, likely benign
g.32986041_32986061del
g.32986043_32986063del
484-25_484-5del21,
1 more item
-
APTX_000032, APTX_000072
delGTTTTTTTTTTTGTTTTTTTT, VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
-/., -?/.
3
-
c.484-25_484-4del
r.spl?
p.?
-
benign, likely benign
g.32986041_32986062del
g.32986043_32986064del
1 more item
-
APTX_000071
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
,
VKGL-NL_AMC
-/.
1
-
c.484-21_484-20insGT
r.(=)
p.(=)
-
benign
g.32986049_32986050insCA
g.32986051_32986052insCA
APTX(NM_001195249.1):c.484-21_484-20insGT
-
APTX_000094
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/.
1
-
c.484-13del
r.(=)
p.(=)
-
likely benign
g.32986041del
g.32986043del
APTX(NM_001195249.2):c.484-25_484-13delGTTTTTTTTTTTGinsGTTTTTTTTTTT
-
APTX_000076
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-/., -?/.
2
-
c.484-13G>T
r.(=)
p.(=)
-
benign, likely benign
g.32986041C>A
g.32986043C>A
APTX(NM_001195249.1):c.484-13G>T
-
APTX_000070
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_Nijmegen
-/.
2
-
c.484-12T>G
r.(=)
p.(=)
-
benign
g.32986040A>C
g.32986042A>C
APTX(NM_001195249.1):c.484-12T>G
-
APTX_000075
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_AMC
-/., -?/.
2
-
c.484-12_484-11insG
r.(=)
p.(=)
-
benign, likely benign
g.32986039_32986040insC
g.32986041_32986042insC
APTX(NM_001195249.1):c.484-12_484-11insG, APTX(NM_001195249.2):c.484-12_484-11insG
-
APTX_000090
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
,
VKGL-NL_AMC
-/., -?/.
3
-
c.484-3del
r.spl?
p.?
-
benign, likely benign
g.32986040del
g.32986042del
APTX(NM_001195249.1):c.484-3delT
-
APTX_000069
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
,
VKGL-NL_AMC
-?/.
1
-
c.484-3T>C
r.spl?
p.?
-
likely benign
g.32986031A>G
g.32986033A>G
APTX(NM_001195248.1):c.526-3T>C (p.?)
-
APTX_000089
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
?/.
1
-
c.493G>T
r.(?)
p.(Gly165Cys)
-
VUS
g.32986019C>A
g.32986021C>A
APTX(NM_001195248.1):c.535G>T (p.(Gly179Cys))
-
APTX_000100
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
?/.
1
-
c.505C>T
r.(?)
p.(Gln169Ter)
-
VUS
g.32986007G>A
g.32986009G>A
APTX(NM_001195248.1):c.547C>T (p.(Gln183Ter))
-
APTX_000099
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/+
1
6
c.541C>T
r.(?)
p.(Gln181*)
-
pathogenic (recessive)
g.32985971G>A
g.32985973G>A
-
-
APTX_000026
-
PubMed: Castellotti 2011
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
-/-, -/.
2
6i
c.543+30A>C
r.(=), r.(?)
p.(=)
-
benign
g.32985939T>G
g.32985941T>G
APTX(NM_175073.2):c.543+30A>C
-
APTX_000034, APTX_000064
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
+/+, +/.
4
7
c.559C>T
r.(?)
p.(Gln187*), p.(Gln187Ter)
-
pathogenic, pathogenic (recessive)
g.32984840G>A
g.32984842G>A
APTX(NM_001195249.1):c.559C>T (p.Q187*), APTX(NM_175073.2):c.559C>T (p.Q187*)
-
APTX_000038, APTX_000063
VKGL data sharing initiative Nederland
PubMed: van Minkelen 2015
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
+/+
1
7
c.589A>C
r.(?)
p.(Lys197Gln)
-
pathogenic (recessive)
g.32984810T>G
g.32984812T>G
-
-
APTX_000003
-
PubMed: Tranchant 2003
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+, +/.
3
7
c.593C>T
r.(?)
p.(Ala198Val)
-
pathogenic, pathogenic (recessive)
g.32984806G>A
g.32984808G>A
APTX(NM_175073.2):c.593C>T (p.A198V)
-
APTX_000005, APTX_000062
VKGL data sharing initiative Nederland
PubMed: Le Ber 2003
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sergio Piñeiro
,
Rick van Minkelen
,
VKGL-NL_Rotterdam
+?/.
1
-
c.596del
r.(?)
p.(Arg199Leufs*15)
-
VUS
g.32984803del
g.32984805del
-
-
APTX_000102
-
PubMed: Riazuddin 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
3
7
c.596delG
r.(?)
p.(Arg199LeufsTer15)
-
likely pathogenic
g.32984803del
g.32984805del
-
-
APTX_000102
-
PubMed: Ganapathy 2019
-
rs770007531
Germline
-
-
-
-
-
Johan den Dunnen
+/+, +/., ?/.
4
7
c.596G>A
r.(?)
p.(Arg199His)
-
pathogenic, pathogenic (recessive), VUS
g.32984803C>T
g.32984805C>T
APTX(NM_001195249.1):c.596G>A (p.R199H)
-
APTX_000006
no maternal variant identified, VKGL data sharing initiative Nederland
PubMed: Moreira 2001
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Gerard C.P. Schaafsma
,
Sergio Piñeiro
,
Rick van Minkelen
,
VKGL-NL_Rotterdam
+/+
1
7
c.601del
r.(?)
p.(His201Ilefs*13)
-
pathogenic (recessive)
g.32984799del
g.32984801del
643delC
-
APTX_000029
-
PubMed: Nouri et al 2012
-
-
Germline
-
-
-
-
-
Rick van Minkelen
+/+
1
7
c.602A>G
r.(?)
p.(His201Arg)
-
pathogenic (recessive)
g.32984797T>C
g.32984799T>C
nt 80 (A>G)
-
APTX_000007
-
PubMed: Shimazaki 2002
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
1
7
c.603T>A
r.(?)
p.(His201Gln)
-
pathogenic (recessive)
g.32984796A>T
g.32984798A>T
-
-
APTX_000008
-
PubMed: Criscuolo 2004
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
4
7
c.617C>T
r.(?)
p.(Pro206Leu)
-
pathogenic (recessive)
g.32984782G>A
g.32984784G>A
-
-
APTX_000009
-
PubMed: Date 2001
,
PubMed: Moreira 2001
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
1
7
c.668T>C
r.(?)
p.(Leu223Pro)
-
pathogenic (recessive)
g.32984731A>G
g.32984733A>G
-
-
APTX_000010
-
PubMed: Criscuolo 2005
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/?
1
7
c.683A>G
r.(?)
p.(His228Arg)
-
pathogenic (recessive)
g.32984716T>C
g.32984718T>C
-
-
APTX_000011
-
PubMed: Fogel 2006
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
5
7
c.689dup
r.(?)
p.(Glu232Glyfs*38)
-
pathogenic (recessive)
g.32984710dup
g.32984712dup
689dupT, 689insT, 690insT
-
APTX_000012
-
PubMed: Date 2001
,
PubMed: Moreira 2001
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
1
7
c.689T>G
r.(?)
p.(Val230Gly)
-
pathogenic (recessive)
g.32984710A>C
g.32984712A>C
-
-
APTX_000013
-
PubMed: Ferrarini 2007
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
1
7
c.692G>A
r.(?)
p.(Gly231Glu)
-
pathogenic (recessive)
g.32984707C>T
g.32984709C>T
-
-
APTX_000014
-
PubMed: Ito 2005
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/?
1
7
c.725G>A
r.(?)
p.(Ser242Asn)
-
pathogenic (recessive)
g.32984674C>T
g.32984676C>T
-
-
APTX_000015
-
PubMed: Baba 2007
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
-?/.
1
-
c.731T>C
r.(?)
p.(Leu244Pro)
-
likely benign
g.32984668A>G
g.32984670A>G
APTX(NM_001195249.1):c.731T>C (p.L244P)
-
APTX_000061
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
?/.
1
-
c.734G>A
r.(?)
p.(Arg245His)
-
VUS
g.32984665C>T
g.32984667C>T
APTX(NM_175073.2):c.734G>A (p.R245H)
-
APTX_000060
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+, +/., +?/-?
4
7
c.739C>T
r.(?)
p.(Arg247*), p.(Arg247Ter)
ACMG
likely pathogenic, pathogenic, pathogenic (recessive)
g.32984660G>A
g.32984662G>A
APTX(NM_001195249.1):c.739C>T (p.R247*)
-
APTX_000016, APTX_000059
VKGL data sharing initiative Nederland
Mosesso et al. 2005. Cell 62: 485,
PubMed: Mosesso 2005
-
rs778258042
CLASSIFICATION record, Germline
-
-
-
-
-
Sergio Piñeiro
,
Andreas Laner
,
Rick van Minkelen
,
VKGL-NL_Rotterdam
?/., ?/?
3
7
c.742T>A
r.(?)
p.(Leu248Met)
-
VUS
g.32984657A>T
g.32984659A>T
APTX(NM_001195249.1):c.742T>A (p.L248M)
-
APTX_000037, APTX_000058
VKGL data sharing initiative Nederland
van Minkelen et al. In preparation,
PubMed: van Minkelen 2015
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
?/.
1
-
c.762G>A
r.(?)
p.(Pro254=)
-
VUS
g.32984637C>T
g.32984639C>T
APTX(NM_001195249.1):c.762G>A (p.P254=)
-
APTX_000088
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/+
2
7
c.770+1G>A
r.(?)
p.?
-
pathogenic (recessive)
g.32984628C>T
g.32984630C>T
-
-
APTX_000020
-
PubMed: Le Ber 2003
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
-/.
1
-
c.771-13_771-12dup
r.(=)
p.(=)
-
benign
g.32974578_32974579dup
g.32974580_32974581dup
APTX(NM_001195249.1):c.771-13_771-12dupTT
-
APTX_000086
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/-
1
7i
c.771-12del
r.(?)
p.(=)
-
benign
g.32974579del
g.32974581del
771-11delT
-
APTX_000028
-
PubMed: Moreira 2001
-
-
Germline
-
-
-
-
-
Rick van Minkelen
-/-, -/.
3
7i
c.771-12dup
r.(=), r.(?)
p.(=)
-
benign
g.32974579dup
g.32974581dup
771-12dupT, APTX(NM_001195249.1):c.771-12dupT, APTX(NM_175073.2):c.771-12dupT
-
APTX_000033
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
,
VKGL-NL_Utrecht
?/?
1
8
c.781C>T
r.(?)
p.(Leu261Phe)
-
VUS
g.32974549G>A
g.32974551G>A
-
-
APTX_000017
-
PubMed: H'mida-Ben Brahim 2011
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
1
8
c.788T>G
r.(?)
p.(Val263Gly)
-
pathogenic (recessive)
g.32974542A>C
g.32974544A>C
-
-
APTX_000018
-
PubMed: Date 2001
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/?
2
8
c.800A>G
r.(?)
p.(Asp267Gly)
-
pathogenic (recessive)
g.32974530T>C
g.32974532T>C
-
-
APTX_000019
-
PubMed: Le Ber 2003
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
2
8
c.835T>C
r.(?)
p.(Trp279Arg)
-
pathogenic (recessive)
g.32974495A>G
g.32974497A>G
-
-
APTX_000021
-
PubMed: Le Ber 2003
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+, +/.
19
8
c.837G>A
r.(?)
p.(Trp279*), p.(Trp279Ter)
ACMG
pathogenic, pathogenic (recessive)
g.32974493C>T
g.32974495C>T
APTX(NM_001368999.1):c.837G>A (p.W279*), APTX(NM_175073.2):c.837G>A (p.W279*)
-
APTX_000004
ACMG grading: PM2,PM3,PVS1,PP5, VKGL data sharing initiative Nederland
PubMed: Moreira 2001
-
rs104894103
CLASSIFICATION record, Germline
-
-
-
-
-
Sergio Piñeiro
,
Andreas Laner
,
Rick van Minkelen
,
VKGL-NL_Rotterdam
,
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
+/+
1
8
c.841del
r.(?)
p.(Ser281Leufs*8)
-
pathogenic (recessive)
g.32974490del
g.32974492del
840delT
-
APTX_000022
-
PubMed: Date 2001
,
PubMed: Seidle et al 2005
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
1
7
c.845delT
r.(?)
p.(Phe282Serfs*7)
-
pathogenic (recessive)
g.32974487del
g.32974489del
887delT
-
APTX_000107
-
-
-
-
Germline
yes
-
-
-
-
Sherifa Ahmed Hamed
-?/., ?/., ?/?
3
8
c.847A>G
r.(?)
p.(Asn283Asp)
-
likely benign, VUS
g.32974483T>C
g.32974485T>C
APTX(NM_001195248.1):c.889A>G (p.(Asn297Asp)), APTX(NM_175073.2):c.847A>G (p.N283D)
-
APTX_000039, APTX_000055
VKGL data sharing initiative Nederland
PubMed: Avan Minkelen 2015
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
VKGL-NL_Leiden
,
Rick van Minkelen
,
VKGL-NL_Rotterdam
-/.
1
-
c.875-60del
r.(=)
p.(=)
-
benign
g.32973727del
g.32973729del
APTX(NM_001195249.1):c.875-60delT
-
APTX_000054
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+?/.
1
8i
c.875-2A>G
r.spl
p.?
-
likely pathogenic
g.32973652T>C
g.32973654T>C
-
-
APTX_000104
-
PubMed: Ganapathy 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
8i
c.875-1G>A
r.spl
p.?
-
pathogenic (recessive)
g.32973651C>T
g.32973653C>T
-
-
APTX_000085
-
PubMed: Amouri 2004
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
+/+
1
9
c.892C>T
r.(?)
p.(Gln298*)
-
pathogenic (recessive)
g.32973633G>A
g.32973635G>A
-
-
APTX_000023
-
PubMed: Crimella 2011
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
+/+
2
9
c.916C>T
r.(?)
p.(Arg306*)
-
pathogenic (recessive)
g.32973609G>A
g.32973611G>A
-
-
APTX_000024
-
PubMed: Castellotti 2011
-
-
Germline
-
-
-
-
-
Sergio Piñeiro
-?/.
1
-
c.918A>G
r.(?)
p.(Arg306=)
-
likely benign
g.32973607T>C
g.32973609T>C
APTX(NM_001195249.1):c.918A>G (p.R306=)
-
APTX_000053
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/+
1
9
c.940_956del
r.(?)
p.(Lys314Serfs*2)
-
pathogenic (recessive)
g.32973572_32973588del
g.32973574_32973590del
940_956del17
-
APTX_000043
-
PubMed: Avan Minkelen 2015
-
-
Germline
-
-
-
-
-
Rick van Minkelen
-/-, -/., -?/.
4
9
c.971A>T
r.(?)
p.(Gln324Leu)
-
benign, likely benign
g.32973554T>A
g.32973556T>A
APTX(NM_001195249.1):c.971A>T (p.Q324L), APTX(NM_001195249.2):c.971A>T (p.Q324L)
-
APTX_000031, APTX_000052
VKGL data sharing initiative Nederland
PubMed: van Minkelen 2015
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Rick van Minkelen
,
VKGL-NL_Rotterdam
,
VKGL-NL_Groningen
,
VKGL-NL_Utrecht
-?/.
1
-
c.985A>G
r.(?)
p.(Ile329Val)
-
likely benign
g.32973540T>C
-
APTX(NM_001195249.1):c.985A>G (p.I329V)
-
APTX_000105
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
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