Global Variome shared LOVD
SGCA (sarcoglycan, alpha (50kDa dystrophin-associa...))
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Unique variants in the SGCA gene
This database is one of the gene variant databases from the
Leiden Muscular Dystrophy pages
The variants shown are described using the NM_000023.2 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)
conflicting
association
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%)
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Operator
Column type
Example
Matches
Text
Arg
all entries containing 'Arg'
space
Text
Arg Ser
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|
Text
Arg|Ser
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!
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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237 entries on 3 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
_1_7i
c.-36_(956+1_957-1)dup
r.?
p.?
ACMG
pathogenic (recessive)
g.(?_48243366)_(48247713_48248000)dup
g.(?_50166005)_50170352_50170639)dup
duplication ex1-7
-
SGCA_000204
ACMG PVS1, PM3, PP1, PP4
PubMed: Xie 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
5' UTR
c.-5C>G
r.(?)
p.(=)
-
VUS
g.48243397C>G
g.50166036C>G
-
-
SGCA_000140
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
1
_1_10_
c.(?_-1)_(*1_?)del
r.0?
p.0?
-
pathogenic
g.(?_48243401)_(48252799_?)del
-
-
-
SGCA_000000
-
PubMed: Duggan
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
_1_3i
c.-36_(312+1_313-1){0}
r.0?
p.0?
-
pathogenic (recessive)
g.(?_48243366)_(48245098_48245307)del
g.(?_50166005)_(50167737_50167946)del
del ex1-3
-
SGCA_000236
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Nguyen Hoang
-/.
1
6i
c.747+161_747+192AC[15_21]
r.(=)
p.(=)
-
benign
g.48246776_48246807AC[15_21]
g.50169415_50169446AC[15_21]
-
-
SGCA_000055
-
PubMed: Roberds
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
1
c.1A>G
r.(?)
p.(Met1?), p.0?
ACMG
pathogenic, pathogenic (recessive)
g.48243402A>G
g.50166041A>G
SGCA(NM_000023.4):c.1A>G (p.M1?)
-
SGCA_000208
ACMG PVS1, PM2, PP1, PP3, PP4, VKGL data sharing initiative Nederland
PubMed: Karthikeyan 2024
,
PubMed: Xie 2019
-
-
CLASSIFICATION record, Germline, Germline/De novo (untested)
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_VUmc
,
Lakshmi Bremadesam
+?/.
1
-
c.2T>C
r.(?)
p.0?
-
likely pathogenic
g.48243403T>C
g.50166042T>C
-
-
SGCA_000223
combination of variants not reported
PubMed: Topf 2020
-
-
Germline
-
1/1001 cases
-
-
-
Johan den Dunnen
?/.
2
1
c.34G>A
r.(?)
p.(Val12Met)
-
VUS
g.48243435G>A
g.50166074G>A
-
-
SGCA_000141
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
1
1i
c.37+1G>C
r.spl?
p.(?)
-
pathogenic
g.48243439G>C
g.50166078G>C
IVS1+G>C
-
SGCA_000083
-
-
-
-
Germline
-
-
-
-
-
Gabriele Dekomien
+/.
1
1i
c.37+2C>G
r.spl
p.?
-
pathogenic
g.48243440C>G
g.50166079C>G
-
-
SGCA_000142
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/., ?/.
9
1, 1i
c.(37+3A>T), c.37+3A>T
r.(spl?), r.spl, r.spl?
p.(?), p.?
-
pathogenic, VUS
g.48243441A>T
g.50166080A>T
IVS1 splice, IVS1+3A>T
-
SGCA_000029
aberrant splicing
PubMed: Carrie 1997
,
PubMed: Eymard 1997
,
PubMed: Trabelsi 2008
-
-
Germline
-
-
MaeI+
-
-
Johan den Dunnen
,
Gabriele Dekomien
?/.
3
1i
c.37+6T>C
r.(?), r.(spl?)
p.(?)
-
VUS
g.48243444T>C
g.50166083T>C
-
-
SGCA_000117
father and mother heterozygous
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Madhuri Hegde
-/., -?/., ?/.
7
1i
c.37+23G>A
r.(=), r.(?)
p.(=)
ACMG
benign, likely benign, VUS
g.48243461G>A
g.50166100G>A
-
-
SGCA_000112
father homozygous, mother heterozygous
from website {DBsub-Emory}
254719, VCV000254719.5
-
Germline, Germline/De novo (untested), Unknown
-
-
-
-
-
Johan den Dunnen
,
Marina Fanin
,
Madhuri Hegde
,
Micaela Carcione
-/.
1
1i
c.37+23G>T
r.(=)
p.(=)
-
benign
g.48243461G>T
g.50166100G>T
-
-
SGCA_000062
-
-
-
-
Germline
-
-
-
-
-
Ieke Ginjaar
-/.
2
1i
c.37+27A>G
r.(=)
p.(=)
-
benign
g.48243465A>G
g.50166104A>G
IVS1+27G>A
-
SGCA_000043
-
{DB: Berne},
PubMed: Carrie 1997
-
-
Germline
-
0.05, 6/128
AciI-
-
-
Johan den Dunnen
-/., -?/.
7
1i
c.37+66C>T
r.(=)
p.(=)
ACMG
benign, likely benign
g.48243504C>T
g.50166143C>T
SGCA(NM_000023.4):c.37+66C>T
-
SGCA_000061
parents homozygous, VKGL data sharing initiative Nederland
-
669838, VCV000669838.3
rs9911548
CLASSIFICATION record, Germline, Germline/De novo (untested)
-
-
-
-
-
Johan den Dunnen
,
VKGL-NL_Groningen
,
Micaela Carcione
?/.
1
1i
c.38-46G>C
r.(?)
p.(=)
-
VUS
g.48244683G>C
g.50167322G>C
-
-
SGCA_000113
-
from website {DBsub-Emory}
-
-
Germline
-
-
-
-
-
Madhuri Hegde
-?/., ?/.
2
2
c.62C>T
r.(?)
p.(Thr21Ile)
-
likely benign, VUS
g.48244753C>T
g.50167392C>T
SGCA(NM_000023.2):c.62C>T (p.T21I)
-
SGCA_000131
VKGL data sharing initiative Nederland
PubMed: Nallamilli 2018
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Madhuri Hegde
,
VKGL-NL_Utrecht
+/.
2
2
c.73C>T
r.(?)
p.(Gln25*)
-
pathogenic
g.48244764C>T
g.50167403C>T
-
-
SGCA_000069
-
PubMed: Gouveia 2006
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
2
c.80C>T
r.(?)
p.(Thr27Met)
-
VUS
g.48244771C>T
g.50167410C>T
-
-
SGCA_000143
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
?/.
1
2
c.85C>T
r.(?)
p.(His29Tyr)
-
VUS
g.48244776C>T
g.50167415C>T
-
-
SGCA_000144
-
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
6
2
c.86dup
r.(?), r.86dup
p.(His29Glnfs*15), p.His29Glnfs*15
-
pathogenic
g.48244777dup
g.50167416dup
86insA
-
SGCA_000053
-
PubMed: Boito
,
PubMed: Ramelli 2006
,
PubMed: Trabelsi 2008
-
-
Germline, Unknown
-
-
-
-
-
Johan den Dunnen
,
Marina Fanin
+/., ?/.
3
2
c.88C>A
r.(?)
p.(Pro30Thr)
-
pathogenic, VUS
g.48244779C>A
g.50167418C>A
-
-
SGCA_000063
-
-
-
rs1327595249
CLASSIFICATION record, Germline
-
-
-
-
-
Ieke Ginjaar
,
MobiDetails
+/.
1
2
c.88_112del
r.(?)
p.(Pro30Thrfs*9)
-
pathogenic
g.48244779_48244803del
g.50167418_50167442del
87_111del
-
SGCA_000095
-
PubMed: Trabelsi 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
2
2
c.89C>T
r.(?)
p.(Pro30Leu)
-
VUS
g.48244780C>T
g.50167419C>T
-
-
SGCA_000030
-
PubMed: Carrie 1997
,
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Madhuri Hegde
+/., +?/.
8
2
c.92T>C
r.(?), r.92u>c
p.(Leu31Pro), p.Leu31Pro
-
likely pathogenic, pathogenic
g.48244783T>C
g.50167422T>C
-
-
SGCA_000017
combination of variants not reported
PubMed: Duggan
,
PubMed: Guglieri 2007
,
PubMed: Moreira 2003
,
PubMed: Topf 2020
,
PubMed: Trabelsi 2008
-
-
Germline
-
1/1001 cases
-
-
-
Johan den Dunnen
,
Tom Winder
+/.
5
2
c.95T>C
r.(?)
p.(Val32Ala)
-
pathogenic (recessive)
g.48244786T>C
g.50167425T>C
-
-
SGCA_000209
-
PubMed: Xie 2019
,
PubMed: Yu 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., +?/., ?/.
10
2, 3
c.100C>T
r.(?)
p.(Arg34Cys)
-
likely pathogenic, pathogenic, VUS
g.48244791C>T
g.50167430C>T
-
-
SGCA_000031
combination of variants not reported, variant apparently homozygous
PubMed: Carrie 1997
,
PubMed: Eymard 1997
,
PubMed: Nallamilli 2018
,
PubMed: Topf 2020
-
-
Germline
-
1/1001 cases
HaeIII-
-
-
Johan den Dunnen
,
Gabriele Dekomien
,
Madhuri Hegde
+/., ?/.
25
2
c.101G>A
r.(?), r.101g>a
p.(Arg34His), p.Arg34His
ACMG
pathogenic, pathogenic (recessive), VUS
g.48244792G>A
g.50167431G>A
SGCA(NM_000023.2):c.101G>A (p.(Arg34His))
-
SGCA_000006
ACMG PM2, PP1-S, PM3, PP1-M, PP1, PP2, PP3, PP4, VKGL data sharing initiative Nederland
from website {DBsub-Emory},
PubMed: Carrie 1997
,
PubMed: Duggan
,
PubMed: Monies 2016
,
PubMed: Xie 2019
,
6 more items
-
-
CLASSIFICATION record, Germline
-
-
NlaIII+
-
-
Johan den Dunnen
,
Ieke Ginjaar
,
Gabriele Dekomien
,
Madhuri Hegde
,
VKGL-NL_Leiden
,
VKGL-NL_Nijmegen
+/.
11
2
c.101G>T
r.(?)
p.(Arg34Leu)
-
pathogenic
g.48244792G>T
g.50167431G>T
-
-
SGCA_000091
-
PubMed: Liang 2016
,
Journal: Liang 2016
,
PubMed: Liang 2020
-
-
Germline
yes
-
-
-
-
Johan den Dunnen
,
Jamie Zeegers
+/.
1
-
c.109G>T
r.(?)
p.(Val37Leu)
-
pathogenic (recessive)
g.48244800G>T
g.50167439G>T
-
-
SGCA_000200
-
PubMed: Reddy 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
2
c.132G>A
r.(?)
p.(=)
-
VUS
g.48244823G>A
g.50167462G>A
-
-
SGCA_000145
-
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
?/.
2
2
c.155T>G
r.(?)
p.(Val52Gly)
-
VUS
g.48244846T>G
g.50167485T>G
-
-
SGCA_000146
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/., +?/., ?/.
13
2
c.157G>A
r.(?), r.(spl?)
p.(Ala53Thr), p.(Ala53Thr?)
-
likely pathogenic, pathogenic, VUS
g.48244848G>A
g.50167487G>A
-
-
SGCA_000042
not in 460 control chromosomes, variant apparently homozygous
PubMed: Dos Santos 2001
,
PubMed: Fendri 2006
,
PubMed: Nallamilli 2018
,
PubMed: Trabelsi 2008
-
rs60407644
CLASSIFICATION record, Germline
-
0/340
HphI
-
-
Johan den Dunnen
,
Rosário dos Santos
,
Madhuri Hegde
,
MobiDetails
+/.
11
2i
c.157+1G>A
r.spl, r.spl?
p.(?), p.(del?), p.?
-
pathogenic, pathogenic (recessive)
g.48244849G>A
g.50167488G>A
-
-
SGCA_000070
-
ESHG2010 Stehlikova P2.117, Ginjaar WMS2005,
PubMed: Ten Dam 2019
,
PubMed: Chakravorty 2020
,
2 more items
-
-
Germline
-
-
TaqI+
-
-
Johan den Dunnen
,
Ieke Ginjaar
,
Jana Zidkova
,
Micaela Carcione
-/.
1
-
c.158-11G>A
r.(=)
p.(=)
-
benign
g.48244932G>A
g.50167571G>A
SGCA(NM_000023.2):c.158-11G>A
-
SGCA_000132
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
-?/.
1
-
c.158-10C>G
r.(=)
p.(=)
-
likely benign
g.48244933C>G
g.50167572C>G
SGCA(NM_000023.2):c.158-10C>G
-
SGCA_000133
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+?/.
1
2i_3
c.158-10_160del
r.spl
p.?
ACMG
likely pathogenic (recessive)
g.48244933_48244945del
g.50167572_50167584del
-
-
SGCA_000210
ACMG PM2, PM3, PP1, PP3, PP4
PubMed: Xie 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3
c.(157+1_158-1)_(312+1_313-1)?
r.158_312del
p.Ala53Glyfs*10
-
pathogenic
g.(48244849_48244942)_(48245098_48245307)?
-
-
-
SGCA_000000
-
PubMed: Bueno 1995
-
-
Germline
-
-
NlaIV-
-
-
Johan den Dunnen
+/.
3
3
c.161del
r.(?)
p.(Val54Alafs*157)
-
pathogenic
g.48244946del
g.50167585del
161delT
-
SGCA_000032, SGCA_000147
-
PubMed: Carrie 1997
,
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Madhuri Hegde
+/.
1
3
c.168del
r.(?)
p.(Ala57Leufs*154)
-
pathogenic
g.48244953del
g.50167592del
168delC
-
SGCA_000148
-
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
?/.
1
3
c.172G>C
r.(?)
p.(Val58Leu)
-
VUS
g.48244957G>C
g.50167596G>C
-
-
SGCA_000149
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
1
3
c.183dup
r.(?)
p.(Tyr62Leufs*43)
-
pathogenic
g.48244968dup
g.50167607dup
183dupC
-
SGCA_000150
-
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
1
3
c.184T>C
r.(?)
p.(Tyr62His)
-
pathogenic
g.48244969T>C
g.50167608T>C
-
-
SGCA_000007
-
PubMed: Piccolo
,
PubMed: Eymard 1997
,
PubMed: Crosbie 2000
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/., ?/.
2
3
c.190G>A
r.(?)
p.(Ala64Thr)
-
likely pathogenic, VUS
g.48244975G>A
g.50167614G>A
-
-
SGCA_000129
-
PubMed: Nallamilli 2018
-
-
Germline
?
-
-
-
-
Madhuri Hegde
,
Aurelio Hernández-LaÃn
+?/., ?/.
4
3
c.197T>A
r.(?)
p.(Leu66His)
ACMG
likely pathogenic, VUS
g.48244982T>A
g.50167621T>A
-
-
SGCA_000151
variant apparently homozygous; no second variant
PubMed: Ganapathy 2019
,
PubMed: Nallamilli 2018
,
PubMed: Nerakh 2021
ClinVar-RCV000384383.1
,
ClinVar-RCV000384383
rs767928766
Germline
-
-
-
-
-
Johan den Dunnen
,
Madhuri Hegde
-?/.
1
-
c.199C>G
r.(?)
p.(Gln67Glu)
-
likely benign
g.48244984C>G
g.50167623C>G
-
-
SGCA_000193
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
1
3
c.203G>A
r.(?)
p.(Gly68Gln)
-
pathogenic
g.48244988G>A
g.50167627G>A
-
-
SGCA_000008
-
PubMed: Piccolo
,
PubMed: Eymard 1997
,
PubMed: Crosbie 2000
-
-
Germline
-
-
BsmFI-
-
-
Johan den Dunnen
+?/.
1
3
c.218C>G
r.(?)
p.(Pro73Arg)
ACMG
likely pathogenic (recessive)
g.48245003C>G
g.50167642C>G
-
-
SGCA_000211
ACMG PM1, PM2, PM3, PP1, PP3, PP4
PubMed: Xie 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
1
3
c.218C>T
r.(?)
p.(Pro73Leu)
ACMG
likely pathogenic (recessive)
g.48245003C>T
g.50167642C>T
-
-
SGCA_000212
ACMG PM1, PM2, PM3, PP1, PP3, PP4
PubMed: Xie 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
9
3
c.220C>T
r.(?)
p.(Arg74Trp)
-
pathogenic, pathogenic (recessive)
g.48245005C>T
g.50167644C>T
-
-
SGCA_000038
not in 200 control chromosomes
0,
PubMed: Ginjaar 2000
,
PubMed: Higuchi
,
PubMed: Higuchi
,
PubMed: Saha 2018
,
Journal: Saha 2018
,
1 more item
-
rs757888349
Germline
-
-
-
-
-
Johan den Dunnen
,
Ieke Ginjaar
,
Gabriele Dekomien
?/.
1
3
c.221G>A
r.(?)
p.(Arg74Gln)
-
VUS
g.48245006G>A
g.50167645G>A
-
-
SGCA_000118
-
-
-
-
Unknown
-
-
-
-
-
Marina Fanin
+/.
2
-
c.226C>T
r.(?)
p.(Leu76Phe)
-
pathogenic (recessive)
g.48245011C>T
g.50167650C>T
-
-
SGCA_000139
-
PubMed: Saha 2018
,
Journal: Saha 2018
,
PubMed: Yis 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/+, +/., +?/., ?/.
208
2, 3
c.(229C>T), c.229C>T
r.(229C>T), r.(?), r.0, r.229c>u
p.(Arg77Cys), p.0, p.Arg77Cys
ACMG
likely pathogenic, pathogenic, pathogenic (recessive), VUS
g.48245014C>T
g.50167653C>T
299C>T, SGCA(NM_000023.2):c.229C>T (p.(Arg77Cys))
-
SGCA_000003
aberrant band exon 2, no variant identified, ACMG PP3, PP4_mod, PM3_very strong, no second variant,
8 more items
ESHG2010 Stehlikova P2.117, from website {DBsub-Emory}, Ginjaar WMS2005,
PubMed: Ten Dam 2019
,
40 more items
-
rs28933693
CLASSIFICATION record, Germline, Unknown
yes
8/1001 cases
BspLI-, NlaIV-
-
-
Johan den Dunnen
,
Ieke Ginjaar
,
Rosário dos Santos
,
Gabriele Dekomien
,
Madhuri Hegde
,
Human Genetics Diagnostic Laboratory - Cochin Hosp J Chelly, F Leturcq
,
Jana Zidkova
,
Florencia Giliberto
,
Tom Winder
,
VKGL-NL_Leiden
,
Miguel Angel Alcántara-Ortigoza
,
VKGL-NL_Nijmegen
,
Valeria Guzman Olvera
?/.
1
3
c.230G>A
r.(?)
p.(Arg77His)
-
VUS
g.48245015G>A
g.50167654G>A
-
-
SGCA_000152
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/., +?/.
2
-
c.232_238del
r.(?)
p.(Tyr78Serfs*131)
-
likely pathogenic, pathogenic (recessive)
g.48245017_48245023del
g.50167656_50167662del
232_238delTACACCC
-
SGCA_000224
combination of variants not reported
PubMed: Topf 2020
,
PubMed: Yis 2018
-
-
Germline
-
2/1001 cases
-
-
-
Johan den Dunnen
+/.
1
3
c.233_234delinsGA
r.(?)
p.(Tyr78*)
-
pathogenic (recessive)
g.48245018_48245019delinsGA
g.50167657_50167658delinsGA
-
-
SGCA_000213
-
PubMed: Xie 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.233_234insGA
r.(?)
p.(Tyr78*)
-
pathogenic (recessive)
g.48245018_48245019insGA
g.50167657_50167658insGA
-
-
SGCA_000214
-
PubMed: Yu 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3
c.234C>A
r.(?)
p.(Tyr78*)
ACMG
pathogenic (recessive)
g.48245019C>A
g.50167658C>A
-
-
SGCA_000215
ACMG PVS1, PM2, PP4
PubMed: Xie 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3
c.238C>T
r.(?)
p.(Gln80*)
-
pathogenic
g.48245023C>T
g.50167662C>T
-
-
SGCA_000011
-
PubMed: Piccolo
,
PubMed: CarriÈ
,
PubMed: Eymard 1997
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., +?/., ?/.
9
3, 4
c.241C>T
r.(?)
p.(Arg81Cys), p.Arg81Cys
ACMG
likely pathogenic, pathogenic, pathogenic (recessive), VUS
g.48245026C>T
g.50167665C>T
Arg81Ser
-
SGCA_000092
combination of variants not reported, VKGL data sharing initiative Nederland,
1 more item
PubMed: Ganapathy 2019
,
PubMed: Guglieri 2007
,
PubMed: Magri 2015
,
PubMed: Nallamilli 2018
,
2 more items
ClinVar-RCV000077938
rs398123098
CLASSIFICATION record, Germline
-
1/1001 cases
-
-
-
Johan den Dunnen
,
Madhuri Hegde
,
Andreas Laner
,
VKGL-NL_Nijmegen
+?/.
1
-
c.242G>A
r.(?)
p.(Arg81His)
-
likely pathogenic
g.48245027G>A
-
-
-
SGCA_000240
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
?/.
3
3
c.250dup
r.(?)
p.(His84Profs*21)
-
VUS
g.48245035dup
g.50167674dup
250dupC
-
SGCA_000080
-
-
-
-
Germline
-
-
-
-
-
Gabriele Dekomien
+/.
1
-
c.257C>T
r.(?)
p.(Pro86Leu)
-
pathogenic
g.48245042C>T
-
-
-
SGCA_000221
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/., ?/.
2
3
c.265C>T
r.(?)
p.(Leu89Phe)
-
pathogenic, VUS
g.48245050C>T
g.50167689C>T
-
-
SGCA_000081
-
PubMed: Klinge 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Gabriele Dekomien
+/.
1
3
c.266_267inv
r.(?)
p.(Leu89Arg)
-
pathogenic
g.48245051_48245052inv
g.50167690_50167691inv
-
-
SGCA_000039
-
{DB: Newcastle}
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
6
3
c.269A>G
r.(?)
p.(Tyr90Cys)
-
pathogenic
g.48245054A>G
g.50167693A>G
-
-
SGCA_000041
-
{DB: Porto},
PubMed: Moreira 2003
-
-
Germline
-
0/260
Fnu4HI
-
-
Johan den Dunnen
+/., +?/.
6
3
c.271G>A
r.(?)
p.(Gly91Ser)
-
likely pathogenic, pathogenic, pathogenic (recessive)
g.48245056G>A
g.50167695G>A
-
-
SGCA_000076
not in 320 control chromosomes
PubMed: Guglieri 2007
,
PubMed: Karthikeyan 2024
,
PubMed: Magri 2015
-
-
Germline, Germline/De novo (untested)
-
-
-
-
-
Johan den Dunnen
,
Marina Fanin
,
Lakshmi Bremadesam
+/.
1
3
c.271G>C
r.(?)
p.(Gly91Arg)
-
pathogenic
g.48245056G>C
g.50167695G>C
-
-
SGCA_000033
-
PubMed: Carrie 1997
-
-
Germline
-
-
BsrBI+
-
-
Johan den Dunnen
?/.
1
3
c.272G>A
r.(?)
p.(Gly91Asp)
-
VUS
g.48245057G>A
g.50167696G>A
-
-
SGCA_000153
variant apparently homozygous
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
2
3
c.278C>T
r.(?), r.278c>u
p.(Ala93Val), p.Ala93Val
-
pathogenic
g.48245063C>T
g.50167702C>T
-
-
SGCA_000018
-
PubMed: Duggan
,
PubMed: Trabelsi 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
2
3
c.288_290del
r.(?)
p.(Glu96del)
-
VUS
g.48245073_48245075del
g.50167712_50167714del
288_290delAGA
-
SGCA_000111
-
-
-
-
Germline, Unknown
-
-
-
-
-
Johan den Dunnen
,
Tom Winder
+/.
4
3
c.290A>G
r.(?), r.290a>g
p.(Asp97Gly), p.Asp97Gly
-
pathogenic, pathogenic (recessive)
g.48245075A>G
g.50167714A>G
-
-
SGCA_000019
-
PubMed: Duggan
,
PubMed: Guglieri 2007
,
PubMed: Stehlikova 2014
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., ?/.
4
3
c.292C>A
r.(?)
p.(Arg98Ser)
-
pathogenic, VUS
g.48245077C>A
g.50167716C>A
-
-
SGCA_000082
-
PubMed: Klinge 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Gabriele Dekomien
+/., +?/.
10
3
c.292C>T
r.(?), r.292c>u
p.(Arg98Cys), p.Arg98Cys
-
likely pathogenic, pathogenic, pathogenic (recessive)
g.48245077C>T
g.50167716C>T
-
-
SGCA_000020
variant apparently homozygous
PubMed: Duggan
,
PubMed: Guglieri 2007
,
PubMed: Ljunggren
,
PubMed: Magri 2015
,
PubMed: Nallamilli 2018
,
2 more items
-
-
Germline
-
-
Sau3A-
-
-
Johan den Dunnen
,
Madhuri Hegde
+/., +?/., ?/.
17
3
c.293G>A
r.(?), r.293g>a
p.(Arg98His), p.Arg98His
ACMG
likely pathogenic, pathogenic, pathogenic (recessive), VUS
g.48245078G>A
g.50167717G>A
293C>A
-
SGCA_000001
ACMG PM1 PM2 PM5 PP3 PP5, combination of variants not reported
PubMed: Boito
,
PubMed: Carrie 1997
,
PubMed: Cavdarli 2023
,
PubMed: Eymard 1997
,
PubMed: Klinge 2008
,
5 more items
-
rs137852621
Germline
-
2/1001 cases
NlaIII+
-
-
Johan den Dunnen
,
Gabriele Dekomien
,
Madhuri Hegde
?/.
1
3
c.293G>C
r.(?)
p.(Arg98Pro)
-
VUS
g.48245078G>C
g.50167717G>C
-
-
SGCA_000154
-
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
1
3
c.301C>T
r.(?)
p.(Gln101*)
-
pathogenic
g.48245086C>T
g.50167725C>T
-
-
SGCA_000096
-
PubMed: Trabelsi 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
1
-
c.302A>G
r.(?)
p.(Gln101Arg)
-
likely pathogenic
g.48245087A>G
g.50167726A>G
-
-
SGCA_000225
combination of variants not reported
PubMed: Topf 2020
-
-
Germline
-
2/1001 cases
-
-
-
Johan den Dunnen
+/.
1
-
c.304dup
r.(?)
p.(Val102GlyfsTer3)
-
pathogenic (recessive)
g.48245089dup
g.50167728dup
-
-
SGCA_000239
-
PubMed: Stehlikova 2014
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
-
c.304G>T
r.(?)
p.(Val102Phe)
ACMG
pathogenic, pathogenic (recessive)
g.48245089G>T
g.50167728G>T
-
-
SGCA_000235
ACMG PM1 PM2 PM5 PP3 PP2
PubMed: Cavdarli 2023
-
rs1266940329
Germline
-
-
-
-
-
Johan den Dunnen
+?/., ?/.
3
3
c.307A>G
r.(?)
p.(Ile103Val)
-
likely pathogenic, VUS
g.48245092A>G
g.50167731A>G
-
-
SGCA_000155
-
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
3
3
c.307A>T
r.(?)
p.(Ile103Phe)
-
pathogenic, pathogenic (recessive)
g.48245092A>T
g.50167731A>T
Ile307Trp
-
SGCA_000074
not in 320 control chromosomes
PubMed: Guglieri 2007
,
PubMed: Magri 2015
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/., ?/.
6
3
c.308T>C
r.(?), r.308u>c
p.(Ile103Thr), p.Ile103Thr
-
pathogenic, pathogenic (recessive), VUS
g.48245093T>C
g.50167732T>C
-
-
SGCA_000021
-
PubMed: Duggan
,
PubMed: Stehlikova 2014
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Gabriele Dekomien
?/.
2
3
c.312G>A
r.(?)
p.(=)
-
VUS
g.48245097G>A
g.50167736G>A
-
-
SGCA_000156
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
+/.
1
3i
c.312_313ins(NEO)
r.0
p.0
-
NA
g.48245097_48245308ins(NEO)
-
-
-
SGCA_000000
1 more item
PubMed: Kobuke 2008
-
-
In vitro (cloned)
-
-
-
-
-
Johan den Dunnen
-/.
2
3i
c.312+83C>T
r.(=)
p.(=)
-
benign
g.48245180C>T
g.50167819C>T
-
-
SGCA_000060
-
-
-
rs2696297
Germline
-
-
-
-
-
Johan den Dunnen
,
Ieke Ginjaar
-/., -?/.
4
3i
c.313-39C>A
r.(=), r.(?)
p.(=)
-
benign, likely benign
g.48245269C>A
g.50167908C>A
131-39C>A
-
SGCA_000064
parents homozygous
from website {DBsub-Emory}
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Ieke Ginjaar
,
Madhuri Hegde
-?/.
1
-
c.313-11C>T
r.(=)
p.(=)
-
likely benign
g.48245297C>T
g.50167936C>T
-
-
SGCA_000194
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/.
2
3i
c.313-2A>G
r.spl
p.?
-
pathogenic (recessive)
g.48245306A>G
g.50167945A>G
-
-
SGCA_000216
-
PubMed: Xie 2019
,
PubMed: Yu 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
3i_8i
c.(312+1_313-1)_(983+1_984-1)del
r.?
p.?
ACMG
pathogenic (recessive)
g.(48245098_48245307)_(48248028_48252617)del
g.(50167737_50167946)_(50170667_50175256)del
deletion ex4-8
-
SGCA_000205
ACMG PVS1, PM3, PP1, PP4
PubMed: Xie 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
3
-
c.319_329del
r.(?)
p.(Ala107Glyfs*4)
ACMG
pathogenic (recessive)
g.48245315_48245325del
g.50167954_50167964del
-
-
SGCA_000124
-
PubMed: Mojbafan 2020
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
4
c.320C>T
r.(?)
p.(Ala107Val)
-
pathogenic (recessive)
g.48245315C>T
g.50167954C>T
-
-
SGCA_000217
-
PubMed: Xie 2019
,
PubMed: Yu 2017
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+?/.
2
4
c.320_330del
r.(?)
p.(Ala107Glyfs*4)
-
likely pathogenic
g.48245315_48245325del
g.50167954_50167964del
319_329delGCCTACAATCG
-
SGCA_000124
-
author, submitted
-
-
Germline
yes
-
-
-
-
Zohreh Fattahi
+?/.
1
4
c.322_325dup
r.(?)
p.(Asn109Ilefs*7)
-
likely pathogenic
g.48245317_48245320dup
g.50167956_50167959dup
322_325dupTACA
-
SGCA_000157
variant apparently homozygous
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
?/.
1
4
c.328C>T
r.(?)
p.(Arg110Trp)
-
VUS
g.48245323C>T
g.50167962C>T
-
-
SGCA_000158
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
-?/.
1
-
c.329G>A
r.(?)
p.(Arg110Gln)
-
likely benign
g.48245324G>A
-
SGCA(NM_000023.2):c.329G>A (p.(Arg110Gln))
-
SGCA_000241
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
1
4
c.329G>T
r.(?)
p.(Arg110Leu)
-
pathogenic
g.48245324G>T
g.50167963G>T
-
-
SGCA_000056
-
PubMed: Moreira 2003
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
7
4
c.(348_352dup), c.348_352dup
r.(?), r.348_352dup
p.(Gln118Leufs*95), p.Gln118Leufs*95
-
pathogenic
g.48245343_48245347dup
g.50167982_50167986dup
347_351dupCTCGG, p.fs118toX212
-
SGCA_000022
-
PubMed: Crosbie 2000
,
PubMed: Duggan
,
PubMed: Klinge 2008
-
-
Germline
-
-
-
-
-
Johan den Dunnen
,
Gabriele Dekomien
?/.
3
4
c.350G>A
r.(?)
p.(Arg117Gln)
-
VUS
g.48245345G>A
g.50167984G>A
-
-
SGCA_000159
no second variant
PubMed: Nallamilli 2018
-
-
Germline
-
-
-
-
-
Madhuri Hegde
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