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.
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
Allele: On which allele is the variant located? Does not necessarily imply inheritance! 'Paternal' (confirmed or inferred), 'Maternal' (confirmed or inferred), 'Parent #1' or #2 for compound heterozygosity without having screened the parents, 'Unknown' for heterozygosity without having screened the parents, 'Both' for homozygozity.
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%)

 Effect
|

 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_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Yen 1987 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Bonifas 1987 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Conary 1987 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Gillard 1987 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Ballabio 1989 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Shapiro 1989 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Sugawara 1993 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Morita 1997 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
Female homozygous gene deletion included in family D2 |
PubMed: Murtaza 2014 |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
- |
- |
STS_000046 |
- |
PubMed: Diociaiuti 2016 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
1.6 Mb interstitial deletion |
- |
STS_000046 |
Female patient homozygous for STS deletion |
PubMed: Nagtzaam 2012 |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Saeki 1998 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Canueta 2010 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete STS and HDHD1A gene deletion |
- |
STS_000046 |
- |
PubMed: Idkowiak 2016 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
- |
PubMed: Diociaiuti 2018 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic (recessive) |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
complete gene deletion |
- |
STS_000046 |
represents 57 individual patients |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
?/. |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
ACMG |
VUS |
g.5748782_10477366del |
g.5830745_10559329del |
chrX, g.5748782_10477366del, arr[GRCh37] Xp22.32p22.2(5748782-10477366)x1, heterozygous | heterozygous |
- |
NLGN4X_000080 |
no gene indicated in publication! |
PubMed: Perea-Romero 2021 |
- |
- |
Germline |
yes |
- |
- |
- |
- |
LOVD |
+/+ |
- |
c.1118-7542_*4380{0} |
r.0? |
p.0? |
- |
pathogenic |
g.7235838_7425134del |
g.7317797_7507093del |
partial deletion intron 7 and 3' end gene |
- |
STS_000051 |
- |
PubMed: Bernatowicz 1992 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
+/+? |
_1_7i |
c.?_?ins[-505_(1117+426_?){2}] |
r.? |
p.? |
- |
likely pathogenic |
g.?_?ins(?_7103282)_(7223650_?) |
g.?_?ins(?_7185241)_(7305609_?) |
hg18 (7113282-7233650)x2 |
- |
STS_000074 |
0.12Mb duplication ex1-6 (NM_000351.4) |
PubMed: Bruno 2011 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_0c_10_ |
c.(-252+1_-251-1)_(*4382_?)del |
r.0? |
p.0? |
- |
pathogenic (recessive) |
g.(7066125_7077940)_(7272684_?)del |
- |
- |
- |
STS_000113 |
complete gene deletion without HDHD1 (breakpoint between exon 0b and 0c) |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
_1_5i |
c.(?_-245)_(842+1_843-1)del |
r.? |
p.? |
- |
pathogenic |
g.(?_7063293)_(7177814_7193991)del |
- |
exon 1-5 deletion |
- |
STS_000059 |
lack of STS enzymatic activity |
PubMed: Valdes-Flores 2001 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
-/. |
- |
c.-207A>C |
r.(?) |
p.(=) |
- |
benign |
g.7066051A>C |
- |
STS(NM_001320751.2):c.-325A>C |
- |
STS_000122 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
-?/. |
- |
c.-207A>C |
r.(?) |
p.(=) |
- |
likely benign |
g.7066051A>C |
- |
STS(NM_001320751.2):c.-325A>C |
- |
STS_000122 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Groningen |
?/. |
- |
c.-150T>A |
r.(?) |
p.(=) |
- |
VUS |
g.7066108T>A |
- |
STS(NM_001320751.2):c.-268T>A |
- |
STS_000126 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Groningen |
-/. |
- |
c.-5+34G>A |
r.(=) |
p.(=) |
- |
benign |
g.7109083G>A |
- |
- |
- |
STS_000123 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
./. |
- |
c.-5+26859T>C |
r.(=) |
p.(=) |
- |
VUS |
g.7135908T>C |
g.7217867T>C |
- |
- |
STS_000031 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
./. |
- |
c.-5+26859T>C |
r.(=) |
p.(=) |
- |
VUS |
g.7135908T>C |
g.7217867T>C |
- |
- |
STS_000031 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
-?/. |
- |
c.-5+28685G>A |
r.(=) |
p.(=) |
- |
likely benign |
g.7137734G>A |
- |
STS(NM_000351.7):c.-5+7G>A |
- |
HDHD1_000014 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Leiden |
+/+ |
2i_7i |
c.(32+1_33-4967)_979+8746_980-1)del |
r.? |
p.? |
- |
pathogenic |
g.(?_7166270)_(7202874_?)del |
g.(?_7248229)_(7284833_?)del |
hg18 7176270-7212874del |
- |
STS_000075 |
intragenic 37kb deletion ex2-6 (NM_000351.4) |
PubMed: Bruno 2011 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/. |
_1_10_ |
c.-245_*4380{0} |
r.0 |
p.0 |
- |
pathogenic (recessive) |
g.(?_6887519)_(7873728_?)del |
g.(?_6969478)_(7955687_?)del |
arr[hg38] Xp22.31 (6,969,478–7,955,687)×1 |
- |
STS_000116 |
986 Kb deletion involving STS, PUDP1, VCX, PNPLA4 |
PubMed: Chouk 2022 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Hamza Chouk |
+/. |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic (recessive) |
g.(?_6551155)_(7982120_?)del |
g.(?_6633114)_(8064079_?)del |
arr[hg38] Xp22.31 (6,633,114–8,064,079)×1 |
- |
STS_000124 |
- |
PubMed: Chouk 2022 |
- |
- |
Germline |
yes |
- |
- |
- |
1.4 Mb deletion involving STS, PUDP1, VCX, PNPLA4 |
Hamza Chouk |
+/. |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic (recessive) |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
del STS gene |
- |
STS_000046 |
- |
PubMed: Chouk 2022 |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Hamza Chouk |
+/. |
_1_11_ |
c.-505_*4380{0} |
r.0 |
p.0 |
- |
pathogenic (recessive) |
g.(?_7137472)_(7272682_?)del |
g.(?_7219431)_(7354641_?)del |
del STS gene |
- |
STS_000046 |
- |
PubMed: Zhang 2022 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Johan den Dunnen |
+/. |
- |
c.? |
r.? |
p.? |
- |
pathogenic (recessive) |
g.? |
- |
del ex7-10 |
- |
CLCN5_000000 |
- |
- |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Johan den Dunnen |
+/+ |
2i_6i |
c.[32+5522_32+5529dup;32+5537_842+5507del] |
r.? |
p.? |
- |
pathogenic |
g.[7143249_7143256dup;7143264_7183320del] |
g.[7225208_7225215dup;7225223_7281467del] |
intragenic exon 2-5 deletion |
- |
STS_000047 |
- |
PubMed: Shapiro 1989 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
?/. |
- |
c.33-312C>G |
r.(=) |
p.? |
- |
VUS |
g.7170925C>G |
g.7252884C>G |
NM_000351.4:c.12-312C>G |
- |
STS_000001 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
+/+ |
- |
c.127G>A |
r.(?) |
p.(Asp43Asn) |
- |
pathogenic (recessive) |
g.7171331G>A |
- |
NM_000351.4:c.106G>A |
- |
STS_000043 |
No STS enzymatic activity in leucocytes |
Nagtzaam et al, submitted |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
-?/. |
- |
c.138G>A |
r.(?) |
p.(Arg46=) |
- |
likely benign |
g.7175283G>A |
- |
STS(NM_001320750.1):c.174G>A (p.R58=) |
- |
STS_000117 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
+/+ |
- |
c.205G>A |
r.(?) |
p.(Gly69Arg) |
- |
pathogenic |
g.7175314G>A |
g.7257273G>A |
NM_000351.4:c.184G>A |
- |
STS_000078 |
lack of STS enzymatic activity |
PubMed: Ohyama 2019 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+?/. |
- |
c.241C>T |
r.(?) |
p.(Arg81Trp) |
- |
likely pathogenic |
g.7175386C>T |
- |
- |
- |
STS_000108 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
+?/+? |
- |
c.277C>T |
r.(?) |
p.(Arg93Trp) |
- |
likely pathogenic (recessive) |
g.7175386C>T |
- |
NM_000351.4:c.256C>T |
- |
STS_000108 |
Missense variant published as pathogenic at equivalent position in paralogue sulfatase gene GALNS |
Nagtzaam et al, submitted |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.282C>G |
r.(?) |
p.(Tyr94Ter) |
- |
pathogenic |
g.7175391C>G |
g.7257350C>G |
NM_000351.4:c.261C>G |
- |
STS_000066 |
lack of STS enzymatic activity |
PubMed: del Refugio Rivera Vega 2015 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.289C>T |
r.(?) |
p.(Arg97Ter) |
- |
pathogenic |
g.7175398C>T |
g.7257357C>T |
NM_000351.4:c.268C>T |
- |
STS_000044 |
- |
PubMed: Winge 2011 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+?/. |
- |
c.308C>T |
r.(?) |
p.(Ser103Leu) |
- |
likely pathogenic |
g.7175555C>T |
- |
- |
- |
STS_000079 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
+/+ |
- |
c.308G>A |
r.(?) |
p.(Trp103Ter) |
- |
pathogenic (recessive) |
g.7175519G>A |
- |
NM_000351.4:c.287G>A |
- |
STS_000104 |
- |
PubMed: Afzal 2020 |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Michel van Geel |
-?/. |
- |
c.324C>T |
r.(?) |
p.(Thr108=) |
- |
likely benign |
g.7175571C>T |
- |
STS(NM_001320750.1):c.360C>T (p.T120=) |
- |
STS_000118 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
+/+? |
- |
c.344C>T |
r.(?) |
p.(Ser115Leu) |
- |
likely pathogenic |
g.7175555C>T |
g.7257514C>T |
NM_000351.4:c.323C>T |
- |
STS_000079 |
- |
PubMed: Diociaiuti 2018 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+?/+? |
- |
c.349G>A |
r.(?) |
p.(Gly117Arg) |
- |
likely pathogenic (recessive) |
g.7175560G>A |
- |
NM_000351.4:c.328G>A |
- |
STS_000109 |
Missense variants published as pathogenic at equivalent position in paralogue sulfatase gene GALNS |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
?/. |
- |
c.374_386del |
r.(?) |
p.(Phe125Ter) |
- |
benign (!) |
g.7175585_7175597del |
g.7257544_7257556del |
- |
- |
STS_000125 |
variant an artefact; gene deletion gives amplification Y-chromosome STS pseudogene |
PubMed: Chouk 2022 |
- |
- |
Artefact |
- |
- |
- |
- |
- |
Johan den Dunnen |
?/. |
- |
c.374_386del |
r.(?) |
p.(Phe125Ter) |
- |
benign (!) |
g.7175585_7175597del |
g.7257544_7257556del |
- |
- |
STS_000125 |
variant an artefact; gene deletion gives amplification Y-chromosome |
PubMed: Chouk 2022 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Johan den Dunnen |
?/. |
- |
c.374_386del |
r.(?) |
p.(Phe125Ter) |
- |
benign (!) |
g.7175585_7175597del |
g.7257544_7257556del |
- |
- |
STS_000125 |
variant an artefact; gene deletion gives amplification Y-chromosome |
PubMed: Chouk 2022 |
- |
- |
Artefact |
- |
- |
- |
- |
- |
Johan den Dunnen |
+?/. |
- |
c.382+1G>T |
r.spl? |
p.? |
- |
likely pathogenic |
g.7175630G>T |
- |
- |
- |
HDHD1_000013 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
?/. |
- |
c.418+240_418+241del |
r.(?) |
p.(=) |
- |
VUS |
g.7175869_7175870del |
g.7257828_7257829del |
NM_000351.4:c.397+240_397+241del |
- |
STS_000028 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.418+240_418+241del |
r.(?) |
p.(=) |
- |
VUS |
g.7175869_7175870del |
g.7257828_7257829del |
NM_000351.4:c.397+240_397+241del |
- |
STS_000028 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.418+253_418+254del |
r.(?) |
p.(=) |
- |
VUS |
g.7175882_7175883del |
g.7257841_7257842del |
NM_000351.4:c.397+253_397+254del |
- |
STS_000004 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.418+253_418+254del |
r.(?) |
p.(=) |
- |
VUS |
g.7175882_7175883del |
g.7257841_7257842del |
NM_000351.4:c.397+253_397+254del |
- |
STS_000004 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.428G>C |
r.(?) |
p.(Cys143Ser) |
- |
VUS |
g.7177435G>C |
- |
STS(NM_001320752.2):c.428G>C (p.(Cys143Ser)) |
- |
HDHD1_000012 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Leiden |
+/+? |
- |
c.473C>G |
r.(?) |
p.(Pro158Arg) |
- |
likely pathogenic |
g.7177444C>G |
g.7259403C>G |
NM_000351.4:c.452C>G |
- |
STS_000067 |
- |
PubMed: Diociaiuti 2016 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+? |
- |
c.473C>G |
r.(?) |
p.(Pro158Arg) |
- |
likely pathogenic |
g.7177444C>G |
g.7259403C>G |
NM_000351.4:c.452C>G |
- |
STS_000067 |
- |
PubMed: Diociaiuti 2018 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.515C>T |
r.(?) |
p.(Thr172Ile) |
- |
pathogenic |
g.7177486C>T |
g.7259445C>T |
NM_000351.4:c.494C>T |
- |
STS_000063 |
lack of STS enzymatic activity, includes heterozygous p.Arg501* FLG mutation |
PubMed: Liao 2007 |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.550_553delinsAG |
r.(?) |
p.(Val184SerfsTer81) |
- |
pathogenic |
g.7177521_7177524delinsAG |
g.7259480_7259483delinsAG |
- |
- |
STS_000065 |
- |
PubMed: Takeichi 2015 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.670_671delinsG |
r.(?) |
p.(Phe224AlafsTer6) |
- |
pathogenic (recessive) |
g.7177641_7177642delinsG |
- |
NM_000351.4:c.649_650delinsG |
- |
STS_000112 |
- |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.670_671delinsG |
r.(?) |
p.(Phe224AlafsTer6) |
- |
pathogenic (recessive) |
g.7177641_7177642delinsG |
- |
NM_000351.4:c.649_650delinsG |
- |
STS_000112 |
- |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.670_671delinsG |
r.(?) |
p.(Phe224AlafsTer6) |
- |
pathogenic (recessive) |
g.7177641_7177642delinsG |
- |
NM_000351.4:c.649_650delinsG |
- |
STS_000112 |
- |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
-/. |
- |
c.807-5del |
r.spl? |
p.? |
- |
benign |
g.7193987del |
- |
STS(NM_000351.7):c.807-5delT |
- |
STS_000127 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Groningen |
-?/. |
- |
c.822G>A |
r.(?) |
p.(Pro274=) |
- |
likely benign |
g.7194007G>A |
- |
STS(NM_001320750.1):c.858G>A (p.P286=) |
- |
STS_000119 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
?/. |
- |
c.842+214C>T |
r.(?) |
p.(=) |
- |
VUS |
g.7178027C>T |
g.7259986C>T |
NM_000351.4:c.821+214C>T |
- |
STS_000006 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.842+214C>T |
r.(?) |
p.(=) |
- |
VUS |
g.7178027C>T |
g.7259986C>T |
NM_000351.4:c.821+214C>T |
- |
STS_000006 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.842+244T>C |
r.(?) |
p.(=) |
- |
VUS |
g.7178057T>C |
g.7260016T>C |
NM_000351.4:c.821+244T>C |
- |
STS_000009 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.842+244T>C |
r.(?) |
p.(=) |
- |
VUS |
g.7178057T>C |
g.7260016T>C |
NM_000351.4:c.821+244T>C |
- |
STS_000009 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.843-22del |
r.(?) |
p.(=) |
- |
VUS |
g.7193970del |
g.7275929del |
NM_000351.4:c.822-22del |
- |
STS_000030 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
+/+? |
- |
c.843-1G>A |
r.spl |
p.? |
- |
likely pathogenic |
g.7193991G>A |
g.7275950G>A |
NM_000351.4:c.822-1G>A |
- |
STS_000073 |
- |
PubMed: Retterer 2016 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+? |
5i_6i |
c.(842+1_843-1)_(979+1_980-1)del |
r.(?) |
p.(Asn275Alafs*8) |
- |
pathogenic (recessive) |
g.(7177814_7193991)_(7194129_7223086)del |
- |
exon 6 deletion |
- |
STS_000105 |
- |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
-?/. |
- |
c.944-10T>C |
r.(=) |
p.(=) |
- |
likely benign |
g.7223077T>C |
- |
STS(NM_001320750.1):c.980-10T>C, STS(NM_001320752.2):c.944-10T>C |
- |
STS_000120 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-?/. |
- |
c.944-10T>C |
r.(=) |
p.(=) |
- |
likely benign |
g.7223077T>C |
- |
STS(NM_001320750.1):c.980-10T>C, STS(NM_001320752.2):c.944-10T>C |
- |
STS_000120 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Leiden |
+/+ |
- |
c.979+2_1118del |
r.spl |
p.? |
- |
pathogenic |
g.7194130_7243380del |
g.7276089_7325339del |
del ex7 |
- |
STS_000077 |
- |
PubMed: Idkowiak 2016 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.979+2_1118del |
r.spl |
p.? |
- |
pathogenic |
g.7194130_7243380del |
g.7276089_7325339del |
del ex7 |
- |
STS_000077 |
- |
PubMed: Diociaiuti 2018 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
6i_10_ |
c.(979+1_980-1)_(*4382_?)del |
r.? |
p.? |
- |
pathogenic |
g.(7194129_7223086)_(7272684_?)del |
- |
partial deletion STS exon 7-10 |
- |
STS_000076 |
Patient also has homozygous ASPM mutation c.2936+1G>A |
PubMed: Abdel-Hamid 2016 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1043C>T |
r.(?) |
p.(Ser348Leu) |
- |
pathogenic |
g.7223150C>T |
g.7305109C>T |
1226 TCG>TTG |
- |
STS_000048 |
complete lack of STS activity |
PubMed: Basler 1992 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+? |
- |
c.1051G>A |
r.(?) |
p.(Gly351Arg) |
- |
likely pathogenic |
g.7223158G>A |
g.7305117G>A |
NM_000351.4:c.1030G>A |
- |
STS_000080 |
- |
PubMed: Diociaiuti 2018 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1051G>T |
r.(?) |
p.(Gly351Ter) |
- |
pathogenic |
g.7223158G>T |
g.7305117G>T |
G>T 1236 |
- |
STS_000056 |
- |
PubMed: Morita 1997 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1067_1069del |
r.(?) |
p.(Glu356del) |
- |
pathogenic |
g.7223174_7223176del |
g.7305133_7305135del |
AAGdel1252 |
- |
STS_000061 |
lack of STS enzymatic activity |
PubMed: Valdes-Flores 2001 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+? |
- |
c.1070T>G |
r.(?) |
p.(Val357Gly) |
- |
likely pathogenic |
g.7223177T>G |
g.7305136T>G |
NM_000351.4:c.1049T>G |
- |
STS_000069 |
- |
PubMed: Oyama 2016 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1096G>A |
r.(?) |
p.(Gly366Arg) |
- |
pathogenic |
g.7223203G>A |
g.7305162G>A |
NM_000351.4:c.1075G>A |
- |
STS_000068 |
- |
PubMed: Diociaiuti 2016 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1096G>A |
r.(?) |
p.(Gly366Arg) |
- |
pathogenic |
g.7223203G>A |
g.7305162G>A |
NM_000351.4:c.1075G>A |
- |
STS_000068 |
- |
PubMed: Diociaiuti 2016 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1096G>A |
r.(?) |
p.(Gly366Arg) |
- |
pathogenic |
g.7223203G>A |
g.7305162G>A |
NM_000351.4:c.1075G>A |
- |
STS_000068 |
- |
PubMed: Oyama 2016 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+? |
- |
c.1096G>A |
r.(?) |
p.(Gly366Arg) |
- |
pathogenic |
g.7223203G>A |
g.7305162G>A |
NM_000351.4:c.1075G>A |
- |
STS_000068 |
- |
PubMed: Diociaiuti 2018 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
?/. |
- |
c.1118-76G>A |
r.(=) |
p.? |
- |
VUS |
g.7243304G>A |
g.7325263G>A |
NM_000351.4:c.1097-76G>A |
- |
STS_000023 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
- |
c.1118-76G>A |
r.(=) |
p.? |
- |
VUS |
g.7243304G>A |
g.7325263G>A |
NM_000351.4:c.1097-76G>A |
- |
STS_000023 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
+?/+? |
7i_9i |
c.(1117+1_1118-1)_(1420+1_1421-1)dup |
r.(?) |
p.? |
- |
likely pathogenic (recessive) |
g.(7223225_7243379)_(7252149_7267928)dup |
- |
- |
- |
STS_000106 |
exon 8-9 duplication |
Nagtzaam et al, submitted |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+? |
- |
c.1120G>A |
r.(?) |
p.(Gly374Arg) |
- |
likely pathogenic |
g.7243382G>A |
g.7325341G>A |
NM_000351.4:c.1099G>A |
- |
STS_000070 |
- |
PubMed: Wei 2011 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+?/+? |
- |
c.1121G>C |
r.(?) |
p.(Gly374Ala) |
- |
likely pathogenic (recessive) |
g.7243383G>C |
- |
NM_000351.4:c.1100G>C |
- |
STS_000110 |
Missense variant published as pathogenic at equivalent position in paralogue sulfatase genes ARSL |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1126G>C |
r.(?) |
p.(Ala376Pro) |
- |
pathogenic (recessive) |
g.7243388G>C |
- |
NM_000351.4:c.1105G>C |
- |
STS_000088 |
Detemined cholesterol sulfate in plasma was >10x elevated |
Nagtzaam et al, submitted |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1135T>A |
r.(?) |
p.(Trp379Arg) |
- |
pathogenic |
g.7243397T>A |
g.7325356T>A |
1320 TGG>AGG |
- |
STS_000049 |
complete lack of STS activity |
PubMed: Basler 1992 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1136G>C |
r.(?) |
p.(Trp379Ser) |
- |
pathogenic |
g.7243398G>C |
g.7325357G>C |
1336 G>C, 372 Trp>Pro |
- |
STS_000053 |
lack of STS enzymatic activity |
PubMed: Alperin 1997 |
- |
- |
Unknown |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1137G>A |
r.(?) |
p.(Trp379Ter) |
- |
pathogenic |
g.7243399G>A |
- |
NM_000351.4:c.1116G>A |
- |
STS_000101 |
deficient STS enzymatic activity |
PubMed: Diociaiuti 2019 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
-?/. |
- |
c.1143G>C |
r.(?) |
p.(Arg381Ser) |
- |
likely benign |
g.7243441G>C |
- |
STS(NM_001320752.2):c.1143G>C (p.(Arg381Ser)) |
- |
HDHD1_000015 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Leiden |
+/+ |
- |
c.1159G>C |
r.(?) |
p.(Gly387Arg) |
- |
pathogenic |
g.7243421G>C |
g.7325380G>C |
G1344C |
- |
STS_000057 |
lack of STS enzymatic activity |
PubMed: Oyama 2000 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
+/+ |
- |
c.1186C>T |
r.(?) |
p.(Gln396Ter) |
- |
pathogenic |
g.7243448C>T |
g.7325407C>T |
C1371T |
- |
STS_000058 |
lack of STS enzymatic activity |
PubMed: Oyama 2000 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Michel van Geel |
-?/. |
- |
c.1209C>A |
r.(?) |
p.(Ala403=) |
- |
likely benign |
g.7243507C>A |
- |
STS(NM_001320750.1):c.1245C>A (p.A415=) |
- |
STS_000121 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |