Global Variome shared LOVD
RS1 (retinoschisin 1)
LOVD v.3.0 Build 30b [
Current LOVD status
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Curators:
Johan den Dunnen
and
Markus Preising
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This database is one of the
"Eye disease"
gene variant databases.
The variants shown are described using the NM_000330.3 transcript reference sequence.
Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect
: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
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%)
Template
: Template(s) used to detect the sequence variant; DNA (genomic DNA), RNA (cDNA) or protein
All options:
DNA
RNA = RNA (cDNA)
protein
? = unknown
Technique
: technique(s) used to identify the sequence variant.
All options:
? = unknown
ARMS = amplification refractory mutation system
arrayCGH = array for Comparative Genomic Hybridisation
arrayMET = array for methylation analysis
arraySEQ = array for resequencing
arraySNP = array for SNP typing
arrayCNV = array for Copy Number Variation (SNP and CNV probes)
ASO = allele-specific oligo hybridisation
BESS = Base Excision Sequence Scanning
CMC = Chemical Mismatch Cleavage
COBRA = Combined Bisulfite Restriction Analysis
CSCE = Conformation Sensitive Capillary Electrophoresis
CSGE = Conformation Sensitive Gel Electrophoresis
ddF = dideoxy Fingerprinting
DGGE = Denaturing-Gradient Gel-Electrophoresis
DHPLC = Denaturing High-Performance Liquid Chromatography
DOVAM = Detection Of Virtually All Mutations (SSCA variant)
DSCA = Double-Strand DNA Conformation Analysis
DSDI = Detection Small Deletions and Insertions
EMC = Enzymatic Mismatch Cleavage
expr = expression analysis
FISH = Fluorescent In-Situ Hybridisation
FISHf = fiberFISH
HD = HeteroDuplex analysis
HPLC = High-Performance Liquid Chromatography
IEF = IsoElectric Focussing
IHC = Immuno-Histo-Chemistry
Invader = Invader assay
MAPH = Multiplex Amplifiable Probe Hybridisation
MAQ = Multiplex Amplicon Quantification
MCA = Melting Curve Analysis, high-resolution (HRMA)
microscope = microscopic analysis (karyotype)
microsat = microsatellite genotyping
minigene = expression minigene construct
MIP = Molecular Inversion Probe amplification
MIPsm = single molecule Molecular Inversion Probe amplification
MLPA = Multiplex Ligation-dependent Probe Amplification
MLPA-ms = Multiplex Ligation-dependent Probe Amplification, methylation specific
MS = mass spectrometry
Northern = Northern blotting
NUC = nuclease digestion (RNAseT1, S1)
OM = optical mapping
PAGE = Poly-Acrylamide Gel-Electrophoresis
PCR = Polymerase Chain Reaction
PCRdd = PCR, digital droplet
PCRdig = PCR + restriction enzyme digestion
PCRh = PCR, haloplex
PCRlr = PCR, long-range
PCRm = PCR, multiplex
PCRms = PCR, methylation sensitive
PCRq = PCR, quantitative (qPCR)
PCRrp = PCR, repeat-primed (RP-PCR)
PCRsqd = PCR, semi-quantitative duplex
PE = primer extension (APEX, SNaPshot)
PEms = primer extension, methylation-sensitive single-nucleotide
PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
PTT = Protein Truncation Test
RFLP = Restriction Fragment Length Polymorphisms
RT-PCR = Reverse Transcription and PCR
RT-PCRq = Reverse Transcription and PCR, quantitative
SBE = Single Base Extension
SEQ = SEQuencing (Sanger)
SEQb = bisulfite SEQuencing
SEQp = pyroSequencing
SEQms = sequencing, methylation specific
SEQ-ON = next-generation sequencing - Oxford Nanopore
SEQ-NG = next-generation sequencing
SEQ-NG-RNA = next-generation sequencing RNA
SEQ-NG-H = next-generation sequencing - Helicos
SEQ-NG-I = next-generation sequencing - Illumina/Solexa
SEQ-NG-IT = next-generation sequencing - Ion Torrent
SEQ-NG-R = next-generation sequencing - Roche/454
SEQ-NG-S = next-generation sequencing - SOLiD
SEQ-PB = next-generation sequencing - Pacific Biosciences
SNPlex = SNPlex
Southern = Southern blotting
SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
SSCAf = fluorescent SSCA (SSCP)
STR = Short Tandem Repeat
TaqMan = TaqMan assay
Western = Western blotting
- = not applicable
Tissue
: tissue type used for analysis
Remarks
: remarks regarding the screening like WGS (whole genome sequencing), WES (whole exome sequencing, gene panel (incl. a list of genes analysed), etc.
ID_report
: ID of the individual that can be publically shared, e.g. as listed in a publication
Reference
: reference to publication describing the individual/family, possibly giving more phenotypic details than listed in this database entry, incl. link to PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"
Remarks
: remarks about the individual
Gender
: gender individual
All options:
? = unknown
- = not applicable
F = female
M = male
rF = raised as female
rM = raised as male
Consanguinity
: indicates whether the parents are related (consanguineous), not related (non-consanguineous) or whether consanguinity is not known (unknown)
All options:
no = non-consanguineous parents
yes = consanguineous parents
likely = consanguinity likely
? = unknown
- = not applicable
Country
: where (country) does the individual live/recently came from. Give additional details (population, specific sub-group) and when parents come from different countries in "Population". Belgium = individual lives in/recently came from Belgium, (France) = reported by laboratory in France, individual's country of origin not sure
All options:
? (unknown)
- (not applicable)
Afghanistan
(Afghanistan)
Albania
(Albania)
Algeria
(Algeria)
American Samoa
(American Samoa)
Andorra
(Andorra)
Angola
(Angola)
Anguilla
(Anguilla)
Antarctica
(Antarctica)
Antigua and Barbuda
(Antigua and Barbuda)
Argentina
(Argentina)
Armenia
(Armenia)
Aruba
(Aruba)
Australia
(Australia)
Austria
(Austria)
Azerbaijan
(Azerbaijan)
Bahamas
(Bahamas)
Bahrain
(Bahrain)
Bangladesh
(Bangladesh)
Barbados
(Barbados)
Belarus
(Belarus)
Belgium
(Belgium)
Belize
(Belize)
Benin
(Benin)
Bermuda
(Bermuda)
Bhutan
(Bhutan)
Bolivia
(Bolivia)
Bosnia and Herzegovina
(Bosnia and Herzegovina)
Botswana
(Botswana)
Bouvet Island
(Bouvet Island)
Brazil
(Brazil)
British Indian Ocean Territory
(British Indian Ocean Territory)
Brunei Darussalam
(Brunei Darussalam)
Bulgaria
(Bulgaria)
Burkina Faso
(Burkina Faso)
Burundi
(Burundi)
Cambodia
(Cambodia)
Cameroon
(Cameroon)
Canada
(Canada)
Cape Verde
(Cape Verde)
Cayman Islands
(Cayman Islands)
Central African Republic
(Central African Republic)
Central Europe
Chad
(Chad)
Chile
(Chile)
China
(China)
Christmas Island
(Christmas Island)
Cocos (Keeling Islands)
(Cocos (Keeling Islands))
Colombia
(Colombia)
Comoros
(Comoros)
Congo
(Congo)
Cook Islands
(Cook Islands)
Costa Rica
(Costa Rica)
Cote D'Ivoire (Ivory Coast)
(Cote D'Ivoire (Ivory Coast))
Croatia (Hrvatska)
(Croatia (Hrvatska))
Cuba
(Cuba)
Cyprus
(Cyprus)
Czech Republic
(Czech Republic)
Denmark
(Denmark)
Djibouti
(Djibouti)
Dominica
(Dominica)
Dominican Republic
(Dominican Republic)
East Timor
(East Timor)
Ecuador
(Ecuador)
Egypt
(Egypt)
El Salvador
(El Salvador)
England
(England)
Equatorial Guinea
(Equatorial Guinea)
Eritrea
(Eritrea)
Estonia
(Estonia)
Ethiopia
(Ethiopia)
Falkland Islands (Malvinas)
(Falkland Islands (Malvinas))
Faroe Islands
(Faroe Islands)
Fiji
(Fiji)
Finland
(Finland)
France
(France)
Gabon
(Gabon)
Gambia
(Gambia)
Georgia
(Georgia)
Germany
(Germany)
Ghana
(Ghana)
Gibraltar
(Gibraltar)
Greece
(Greece)
Greenland
(Greenland)
Grenada
(Grenada)
Guadeloupe
(Guadeloupe)
Guam
(Guam)
Guatemala
(Guatemala)
Guiana, French
(Guiana, French)
Guinea
(Guinea)
Guinea-Bissau
(Guinea-Bissau)
Guyana
(Guyana)
Haiti
(Haiti)
Heard and McDonald Islands
(Heard and McDonald Islands)
Honduras
(Honduras)
Hong Kong
(Hong Kong)
Hungary
(Hungary)
Iceland
(Iceland)
India
(India)
Indonesia
(Indonesia)
Iran
(Iran)
Iraq
(Iraq)
Ireland
(Ireland)
Israel
(Israel)
Italy
(Italy)
Jamaica
(Jamaica)
Japan
(Japan)
Jordan
(Jordan)
Kazakhstan
(Kazakhstan)
Kenya
(Kenya)
Kiribati
(Kiribati)
Korea
(Korea)
Korea, North (People's Republic)
(Korea, North (People's Republic))
Korea, South (Republic)
(Korea, South (Republic))
Kosovo
(Kosovo)
Kuwait
(Kuwait)
Kyrgyzstan (Kyrgyz Republic)
(Kyrgyzstan (Kyrgyz Republic))
Laos
(Laos)
Latvia
(Latvia)
Lebanon
(Lebanon)
Lesotho
(Lesotho)
Liberia
(Liberia)
Libya
(Libya)
Liechtenstein
(Liechtenstein)
Lithuania
(Lithuania)
Luxembourg
(Luxembourg)
Macau
(Macau)
Macedonia
(Macedonia)
Madagascar
(Madagascar)
Malawi
(Malawi)
Malaysia
(Malaysia)
Maldives
(Maldives)
Mali
(Mali)
Mallorca
(Mallorca)
Malta
(Malta)
Marshall Islands
(Marshall Islands)
Martinique
(Martinique)
Mauritania
(Mauritania)
Mauritius
(Mauritius)
Mayotte
(Mayotte)
Mexico
(Mexico)
Micronesia
(Micronesia)
Moldova
(Moldova)
Monaco
(Monaco)
Mongolia
(Mongolia)
Montserrat
(Montserrat)
Morocco
(Morocco)
Mozambique
(Mozambique)
Myanmar
(Myanmar)
Namibia
(Namibia)
Nauru
(Nauru)
Nepal
(Nepal)
Netherlands
(Netherlands)
Netherlands Antilles
(Netherlands Antilles)
Neutral Zone (Saudia Arabia/Iraq)
(Neutral Zone (Saudia Arabia/Iraq))
New Caledonia
(New Caledonia)
New Zealand
(New Zealand)
Nicaragua
(Nicaragua)
Niger
(Niger)
Nigeria
(Nigeria)
Niue
(Niue)
Norfolk Island
(Norfolk Island)
Northern Ireland
(Northern Ireland)
Northern Mariana Islands
(Northern Mariana Islands)
Norway
(Norway)
Oman
(Oman)
Pakistan
(Pakistan)
Palau
(Palau)
Palestine
(Palestine)
Panama
(Panama)
Papua New Guinea
(Papua New Guinea)
Paraguay
(Paraguay)
Peru
(Peru)
Philippines
(Philippines)
Pitcairn
(Pitcairn)
Poland
(Poland)
Polynesia, French
(Polynesia, French)
Portugal
(Portugal)
Puerto Rico
(Puerto Rico)
Qatar
(Qatar)
Reunion
(Reunion)
Romania
(Romania)
Russia
(Russia)
Russian Federation
(Russian Federation)
Rwanda
(Rwanda)
S. Georgia and S. Sandwich Isls.
(S. Georgia and S. Sandwich Isls.)
Saint Kitts and Nevis
(Saint Kitts and Nevis)
Saint Lucia
(Saint Lucia)
Saint Vincent and The Grenadines
(Saint Vincent and The Grenadines)
Samoa
(Samoa)
San Marino
(San Marino)
Sao Tome and Principe
(Sao Tome and Principe)
Saudi Arabia
(Saudi Arabia)
Scotland
(Scotland)
Senegal
(Senegal)
Serbia
(Serbia)
Seychelles
(Seychelles)
Sierra Leone
(Sierra Leone)
Singapore
(Singapore)
Slovakia (Slovak Republic)
(Slovakia (Slovak Republic))
Slovenia
(Slovenia)
Solomon Islands
(Solomon Islands)
Somalia
(Somalia)
South Africa
(South Africa)
Southern Territories, French
(Southern Territories, French)
Soviet Union (former)
(Soviet Union (former))
Spain
(Spain)
Sri Lanka
(Sri Lanka)
St. Helena, Ascension and Tristan da
Cunha
(St. Helena, Ascension and Tristan da
Cunha)
St. Pierre and Miquelon
(St. Pierre and Miquelon)
Sudan
(Sudan)
Sudan, South
(Sudan, South)
Suriname
(Suriname)
Svalbard and Jan Mayen Islands
(Svalbard and Jan Mayen Islands)
Swaziland
(Swaziland)
Sweden
(Sweden)
Switzerland
(Switzerland)
Syria
(Syria)
Taiwan
(Taiwan)
Tajikistan
(Tajikistan)
Tanzania
(Tanzania)
Thailand
(Thailand)
Togo
(Togo)
Tokelau
(Tokelau)
Tonga
(Tonga)
Trinidad and Tobago
(Trinidad and Tobago)
Tunisia
(Tunisia)
Turkey
(Turkey)
Turkmenistan
(Turkmenistan)
Turks and Caicos Islands
(Turks and Caicos Islands)
Tuvalu
(Tuvalu)
Uganda
(Uganda)
Ukraine
(Ukraine)
United Arab Emirates
(United Arab Emirates)
United Kingdom (Great Britain)
(United Kingdom (Great Britain))
United States
(United States)
Uruguay
(Uruguay)
US Minor Outlying Islands
(US Minor Outlying Islands)
Uzbekistan
(Uzbekistan)
Vanuatu
(Vanuatu)
Vatican City State (Holy See)
(Vatican City State (Holy See))
Venezuela
(Venezuela)
Viet Nam
(Viet Nam)
Virgin Islands (British)
(Virgin Islands (British))
Virgin Islands (US)
(Virgin Islands (US))
Wales
(Wales)
Wallis and Futuna Islands
(Wallis and Futuna Islands)
Western Sahara
(Western Sahara)
Yemen
(Yemen)
Yugoslavia
(Yugoslavia)
Zaire
(Zaire)
Zambia
(Zambia)
Zimbabwe
(Zimbabwe)
Population
: population the individual (or ancestors) belongs to; e.g. white, gypsy, Jewish-Ashkenazi, Africa-N, Sardinia, etc.
Age at death
: age at which the individual deceased (when applicable):
35y = 35 years
>43y = still alive at 43y
04y08m = 4 years and 8 months
00y00m01d12h = 1 day and 12 hours
18y? = around 18 years
30y-40y = between 30 and 40 years
>54y = older than 54
? = unknown
VIP
: individual/phenotype 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.
Data_av
: are additional data available upon request: e.g. pedigree (yes/no/?)
Treatment
: treatment of patient
How to query this table
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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
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$
Text
Ser)$
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=""
Text
=""
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=""
Text
="p.0"
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!=""
Text
!=""
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!=""
Text
!="p.0"
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combination
Text
*|Ter !fs
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Date
2020
all entries matching the year 2020
|
Date
2020-03|2020-04
all entries matching March or April, 2020
!
Date
!2020-03
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<
Date
<2020
all entries before the year 2020
<=
Date
<=2020-06
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>
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
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|
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
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>
Numeric
>23
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>=
Numeric
>=23
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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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39 entries on 1 page. Showing entries 1 - 39.
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Legend
How to query
Effect
Exon
DNA change (cDNA)
RNA change
Protein
Allele
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
Template
Technique
Tissue
Remarks
Disease
ID_report
Reference
Remarks
Gender
Consanguinity
Country
Population
Age at death
VIP
Data_av
Treatment
Panel size
Owner
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
pathogenic
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: RS-consortium 1998, group 2
-
-
Germline
-
-
-BbvI
-
-
DNA
SSCA
-
-
RS1
-
PubMed: RS-consortium 1998, group 2
-
?
-
Austria
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
pathogenic
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: Gehrig 1999
-
-
Germline
-
-
-BbvI
-
-
DNA
SSCA
-
-
RS1
-
PubMed: Gehrig 1999
-
?
-
Austria
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
pathogenic
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: Pimenides 2005
-
-
Germline
-
-
-BbvI
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Pimenides 2005
-
M
-
United Kingdom (Great Britain)
-
-
-
-
-
1
Dorothy Trump
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
pathogenic
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: RS-consortium 1998; group 6
,
PubMed: Pimenides 2005
-
-
Germline
-
-
-BbvI
-
-
DNA
SEQ
-
-
RS1
-
PubMed: RS-consortium 1998; group 6
,
PubMed: Pimenides 2005
several patients
M
-
United Kingdom (Great Britain)
-
-
-
-
-
1
Dorothy Trump
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
pathogenic
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: RS-consortium 1998, group 3
-
-
Germline
-
-
-BbvI
-
-
DNA
SEQ
-
-
RS1
-
PubMed: RS-consortium 1998, group 3
-
?
-
United States
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
pathogenic
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: Tsang 2007
-
-
Germline
-
-
-BbvI
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Tsang 2007
-
M
-
United States
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Both (homozygous)
-
pathogenic
g.18660225dup
g.18642105dup
588-593incC
-
RS1_000070
-
PubMed: Ali 2003
,
PubMed: Saleheen 2008
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
?;FamPatIV2/3/4/5
PubMed: Ali 2003
,
PubMed: Saleheen 2008
4 affected females
F
yes
Pakistan
-
-
-
-
-
4
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (confirmed)
-
pathogenic
g.18660225dup
g.18642105dup
578_579insC
-
RS1_000070
-
PubMed: Riveiro 2005
,
PubMed: Riveiro-Alvarez 2009
;Riveiro-Alvarez ESHG2008 P05.213
-
-
Germline
-
-
-BbvI
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Riveiro 2005
,
PubMed: Riveiro-Alvarez 2009
;Riveiro-Alvarez ESHG2008 P05.213
3-generation family, 3 affecteds, 2 carriers
M
-
Spain
-
-
-
-
-
5
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (confirmed)
-
pathogenic
g.18660225dup
g.18642105dup
578_579insC
-
RS1_000070
-
PubMed: Riveiro 2005
,
PubMed: Riveiro-Alvarez 2009
;Riveiro-Alvarez ESHG2008 P05.213
-
-
Germline
-
-
-BbvI
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Riveiro 2005
,
PubMed: Riveiro-Alvarez 2009
;Riveiro-Alvarez ESHG2008 P05.213
carrier mother/sister, 3 affected brothers
M
-
Spain
-
-
-
-
-
5
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (confirmed)
-
pathogenic
g.18660225dup
g.18642105dup
578_579insC
-
RS1_000070
-
PubMed: Riveiro 2005
,
PubMed: Riveiro-Alvarez 2009
;Riveiro-Alvarez ESHG2008 P05.213
-
-
Germline
-
-
-BbvI
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Riveiro 2005
,
PubMed: Riveiro-Alvarez 2009
;Riveiro-Alvarez ESHG2008 P05.213
3-generation family, 2 affecteds, 3 carriers
M
-
Spain
-
-
-
-
-
5
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (confirmed)
-
pathogenic
g.18660225dup
g.18642105dup
588-593incC
-
RS1_000070
-
PubMed: Ali 2003
,
PubMed: Saleheen 2008
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
?;family
PubMed: Ali 2003
,
PubMed: Saleheen 2008
4-generation family, 5 affected males, 4, affected females, 6 unaffected carriers
F;M
yes
Pakistan
-
-
-
-
-
9
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (confirmed)
-
pathogenic
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: Lesch 2008
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
Fam11
PubMed: Lesch 2008
3-generation family, 1 affected, 3 carriers
M
-
Hungary
-
-
-
-
-
1
Johan den Dunnen
+?/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Parent #1
-
likely pathogenic
g.18660225dup
g.18642105dup
c.579dupC
-
RS1_000070
-
PubMed: Holtan 2020
-
-
Germline
-
1/899 cases
-
-
-
DNA
SEQ
-
-
retinal disease
-
PubMed: Holtan 2020
1 patient with variant in heterozygous or compound heterozygous form
-
-
Norway
-
-
-
-
-
1
Global Variome, with Curator vacancy
?/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
VUS
g.18660225dup
g.18642105dup
RS1 nucleotide 1, protein 1:c.579dupC, p.Ile194Hisfsext51
-
RS1_000070
error in annotation: c.579dup causes p.(Ile194Hisfs*70) and not p.(Ile194Hisfsext51), hemizygous, ACMG unclassified - no access to supplementary table 2
PubMed: Hull 2020
-
-
Germline
?
-
-
-
-
DNA
?
blood
NGS gene panel investigation in 60 families, Sanger sequencing in 27 families, and Asper microarray in 25 families
retinal disease
11
PubMed: Hull 2020
-
-
-
New Zealand
white
-
-
-
-
1
LOVD
+?/.
-
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
-
likely pathogenic
g.18660225dup
g.18642105dup
c.579dupC; p.Ile194Hisfs
-
RS1_000070
-
PubMed: Duncan 2011
-
-
Unknown
?
-
-
-
-
DNA
SEQ
blood
-
retinal disease
2
PubMed: Duncan 2011
-
?
-
United States
-
-
-
-
-
1
LOVD
+?/.
-
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
likely pathogenic
g.18660225dup
g.18642105dup
Insertion c.579insC
-
RS1_000070
error in annotation, variant c.579insC is c.579dupC and causes p.(Ile194Hisfs*70) and not p.(His194fs*263)
PubMed: Sergeev 2013
-
-
Unknown
?
-
-
-
-
DNA
SEQ
blood
-
retinal disease
17
PubMed: Sergeev 2013
patient ID ascribed consecutively (no ID in the paper)
M
-
(United Kingdom (Great Britain))
-
-
-
-
-
1
LOVD
+?/.
-
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
likely pathogenic
g.18660225dup
g.18642105dup
Duplication 579dupC
-
RS1_000070
error in annotation, variant c.579insC is c.579dupC and causes p.(Ile194Hisfs*70) and not p.(His194fs*263)
PubMed: Sergeev 2013
-
-
Unknown
?
-
-
-
-
DNA
SEQ
blood
-
retinal disease
21
PubMed: Sergeev 2013
patient ID ascribed consecutively (no ID in the paper)
M
-
(United Kingdom (Great Britain))
-
-
-
-
-
1
LOVD
+?/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
likely pathogenic
g.18660225dup
g.18642105dup
X6, 579insC
-
RS1_000070
-
PubMed: Khan 2001
-
-
Unknown
?
-
-
-
-
DNA
SEQ
blood
-
retinal disease
108
PubMed: Khan 2001
-
M
-
(United States)
-
-
-
-
-
1
LOVD
+?/.
-
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
likely pathogenic
g.18660225dup
g.18642105dup
RS1 c.579dupC, p.(Ile194fs)
-
RS1_000070
-
PubMed: Fahim 2017
-
-
Unknown
?
-
-
-
-
DNA
?
-
retrospective study
retinal disease
51
PubMed: Fahim 2017
no patient numbers in paper, consecutive numbers given
M
-
-
-
-
-
-
-
1
LOVD
+?/.
-
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
likely pathogenic
g.18660225dup
g.18642105dup
RS1 c.579dupC, p.(Ile194fs)
-
RS1_000070
-
PubMed: Fahim 2017
-
-
Unknown
?
-
-
-
-
DNA
?
-
retrospective study
retinal disease
52
PubMed: Fahim 2017
no patient numbers in paper, consecutive numbers given
M
-
-
-
-
-
-
-
1
LOVD
+?/.
-
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
likely pathogenic
g.18660225dup
g.18642105dup
RS1 c.579dupC, p.(Ile194fs)
-
RS1_000070
-
PubMed: Fahim 2017
-
-
Unknown
?
-
-
-
-
DNA
?
-
retrospective study
retinal disease
53
PubMed: Fahim 2017
no patient numbers in paper, consecutive numbers given
M
-
-
-
-
-
-
-
1
LOVD
+?/.
-
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
-
likely pathogenic
g.18660225dup
g.18642105dup
579DupC, p.Ile194His
-
RS1_000070
error in annotation both in cDNA (no ""c."" and protein change should be p.Ile194Hisfs*70 and not p.Ile194His
PubMed: Pennesi 2018
-
-
Unknown
?
-
-
-
-
DNA
?
-
-
retinal disease
CEI-010
PubMed: Pennesi 2018
-
M
-
United States
-
-
-
-
-
1
LOVD
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Maternal (confirmed)
-
pathogenic
g.18660225dup
g.18642105dup
c.578_579incC;p.HisfsX264
-
RS1_000070
c.578_579insC automapped to NM_000330.4:c.579dupC
PubMed: Christodoulou 2019
-
-
Germline
yes
-
-
-
-
DNA
SEQ-NG
-
-
-
-
PubMed: Almomani 2011
-
-
-
-
-
-
-
-
-
1
Global Variome, with Curator vacancy
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (inferred)
ACMG
pathogenic
g.18660225dup
g.18642105dup
RS1 c.579_580insC , p.X225Lext 38
-
RS1_000070
error in annotation: c.579_580insC automapped to c.579dup and causes p.Ile194Hisfs*70 and not p.*225Leuext 38; number of alleles does not match number of patients (91 vs 90)
PubMed: Chen 2020
-
-
Unknown
?
1/90
-
-
-
DNA
SEQ, SEQ-NG
blood
Sanger-DNA sequencing of RS1 and targeted next-generation sequencing
retinal disease
63
PubMed: Chen 2020
no patient numbering in the paper, numbers given consecutively; actual number in table does not match number of patients in text (91 vs 90)
M
-
China
-
-
-
-
-
1
LOVD
+/.
-
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Unknown
-
pathogenic
g.18660225dup
-
-
-
RS1_000070
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
-
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
ACMG
pathogenic (recessive)
g.18660225dup
g.18642105dup
579dupC
-
RS1_000070
ACMG PVS1, PP5, PM2, PM3
PubMed: D'Anna Mardero 2024
-
-
Germline/De novo (untested)
-
-
-
-
-
DNA
SEQ
-
-
RS1
Pat3
PubMed: D'Anna Mardero 2024
patient, no family history
M
-
Spain
Europe
-
-
-
-
1
Johan den Dunnen
+/.
-
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
ACMG
pathogenic (recessive)
g.18660225dup
g.18642105dup
(I194H )
-
RS1_000070
-
PubMed: Wey 2023
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Wey 2023
patient
M
-
United States
-
-
-
-
-
1
Johan den Dunnen
+/.
-
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
ACMG
pathogenic (recessive)
g.18660225dup
g.18642105dup
(I194H )
-
RS1_000070
-
PubMed: Wey 2023
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Wey 2023
patient
M
-
United States
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
-
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: Fortunato 2023
-
rs199469697
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
Fam3Pat5
PubMed: Fortunato 2023
patient
M
-
Italy
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
-
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
-
PubMed: Fortunato 2023
-
rs199469697
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
Fam17Pat22
PubMed: Fortunato 2023
patient
M
-
Italy
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
-
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
ACMG PVS1, PM2, PP1, PP3, PP4, PP5
PubMed: Georgiou 2022
-
rs199469697
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Georgiou 2022
family, 1 affected
M
-
United Kingdom (Great Britain)
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
-
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
ACMG PVS1, PM2, PP1, PP3, PP4, PP5
PubMed: Georgiou 2022
-
rs199469697
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Georgiou 2022
family, 1 affected
M
-
United Kingdom (Great Britain)
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
-
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
ACMG PVS1, PM2, PP1, PP3, PP4, PP5
PubMed: Georgiou 2022
-
rs199469697
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Georgiou 2022
family, 1 affected
M
-
United Kingdom (Great Britain)
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
-
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
ACMG PVS1, PM2, PP1, PP3, PP4, PP5
PubMed: Georgiou 2022
-
rs199469697
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
-
PubMed: Georgiou 2022
family, 1 affected
M
-
United Kingdom (Great Britain)
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194Hisfs*70)
Maternal (confirmed)
-
pathogenic (recessive)
g.18660225dup
g.18642105dup
579dupC
-
RS1_000070
-
PubMed: Lesch 2008
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
RS1
Fam6
PMID:Lesch 2008:19093009}
3-generation family, 2 affected, 3 unaffected carrier females
M
-
Hungary
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
ACMG
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
ACMG PVS1, PS4, PM2, PP4, PM1
PubMed: Bender 2022
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
Var82.1
PubMed: Bender 2022
proband
M
-
-
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
ACMG
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
ACMG PVS1, PS4, PM2, PP4, PM1
PubMed: Bender 2022
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
Var82.2
PubMed: Bender 2022
proband
M
-
-
-
-
-
-
-
1
Johan den Dunnen
+/.
6
c.579dup
r.(?)
p.(Ile194HisfsTer70)
Unknown
ACMG
pathogenic (recessive)
g.18660225dup
g.18642105dup
-
-
RS1_000070
ACMG PVS1, PS4, PM2, PP4, PM1
PubMed: Bender 2022
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RS1
Var82.3
PubMed: Bender 2022
proband
M
-
-
-
-
-
-
-
1
Johan den Dunnen
+/.
-
c.579dup
r.(579dup)
p.(Ile194Hisfs*70)
Maternal (confirmed)
-
pathogenic (recessive)
g.18660225dup
g.18642105dup
Pro192 ins1 cggC
-
RS1_000070
-
PubMed: Pradhan 2009
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
RD
Pat1
PubMed: Pradhan 2009
2-generation family, 1 affected, unaffected carrier mother
M
-
New Zealand
-
-
-
-
-
1
Johan den Dunnen
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