Global Variome shared LOVD
OAT (ornithine aminotransferase)
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This database is one of the
"Eye disease"
gene variant databases.
The variants shown are described using the NM_000274.3 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
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space
Text
Arg Ser
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|
Text
Arg|Ser
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!
Text
!fs
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^
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
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|
Date
2020-03|2020-04
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!
Date
!2020-03
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<
Date
<2020
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<=
Date
<=2020-06
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>
Date
>2020-06
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>=
Date
>=2020-06-15
all entries on or after June 15th, 2020
combination
Date
2019|2020 <2020-03
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Numeric
23
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|
Numeric
23|24
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!
Numeric
!23
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<
Numeric
<23
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<=
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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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
./.
-
c.-9273523_*2935700dup
-
-
Unknown
-
pathogenic
g.123150811_135380935dup
-
-
-
ACADSB_000015
increased gene dosage
PubMed: DDDS 2015
,
Journal: DDDS 2015
-
-
De novo
-
-
-
-
-
DNA
SEQ, SEQ-NG-I
-
-
?
-
PubMed: DDDS 2015
,
Journal: DDDS 2015
family, affected sibling(s)
F
-
United Kingdom (Great Britain)
-
-
-
Decipher
-
2
Johan den Dunnen
-/.
-
c.-94T>G
r.(?)
p.(=)
Unknown
-
benign
g.126107506A>C
g.124418937A>C
-
-
OAT_000081
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.-53C>T
r.(?)
p.(=)
Unknown
-
likely benign
g.126107465G>A
g.124418896G>A
-
-
OAT_000080
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.-53C>T
r.(=)
p.(=)
Parent #1
-
VUS
g.126107465G>A
g.124418896G>A
-
-
OAT_000080
91 heterozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs117824913
Germline
-
91/2793 individuals
-
-
-
DNA
arraySNP
-
Infinium Global Screening Array v1.0
?
-
PubMed: Narang 2020
,
Journal: Narang 2020
analysis 2794 individuals (India)
-
-
India
-
-
-
-
-
91
Mohammed Faruq
?/.
-
c.-53C>T
r.(=)
p.(=)
Both (homozygous)
-
VUS
g.126107465G>A
g.124418896G>A
-
-
OAT_000080
3 homozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs117824913
Germline
-
3/2793 individuals
-
-
-
DNA
arraySNP
-
Infinium Global Screening Array v1.0
?
-
PubMed: Narang 2020
,
Journal: Narang 2020
analysis 2794 individuals (India)
-
-
India
-
-
-
-
-
3
Mohammed Faruq
-?/.
-
c.-30+8C>T
r.(=)
p.(=)
Unknown
-
likely benign
g.126107434G>A
g.124418865G>A
OAT(NM_000274.3):c.-30+8C>T (p.(=))
-
OAT_000082
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/.
-
c.?
r.0
p.0
Paternal (confirmed)
-
likely pathogenic
g.?
g.?
OAT partial deletion EcoRI frgment 5.7 kb to ~5kb
-
CYP2C9_001038
heterozygous; second allele unknown
PubMed: Hotta 1989
-
-
Germline
yes
-
-
-
-
DNA
Southern, Northern, RFLP, SEQ
-
-
GACR;OATD
3
PubMed: Hotta 1989
-
M
-
-
English
-
-
-
-
1
LOVD
+?/.
-
c.?
r.0
p.0
Both (homozygous)
-
likely pathogenic
g.?
g.?
OAT partial deletion EcoRI frgment ~5.4 Kbp; complete absence of mRNA
-
CYP2C9_001038
heterozygous
PubMed: Inana 1988
-
-
Germline
yes
-
-
-
-
DNA
Southern, Northern, RFLP
-
-
GACR;OATD
35
PubMed: Inana 1988
also patients 14, 15, 36 and 37 tested, but not sequenced, so no variants found
-
-
-
-
-
-
-
-
1
LOVD
+?/.
-
c.?
r.0
p.0
Parent #2
-
likely pathogenic
g.?
g.?
OAT promoter ?
-
CYP2C9_001038
Northern 50% of expression, so probably a heterozygous mutation in the promoter or partial deletion
PubMed: Mashima 1999
-
-
Germline
?
-
-
-
-
DNA
DGGE, Northern, SEQ
skin fibroblasts
-
GACR;OATD
patient 3
PubMed: Mashima 1999
-
F
-
-
English/Scottish/Czech
-
-
-
-
1
LOVD
+/+?
2
c.3G>A
r.(3g>a)
p.(Met1?)
Both (homozygous)
-
pathogenic
g.126100738C>T
g.124412169C>T
3G>A: MI1
-
OAT_000039
1 Lebanese Maronite patient and 1 patient of unknown ethnicity. Mutation leads to production of inactive OAT protein.
PubMed: Brody 1992
,
PubMed: Park 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
-
Lebanese Maronite
-
-
-
-
1
Anne Polvi
+/.
-
c.3G>A
r.(?)
p.(Met1?)
Unknown
-
pathogenic
g.126100738C>T
g.124412169C>T
-
-
OAT_000039
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
-
c.3G>A
r.(?)
p.(Met1?)
Both (homozygous)
-
pathogenic
g.126100738C>T
g.124412169C>T
OAT G->A transition, changing the initiator ATG (methionine) codon to ATA
-
OAT_000039
homozygous
PubMed: Mitchell 1988
-
-
Germline
yes
-
-
-
-
DNA
Southern, Northern, RFLP, SEQ
-
-
GACR;OATD
7
PubMed: Mitchell 1988
sibling pair 1, individual 7
F
-
Lebanon
Lebanese Maronite
-
-
-
-
1
LOVD
+/.
-
c.3G>A
r.(?)
p.(Met1?)
Both (homozygous)
-
pathogenic
g.126100738C>T
g.124412169C>T
OAT G->A transition, changing the initiator ATG (methionine) codon to ATA
-
OAT_000039
homozygous
PubMed: Mitchell 1988
-
-
Germline
yes
-
-
-
-
DNA
Southern, Northern, RFLP, SEQ
-
-
GACR;OATD
16
PubMed: Mitchell 1988
sibling pair 1, individual 16
M
-
Lebanon
Lebanese Maronite
-
-
-
-
1
LOVD
+/.
-
c.3G>A
r.(?)
p.(Met1?)
Both (homozygous)
-
pathogenic
g.126100738C>T
g.124412169C>T
OAT G->A transition, changing the initiator ATG (methionine) codon to ATA
-
OAT_000039
homozygous
PubMed: Mitchell 1988
-
-
Germline
yes
-
-
-
-
DNA
Southern, Northern, RFLP, SEQ
-
-
GACR;OATD
25
PubMed: Mitchell 1988
sibling pair 2, individual 25
F
-
Lebanon
Lebanese Maronite
-
-
-
-
1
LOVD
+/.
-
c.3G>A
r.(?)
p.(Met1?)
Both (homozygous)
-
pathogenic
g.126100738C>T
g.124412169C>T
OAT G->A transition, changing the initiator ATG (methionine) codon to ATA
-
OAT_000039
homozygous
PubMed: Mitchell 1988
-
-
Germline
yes
-
-
-
-
DNA
Southern, Northern, RFLP, SEQ
-
-
GACR;OATD
26
PubMed: Mitchell 1988
sibling pair 2, individual 26
M
-
Lebanon
Lebanese Maronite
-
-
-
-
1
LOVD
-?/.
-
c.48C>T
r.(?)
p.(Arg16=)
Unknown
-
likely benign
g.126100693G>A
g.124412124G>A
OAT(NM_000274.4):c.48C>T (p.R16=)
-
OAT_000085
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+?
2
c.152G>A
r.(152g>a)
p.(Gly51Asp)
Parent #2
-
pathogenic (recessive)
g.126100589C>T
g.124412020C>T
-
-
OAT_000003
-
PubMed: Doimo 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Doimo 2012
-
-
-
Italy
Southern Italian
-
-
-
-
1
Anne Polvi
+/+?
2
c.152G>A
r.(152g>a)
p.(Gly51Asp)
Parent #2
-
pathogenic (recessive)
g.126100589C>T
g.124412020C>T
-
-
OAT_000003
-
PubMed: Doimo 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Doimo 2012
-
-
-
Italy
Southern Italian
-
-
-
-
1
Anne Polvi
+/+?
2
c.152G>A
r.(152g>a)
p.(Gly51Asp)
Both (homozygous)
-
pathogenic
g.126100589C>T
g.124412020C>T
-
-
OAT_000003
-
PubMed: Sergouniotis 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Sergouniotis 2012
-
-
-
United Kingdom (Great Britain)
English
-
-
-
-
1
Anne Polvi
+?/.
-
c.152G>A
r.(?)
p.(Gly51Asp)
Unknown
-
likely pathogenic
g.126100589C>T
g.124412020C>T
-
-
OAT_000003
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+?
2
c.159del
r.(?)
p.(His53Glnfs*8)
Both (homozygous)
-
pathogenic
g.126100582del
g.124412013del
159delC: H53fs(-l)
-
OAT_000029
Iraqi Jew mutation
PubMed: Brody 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
-
Iraq;Jewish
-
-
-
-
1
Anne Polvi
+/.
-
c.159del
r.(?)
p.(His53Glnfs*8)
Unknown
ACMG
pathogenic
g.126100582del
-
c.159delC
-
OAT_000029
-
PubMed: Sharon 2019
-
-
Germline
-
2/2420 IRD families
-
-
-
DNA
SEQ
-
-
retinal disease
-
PubMed: Sharon 2019
2 IRD families
-
-
Israel
-
-
-
-
-
2
Global Variome, with Curator vacancy
+?/.
-
c.159delC
r.(?)
p.(His53Glnfs*8)
Both (homozygous)
-
likely pathogenic
g.126100582del
g.124412013del
OAT c.159delC, p.(H53Qfs7*)
-
OAT_000029
homozygous
PubMed: Heller 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
Family-A proband
PubMed: Heller 2017
-
F
-
Israel
Syrian Jewish
-
-
-
-
1
LOVD
+/+?
2
c.162C>A
r.162c>a
p.Asn54Lys
Both (homozygous)
-
pathogenic (recessive)
g.126100579G>T
g.124412010G>T
C>A at 162 bp, Asp54Lys
-
OAT_000030
Mutation leads to inactive OAT protein.
PubMed: Ramesh 1988
-
-
Germline
yes
-
-
-
-
DNA, RNA
RT-PCR, SEQ
-
-
GACR;OATD
-
PubMed: Ramesh 1988
-
-
-
United States
-
-
-
-
-
1
Anne Polvi
+/+?
2
c.163T>C
r.(163u>c)
p.(Tyr55His)
Parent #1
-
pathogenic
g.126100578A>G
g.124412009A>G
163T>C
-
OAT_000031
Australian/Hungarian/English mutation. Mutation leads to very low RNA expression level and production of inactive OAT protein.
PubMed: Ramesh 1988
,
PubMed: Brody 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
-
-
-
-
-
-
1
Anne Polvi
+/+?
2
c.163T>C
r.(163u>c)
p.(Tyr55His)
Parent #1
-
pathogenic
g.126100578A>G
g.124412009A>G
-
-
OAT_000031
-
PubMed: Sergouniotis 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Sergouniotis 2012
-
-
-
United Kingdom (Great Britain)
English
-
-
-
-
1
Anne Polvi
+/.
-
c.192_193del
r.(?)
p.(Gly65Lysfs*15)
Parent #1
-
pathogenic (recessive)
g.126100553_126100554del
g.124411984_124411985del
192_193delAG
-
OAT_000032
-
PubMed: Mashima 1992
-
-
Germline
-
-
-
-
-
DNA
DGGE, SEQ
-
-
GACR;OATD
Pat1
PubMed: Mashima 1992
adopted
-
-
Canada
-
-
-
-
-
1
Johan den Dunnen
-?/.
-
c.199+11_199+16dup
r.(=)
p.(=)
Unknown
-
likely benign
g.126100527_126100532dup
-
OAT(NM_001322966.2):c.199+11_199+16dupAATTAA
-
OAT_000099
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.199+11_199+16dupAATTAA
r.spl?
p.?
Unknown
-
VUS
g.126100527_126100532dup
g.124411958_124411963dup
OAT c.199+11_199+16dupAATTAA
-
OAT_000099
heterozygous; segregation not performed
PubMed: Kim 2013
-
-
Germline
?
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
older twin
PubMed: Kim 2013
identical twin 1
F
-
-
-
-
-
-
B6 (pyridoxine) 300 mg daily and an arginine-restricted diet
1
LOVD
?/.
-
c.199+11_199+16dupAATTAA
r.spl?
p.?
Unknown
-
VUS
g.126100527_126100532dup
g.124411958_124411963dup
OAT c.199+11_199+16dupAATTAA
-
OAT_000099
heterozygous; segregation not performed
PubMed: Kim 2013
-
-
Germline
?
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
younger twin
PubMed: Kim 2013
identical twin 2
F
-
-
-
-
-
-
B6 (pyridoxine) 300 mg daily and an arginine-restricted diet
1
LOVD
-/.
-
c.199+19C>T
r.(=)
p.(=)
Unknown
-
benign
g.126100523G>A
g.124411954G>A
OAT(NM_000274.4):c.199+19C>T
-
OAT_000079
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.199+19C>T
r.(=)
p.(=)
Unknown
-
benign
g.126100523G>A
g.124411954G>A
OAT(NM_000274.4):c.199+19C>T
-
OAT_000079
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.199+20G>A
r.(=)
p.(=)
Unknown
-
benign
g.126100522C>T
g.124411953C>T
OAT(NM_000274.4):c.199+20G>A
-
OAT_000078
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+?
2i
c.199+303C>G
r.199_200ins199+161_199+302
p.(=)
Both (homozygous)
-
pathogenic
g.126100239G>C
g.124411670G>C
OAT G67ins; C>G transition in intron 3: mRNA with 142-bp insertion (new Alu exon"") between exon 3 and 4""
-
OAT_000033
Mutation creates a new donor splice site that activates an upstream cryptic acceptor site. New 142 bp exon"" is created and included into transcript.""
PubMed: Mitchell 1991
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Mitchell 1991
-
-
-
Algeria
Algerian
-
-
-
-
1
Anne Polvi
-/.
-
c.200-10T>C
r.(=)
p.(=)
Unknown
-
benign
g.126097544A>G
g.124408975A>G
OAT(NM_001322966.1):c.200-10T>C, OAT(NM_001322966.2):c.200-10T>C
-
OAT_000077
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.200-10T>C
r.(=)
p.(=)
Unknown
-
benign
g.126097544A>G
g.124408975A>G
OAT(NM_001322966.1):c.200-10T>C, OAT(NM_001322966.2):c.200-10T>C
-
OAT_000077
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/.
3
c.248G>A
r.(?)
p.(Ser83Asn)
Both (homozygous)
-
likely pathogenic
g.126097486C>T
g.124408917C>T
OAT c.G248A:p.S83N
-
OAT_000098
homozygous
PubMed: Huang 2018
-
-
Germline
yes
-
-
-
-
DNA
SEQ-NG, SEQ
blood
targeted next-generation sequencing, 195 genes
GACR;OATD
IV:1
PubMed: Huang 2018
parents first cousins; proband, sister of IV:2
F
yes
China
Chinese
-
-
-
-
1
LOVD
+?/.
3
c.248G>A
r.(?)
p.(Ser83Asn)
Both (homozygous)
-
likely pathogenic
g.126097486C>T
g.124408917C>T
OAT c.G248A:p.S83N
-
OAT_000098
homozygous
PubMed: Huang 2018
-
-
Germline
yes
-
-
-
-
DNA
SEQ-NG, SEQ
blood
targeted next-generation sequencing, 195 genes
GACR;OATD
IV:2
PubMed: Huang 2018
parents first cousins; sister of IV:1
F
yes
China
Chinese
-
-
-
-
1
LOVD
+/+?
3
c.267C>A
r.(267c>a)
p.(Asn89Lys)
Parent #1
-
pathogenic
g.126097467G>T
g.124408898G>T
267C>A
-
OAT_000034
Finnish mutation
PubMed: Brody 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
Finland
Finnish
-
-
-
-
1
Anne Polvi
+/.
-
c.267C>A
r.(?)
p.(Asn89Lys)
Parent #2
-
pathogenic
g.126097467G>T
g.124408898G>T
OAT N89K
-
OAT_000034
no nucleotide annotation, extrapolated from protein and databases; heterozygous
PubMed: Peltola 2001
-
-
Unknown
?
-
-
-
-
DNA
?
-
-
GACR;OATD
20
PubMed: Peltola 2001
-
M
-
-
-
-
-
-
creatine supplementation
1
LOVD
+/+?
3
c.268C>G
r.(268c>G)
p.(Gln90Glu)
Both (homozygous)
-
pathogenic
g.126097466G>C
g.124408897G>C
268C>G: Q90E
-
OAT_000035
Loss of mitocondrial targeting of mutant protein.
PubMed: Kobayashi et al.1995
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Kobayashi et al.1995
1 familie, 1 patient
-
-
Japan
Japanese
-
-
-
-
1
Anne Polvi
+/+?
3
c.272G>A
r.(272g>a)
p.(Gly91Glu)
Both (homozygous)
-
pathogenic
g.126097462C>T
g.124408893C>T
-
-
OAT_000068
-
PubMed: Sergouniotis 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Sergouniotis 2012
-
-
-
United Kingdom (Great Britain)
-
-
-
-
-
1
Anne Polvi
?/.
-
c.272G>A
r.(?)
p.(Gly91Glu)
Unknown
-
VUS
g.126097462C>T
-
OAT(NM_001322966.1):c.272G>A (p.G91E)
-
OAT_000068
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/.
-
c.272G>A
r.(?)
p.(Gly91Glu)
Parent #1
-
likely pathogenic
g.126097462C>T
g.124408893C>T
-
-
OAT_000068
-
PubMed: Stone 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG
-
-
retinal disease
944
PubMed: Stone 2017
1 affected
F
-
(United States)
-
-
-
-
-
1
LOVD
+/+?
3
c.278G>T
r.(278g>u)
p.(Cys93Phe)
Parent #1
-
pathogenic
g.126097456C>A
g.124408887C>A
278G>T
-
OAT_000036
German/Italian mutation
PubMed: Brody 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
-
German/Italian
-
-
-
-
1
Anne Polvi
?/.
-
c.298G>A
r.(?)
p.(Ala100Thr)
Unknown
-
VUS
g.126097436C>T
g.124408867C>T
OAT(NM_001322966.1):c.298G>A (p.A100T)
-
OAT_000084
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
3
c.311A>G
r.311a>g
p.Gln104Arg
Parent #2
-
pathogenic
g.126097423T>C
g.124408854T>C
-
-
OAT_000004
-
-
-
-
Germline
-
-
-
-
-
DNA, RNA
RT-PCR, SEQ
-
-
GACR;OATD
-
-
-
-
-
Greece
Greece
-
-
-
-
1
Eva Trevisson
+/+?
3
c.311A>G
r.(311a>g)
p.(Gln104Arg)
Parent #2
-
pathogenic
g.126097423T>C
g.124408854T>C
-
-
OAT_000004
-
PubMed: Doimo 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Doimo 2012
-
-
-
Greece
-
-
-
-
-
1
Anne Polvi
-?/.
-
c.314T>C
r.(?)
p.(Val105Ala)
Unknown
-
likely benign
g.126097420A>G
-
OAT(NM_001322966.1):c.314T>C (p.V105A)
-
OAT_000088
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
3
c.314T>C
r.(?)
p.(Val105Ala)
Unknown
-
VUS
g.126097420A>G
g.124408851A>G
T314C
-
OAT_000088
-
PubMed: Katagiri 2014
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG-I
-
-
retinal disease
-
PubMed: Katagiri 2014
index patient
M
no
Japan
Japanese
-
-
-
-
1
Rob W.J. Collin
+/+?
3
c.362G>A
r.(362g>a)
p.(Gly121Asp)
Parent #1
-
pathogenic
g.126097372C>T
g.124408803C>T
-
-
OAT_000070
-
PubMed: Sergouniotis 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Sergouniotis 2012
-
-
-
United Kingdom (Great Britain)
English
-
-
-
-
1
Anne Polvi
+/+?
3
c.373_375del
r.(?)
p.(Glu125del)
Parent #1
-
pathogenic
g.126097362_126097364del
g.124408793_124408795del
Codon 125 GAG Glu deletion
-
OAT_000037
-
PubMed: Mashima 1996
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Mashima 1996
-
-
-
Japan
Japanese
-
-
-
-
1
Anne Polvi
+/+?
3
c.381dup
r.381dupu)
p.(Thr128Tyrfs*2)
Parent #1
-
pathogenic
g.126097354dup
g.124408785dup
380-1insT: 1127fs(+l)
-
OAT_000038
Welsh mutation. Reduced RNA expression.
PubMed: Brody 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
-
Welsh
-
-
-
-
1
Anne Polvi
+?/.
-
c.416T>G
r.(?)
p.(Met139Arg)
Both (homozygous)
ACMG
likely pathogenic
g.126097318A>C
g.124408749A>C
OAT c.416T>G, p.(Met139Arg)
-
OAT_000090
homozygous
PubMed: Dineiro 2020
-
-
Germline
?
-
-
-
-
DNA
SEQ-NG-I, SEQ
blood, saliva
targeted sequencing with 1 of 4 panels of OFTALMOgenics probes
retinal disease
OFTALMO.022
PubMed: Dineiro 2020
-
?
-
Spain
-
-
-
-
-
1
LOVD
+/+?
3i_4
c.425-4_429del
r.425_520del
p.Gly142_Ala173del
Parent #1
-
pathogenic
g.126097204_126097212del
g.124408635_124408643del
a 9-bp deletion covering the 3' splice acceptor region of intron 4: exon 5 skipping; McClatchey-1
-
OAT_000041
-
PubMed: McClatchey 1990
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: McClatchey 1990
-
-
-
-
Danish/Swedish
-
-
-
-
1
Anne Polvi
+?/.
-
c.425-4_429del
r.spl
p.?
Parent #2
-
likely pathogenic
g.126097204_126097212del
g.124408635_124408643del
IVS3-6del9cTGATAGGAG
-
OAT_000041
-
PubMed: Stone 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG
-
-
retinal disease
944
PubMed: Stone 2017
1 affected
F
-
(United States)
-
-
-
-
-
1
LOVD
+/+?
3i
c.425-2A>G
r.425_520del
p.Gly142_Ala173del
Parent #2
-
pathogenic (recessive)
g.126097208T>C
g.124408639T>C
Exon 5 skipping
-
OAT_000040
exon 4 skipping (published exon 5)
PubMed: Mashima 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Mashima 1992
2-generation family, 2 affected sisters
F
-
United States
-
-
-
-
-
2
Anne Polvi
+/.
-
c.425-2A>G
r.spl
p.?
Parent #2
-
pathogenic
g.126097208T>C
g.124408639T>C
OAT IVS4 nt-2 a->g
-
OAT_000040
exon 4 (described as exon 5) not spliced in; possible duplicate patient from {PMID:Mashima 1992:1487247}; heterozygous
PubMed: Mashima 1999
-
-
Germline
yes
-
-
-
-
DNA
DGGE, Northern, SEQ
skin fibroblasts
-
GACR;OATD
patient 1
PubMed: Mashima 1999
sibship 1, patient 1
F
-
-
English/German/Scottish
-
-
-
-
1
LOVD
+/.
-
c.425-2A>G
r.spl
p.?
Parent #2
-
pathogenic
g.126097208T>C
g.124408639T>C
OAT IVS4 nt-2 a->g
-
OAT_000040
exon 4 (described as exon 5) not spliced in; possible duplicate patient from {PMID:Mashima 1992:1487247}; heterozygous
PubMed: Mashima 1999
-
-
Germline
yes
-
-
-
-
DNA
DGGE, Northern, SEQ
skin fibroblasts
-
GACR;OATD
patient 2
PubMed: Mashima 1999
sibship 1, patient 2
F
-
-
English/German/Scottish
-
-
-
-
1
LOVD
+/+?
4
c.425G>A
r.(425g>a)
p.(Gly142Glu)
Both (homozygous)
-
pathogenic
g.126097206C>T
g.124408637C>T
Codon 142 GGA>GAA: Gly>Glu
-
OAT_000042
-
PubMed: Mashima 1996
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Mashima 1996
-
-
-
Japan
Japanese
-
-
-
-
1
Anne Polvi
+/.
-
c.425G>A
r.(?)
p.(Gly142Glu)
Unknown
-
pathogenic
g.126097206C>T
g.124408637C>T
OAT c.425G>A
-
OAT_000042
heterozygous; segregation not performed
PubMed: Kim 2013
-
-
Germline
?
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
older twin
PubMed: Kim 2013
identical twin 1
F
-
-
-
-
-
-
B6 (pyridoxine) 300 mg daily and an arginine-restricted diet
1
LOVD
+/.
-
c.425G>A
r.(?)
p.(Gly142Glu)
Unknown
-
pathogenic
g.126097206C>T
g.124408637C>T
OAT c.425G>A
-
OAT_000042
heterozygous; segregation not performed
PubMed: Kim 2013
-
-
Germline
?
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
younger twin
PubMed: Kim 2013
identical twin 2
F
-
-
-
-
-
-
B6 (pyridoxine) 300 mg daily and an arginine-restricted diet
1
LOVD
?/.
-
c.460C>T
r.(?)
p.(Arg154Cys)
Unknown
-
VUS
g.126097171G>A
g.124408602G>A
-
-
OAT_000076
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+?
4
c.461G>T
r.(461g>u)
p.(Arg154Leu)
Both (homozygous)
-
pathogenic
g.126097170C>A
g.124408601C>A
461G>T
-
OAT_000043
English/German mutation. Mutation leads to production of inactive OAT protein.
PubMed: Brody 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
-
English/German
-
-
-
-
1
Anne Polvi
+/+?
4
c.472_486del
r.472_486del
p.Tyr158_Gly162del
Parent #1
-
pathogenic
g.126097149_126097163del
g.124408580_124408594del
15-bp deletion: del YTVKG
-
OAT_000044
-
PubMed: Park 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Park 1992
1 familie, 1 patient
-
-
-
-
-
-
-
-
1
Anne Polvi
+?/.
10
c.473A>C
r.(?)
p.(Tyr158Ser)
Both (homozygous)
-
likely pathogenic
g.126097158T>G
g.124408589T>G
OAT c.473A>C: p.Y158S
-
OAT_000097
homozygous
PubMed: Cui 2018
-
-
Germline
?
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
?
PubMed: Cui 2018
parents first cousins
F
yes
Honduras
-
-
-
-
-
1
LOVD
+?/.
5
c.505_506del
r.(?)
p.(Lys169Aspfs*11)
Maternal (confirmed)
-
likely pathogenic
g.126097126_126097127del
g.124408557_124408558del
OAT c.504_505delAA (exon 5) (p.K169DfsX10)
-
OAT_000096
heterozygous
PubMed: Katagiri 2014
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
II-1 (JU#0213)
PubMed: Katagiri 2014
family JU#0213, individual II-1, brother of II-2
M
-
Japan
Japanese
-
-
-
-
1
LOVD
+?/.
5
c.505_506del
r.(?)
p.(Lys169Aspfs*11)
Maternal (confirmed)
-
likely pathogenic
g.126097126_126097127del
g.124408557_124408558del
OAT c.504_505delAA (exon 5) (p.K169DfsX10)
-
OAT_000096
heterozygous
PubMed: Katagiri 2014
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
II-2 (JU#0213)
PubMed: Katagiri 2014
family JU#0213, individual II-2, brother of II-1
M
-
Japan
Japanese
-
-
-
-
1
LOVD
+/+?
4i_5i
c.521-172_649-744del
r.521_648del
p.Gly175Cysfs*18
Parent #1
-
pathogenic (recessive)
g.126093239_126094310del
g.124404670_124405741del
1,072-bp deletion between 172 bp upstream and 772 bp downstream of exon 6: exon 6 skipping.
-
OAT_000046
very low RNA expression
PubMed: Akaki 1992
-
-
Germline
yes
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
GACR;OATD
patient;Pat2
PubMed: Akaki 1992
,
PubMed: Mashima 1992
2-generation family, 1 affected
-
-
England;France;Germany;Netherlands
Europe
-
-
-
-
1
Anne Polvi
-/.
-
c.521-15_521-12del
r.(=)
p.(=)
Unknown
-
benign
g.126094149_126094152del
g.124405580_124405583del
OAT(NM_000274.4):c.521-15_521-12delGTTT
-
OAT_000075
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+?
5
c.533G>A
r.533g>a
p.(Trp178*)
Both (homozygous)
-
pathogenic
g.126094120C>T
g.124405551C>T
Exon 6 bp +13G>A: W178X and exon 6 skipping
-
OAT_000048
Exon 8 skipping in less than 5% of transcripts.
PubMed: Dietz 1993
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Dietz 1993
-
-
-
-
-
-
-
-
-
1
Anne Polvi
+/+?
5
c.533_537del
r.(?)
p.(Trp178*)
Parent #1
-
pathogenic
g.126094117_126094121del
g.124405548_124405552del
-
-
OAT_000047
-
PubMed: Renner et al.2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Renner et al.2012
-
-
-
Germany
German
-
-
-
-
1
Anne Polvi
+/.
5
c.539G>C
r.539g>c
p.Arg180Thr
Both (homozygous)
-
pathogenic
g.126094114C>G
g.124405545C>G
-
-
OAT_000017
Mutant OAT protein was inactive.
PubMed: Mitchell 1989
-
-
Germline
yes
0/19 FIN CON
-
-
-
DNA
EMC, SEQ, Southern
-
-
GACR;OATD
-
PubMed: Mitchell 1989
Families: Fin 6 and Fin 14
-
-
Finland
Finnish
-
-
-
-
1
Anne Polvi
?/.
5
c.539G>C
r.539g>c
p.Arg180Thr
Both (homozygous)
-
VUS
g.126094114C>G
g.124405545C>G
-
-
OAT_000017
Mutant OAT protein was inactive.
PubMed: Mitchell 1989
-
-
Germline
yes
0/19 FIN CON
-
-
-
DNA
EMC, SEQ, Southern
-
-
GACR;OATD
-
PubMed: Mitchell 1989
-
-
-
United States
American
-
-
-
-
1
Anne Polvi
+/+?
5
c.539G>C
r.(539g>c)
p.(Arg180Thr)
Parent #1
-
pathogenic (recessive)
g.126094114C>G
g.124405545C>G
Codon 180 AGG (Arg) > ACG (Thr)
-
OAT_000017
-
PubMed: Mashima 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
Pat4
PubMed: Mashima 1992
-
-
-
Ireland;Italy;Netherlands
European
-
-
-
-
1
Anne Polvi
+/+?
5
c.539G>C
r.(539g>c)
p.(Arg180Thr)
Both (homozygous)
-
pathogenic
g.126094114C>G
g.124405545C>G
539G>C
-
OAT_000017
-
PubMed: Brody 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
-
Finnish/American
-
-
-
-
1
Anne Polvi
+/.
-
c.539G>C
r.(?)
p.(Arg180Thr)
Parent #2
-
pathogenic
g.126094114C>G
g.124405545C>G
OAT R180T
-
OAT_000017
no nucleotide annotation, extrapolated from protein and databases; heterozygous
PubMed: Peltola 2001
-
-
Unknown
?
-
-
-
-
DNA
?
-
-
GACR;OATD
21
PubMed: Peltola 2001
-
M
-
-
-
-
-
-
-
1
LOVD
+/.
-
c.539G>C
r.(?)
p.(Arg180Thr)
Parent #2
-
pathogenic
g.126094114C>G
g.124405545C>G
OAT R180T
-
OAT_000017
no nucleotide annotation, extrapolated from protein and databases; heterozygous
PubMed: Peltola 2001
-
-
Unknown
?
-
-
-
-
DNA
?
-
-
GACR;OATD
22
PubMed: Peltola 2001
-
M
-
-
-
-
-
-
-
1
LOVD
+/.
-
c.539G>C
r.(?)
p.(Arg180Thr)
Parent #2
-
pathogenic
g.126094114C>G
g.124405545C>G
OAT R180T
-
OAT_000017
no nucleotide annotation, extrapolated from protein and databases; heterozygous
PubMed: Peltola 2001
-
-
Unknown
?
-
-
-
-
DNA
?
-
-
GACR;OATD
28
PubMed: Peltola 2001
-
F
-
-
-
-
-
-
-
1
LOVD
+/+?
5
c.542C>T
r.(542C>u)
p.(Thr181Met)
Both (homozygous)
-
pathogenic
g.126094111G>A
g.124405542G>A
Codon 181 ACG>ATG: Thr>Met
-
OAT_000049
-
PubMed: Mashima 1996
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Mashima 1996
-
-
-
Japan
Japanese
-
-
-
-
1
Anne Polvi
+?/.
5
c.542C>T
r.(?)
p.(Thr181Met)
Unknown
-
likely pathogenic (recessive)
g.126094111G>A
-
c.542C>T
-
OAT_000049
-
PubMed: Liu-2020
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG
-
hereditary eye disease enrichment panel (HEDEP)
retinal disease
-
PubMed: Liu-2020
-
M
-
-
-
-
-
-
-
1
LOVD
+/+?
5
c.550G>A
r.(550g>a)
p.(Ala184Thr)
Parent #1
-
pathogenic
g.126094103C>T
g.124405534C>T
-
-
OAT_000051
-
PubMed: Michaud 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Michaud 1992
1 familie, 1 patient
-
-
-
-
-
-
-
-
1
Anne Polvi
+/+?
5
c.550_552del
r.(?)
p.(Ala184del)
Parent #1
-
pathogenic
g.126094103_126094105del
g.124405534_124405536del
550delGCT
-
OAT_000050
Portugese mutation. Mutation leads to production of inactive OAT protein.
PubMed: Brody 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Brody 1992
1 familie, 1 patient
-
-
Portugal
Portugese
-
-
-
-
1
Anne Polvi
?/.
-
c.578G>A
r.(?)
p.(Ser193Asn)
Unknown
-
VUS
g.126094075C>T
-
-
-
OAT_000102
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.582C>T
r.(?)
p.(Tyr194=)
Unknown
-
likely benign
g.126094071G>A
g.124405502G>A
OAT(NM_001322966.1):c.582C>T (p.Y194=), OAT(NM_001322966.2):c.582C>T (p.Y194=)
-
OAT_000083
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.582C>T
r.(?)
p.(Tyr194=)
Unknown
-
likely benign
g.126094071G>A
-
OAT(NM_001322966.1):c.582C>T (p.Y194=), OAT(NM_001322966.2):c.582C>T (p.Y194=)
-
OAT_000083
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+?
5
c.583G>T
r.(583g>u)
p.(Asp195Tyr)
Parent #1
-
pathogenic
g.126094070C>A
g.124405501C>A
Codon 195: GAT>TAT: Asp>Tyr
-
OAT_000052
-
PubMed: Mashima 1996
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Mashima 1996
-
-
-
Japan
Japanese
-
-
-
-
1
Anne Polvi
+/.
5
c.596C>A
r.596c>a
p.Pro199Gln
Parent #1
-
pathogenic
g.126094057G>T
g.124405488G>T
-
-
OAT_000008
-
-
-
-
Germline
-
-
-
-
-
DNA, RNA
RT-PCR, SEQ
-
-
GACR;OATD
-
-
-
-
-
United Kingdom (Great Britain)
England
-
-
-
-
1
Eva Trevisson
+/+?
5
c.596C>A
r.(596c>a)
p.(Pro199Gln)
Parent #1
-
pathogenic
g.126094057G>T
g.124405488G>T
-
-
OAT_000008
-
PubMed: Doimo 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Doimo 2012
-
-
-
United Kingdom (Great Britain)
English
-
-
-
-
1
Anne Polvi
+/+?
5
c.596C>A
r.(596c>a)
p.(Pro199Gln)
Parent #1
-
pathogenic
g.126094057G>T
g.124405488G>T
-
-
OAT_000008
-
PubMed: Sergouniotis 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Sergouniotis 2012
-
-
-
United Kingdom (Great Britain)
English
-
-
-
-
1
Anne Polvi
+/+?
5
c.596C>A
r.(596c>a)
p.(Pro199Gln)
Parent #1
-
pathogenic
g.126094057G>T
g.124405488G>T
-
-
OAT_000008
-
PubMed: Sergouniotis 2012
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
-
PubMed: Sergouniotis 2012
-
-
-
United Kingdom (Great Britain)
English
-
-
-
-
1
Anne Polvi
+/.
-
c.596C>A
r.(?)
p.(Pro199Gln)
Unknown
-
pathogenic
g.126094057G>T
g.124405488G>T
OAT c.596C>A, p.Pro199Gln
-
OAT_000008
compound heterozygous
PubMed: Bell 2021
-
-
Germline
yes
-
-
-
-
DNA
SEQ-NG
blood
targeted next-generation sequencing
retinal disease
4
PubMed: Bell 2021
-
F
no
(United Kingdom (Great Britain))
-
-
-
-
-
1
LOVD
+/.
-
c.596C>A
r.(?)
p.(Pro199Gln)
Parent #2
-
pathogenic (recessive)
g.126094057G>T
g.124405488G>T
-
-
OAT_000008
-
PubMed: Mashima 1992
-
-
Germline
-
-
-
-
-
DNA
DGGE, SEQ
-
-
GACR;OATD
Pat1
PubMed: Mashima 1992
adopted
-
-
Canada
-
-
-
-
-
1
Johan den Dunnen
+/+?
5
c.627T>A
r.0
p.0
Parent #2
-
pathogenic
g.126094026A>T
g.124405457A>T
Codon 209 (exon 6) TAT (Try) > TAA (stop codon)
-
OAT_000040
-
PubMed: Mashima 1992
-
-
Germline
yes
-
-
-
-
DNA
SEQ
-
-
GACR;OATD
Pat3
PubMed: Mashima 1992
-
-
-
England;Germany
-
-
-
-
-
1
Anne Polvi
+?/.
-
c.627T>A
r.(?)
p.(Tyr209Ter)
Both (homozygous)
-
likely pathogenic
g.126094026A>T
g.124405457A>T
-
-
OAT_000040
-
PubMed: Riera 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ-NG
-
212-gene panel
retinal disease
Fi15/10
PubMed: Riera 2017
patient
-
-
Spain
-
-
-
-
-
1
LOVD
+/.
5
c.627T>A
r.627u>a
p.Tyr209*
Parent #2
-
pathogenic (recessive)
g.126094026A>T
-
-
-
OAT_000040
-
PubMed: Mashima 1992
-
-
Germline
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
GACR;OATD
patient;Pat2
PubMed: Akaki 1992
,
PubMed: Mashima 1992
2-generation family, 1 affected
-
-
England;France;Germany;Netherlands
Europe
-
-
-
-
1
Anne Polvi
-/.
-
c.648+14A>G
r.(=)
p.(=)
Unknown
-
benign
g.126093991T>C
g.124405422T>C
OAT(NM_000274.4):c.648+14A>G
-
OAT_000074
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.648+14A>G
r.(=)
p.(=)
Unknown
-
benign
g.126093991T>C
g.124405422T>C
OAT(NM_000274.4):c.648+14A>G
-
OAT_000074
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/.
6
c.661del
r.(?)
p.(Asp221Ilefs*9)
Unknown
-
likely pathogenic (recessive)
g.126092477del
-
c.661delG
-
OAT_000092
-
PubMed: Liu-2020
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG
-
hereditary eye disease enrichment panel (HEDEP)
retinal disease
-
PubMed: Liu-2020
-
M
-
-
-
-
-
-
-
1
LOVD
+/.
6
c.677C>T
r.(?)
p.(Ala226Val)
Parent #1
-
pathogenic
g.126092461G>A
g.124403892G>A
-
-
OAT_000013
-
PubMed: Brody 1992
-
-
Germline
-
-
-
-
-
DNA
SEQ, SSCA
-
-
GACR;OATD
-
-
-
-
-
-
white
-
-
-
-
1
Eva Trevisson
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