Global Variome shared LOVD
PGAP3 (post-GPI attachment to proteins 3)
LOVD v.3.0 Build 30b [
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Curator:
Philippe Campeau
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The variants shown are described using the NM_033419.3 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
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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
all entries beginning with 'p.(Arg'
$
Text
Ser)$
all entries ending with 'Ser)'
=""
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
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<=
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
all entries lower than, or equal to, 23
>
Numeric
>23
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>=
Numeric
>=23
all entries higher than, or equal to, 23
combination
Numeric
>=20 <30 !23
all entries with values from 20 to 29, but not equal to 23
Some more advanced examples:
Example
Matches
Asian
all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian
all entries containing 'Asian' but not containing 'Caucasian'
Asian|African !Caucasian
all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"
all entries containing 'South Asian', but not containing 'South East Asian'
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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
?/.
-
c.-39951del
r.(?)
p.(=)
Unknown
-
VUS
g.37884223del
g.39727970del
ERBB2(NM_001289936.1):c.3649delG (p.A1217Lfs*70)
-
ERBB2_000012
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.-39909G>T
r.(?)
p.(=)
Unknown
-
benign
g.37884176C>A
-
-
-
ERBB2_000005
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.-39770G>C
r.(?)
p.(=)
Unknown
-
benign
g.37884037C>G
g.39727784C>G
ERBB2(NM_001005862.3):c.3418C>G (p.P1140A)
-
ERBB2_000004
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.-39429G>A
r.(?)
p.(=)
Unknown
-
likely benign
g.37883696C>T
-
ERBB2(NM_001289936.1):c.3263C>T (p.T1088I)
-
ERBB2_000017
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.-38874C>T
r.(?)
p.(=)
Unknown
-
likely benign
g.37883141G>A
g.39726888G>A
ERBB2(NM_001289936.1):c.2999G>A (p.G1000E)
-
ERBB2_000015
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.-37694A>C
r.(?)
p.(=)
Unknown
-
likely benign
g.37881961T>G
g.39725708T>G
ERBB2(NM_001289936.1):c.2682T>G (p.G894=)
-
ERBB2_000003
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.-37349G>A
r.(?)
p.(=)
Unknown
-
VUS
g.37881616C>T
-
-
-
ERBB2_000018
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.-27878G>A
r.(?)
p.(=)
Unknown
-
VUS
g.37872145C>T
g.39715892C>T
ERBB2(NM_001289936.1):c.1421C>T (p.P474L)
-
ERBB2_000010
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.-27447G>A
r.(?)
p.(=)
Unknown
-
VUS
g.37871714C>T
g.39715461C>T
ERBB2(NM_001289936.1):c.1193C>T (p.S398L)
-
ERBB2_000009
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.-27280G>T
r.(?)
p.(=)
Unknown
-
likely benign
g.37871547C>A
g.39715294C>A
ERBB2(NM_001289936.1):c.1112C>A (p.A371D)
-
ERBB2_000008
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.-24448G>A
r.(?)
p.(=)
Unknown
-
benign
g.37868715C>T
g.39712462C>T
ERBB2(NM_001005862.3):c.1058+14C>T
-
ERBB2_000001
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.-21866G>C
r.(?)
p.(=)
Unknown
-
likely benign
g.37866133C>G
g.39709880C>G
ERBB2(NM_001289936.1):c.597C>G (p.S199R)
-
ERBB2_000007
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.100C>T
r.(?)
p.(Leu34=)
Unknown
-
likely benign
g.37844168G>A
g.39687915G>A
PGAP3(NM_033419.4):c.100C>T (p.L34=)
-
ERBB2_000014
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.124T>G
r.(?)
p.(Ser42Ala)
Unknown
-
VUS
g.37844144A>C
-
PGAP3(NM_033419.3):c.124T>G (p.(Ser42Ala))
-
ERBB2_000016
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.200A>G
r.(?)
p.(Asp67Gly)
Unknown
-
VUS
g.37842254T>C
g.39686001T>C
PGAP3(NM_033419.4):c.200A>G (p.D67G), PGAP3(NM_033419.5):c.200A>G (p.(Asp67Gly))
-
ERBB2_000013
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.200A>G
r.(?)
p.(Asp67Gly)
Unknown
-
VUS
g.37842254T>C
-
PGAP3(NM_033419.4):c.200A>G (p.D67G), PGAP3(NM_033419.5):c.200A>G (p.(Asp67Gly))
-
ERBB2_000013
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
-
c.275G>A
r.(?)
p.(Gly92Asp)
Both (homozygous)
-
pathogenic
g.37842179C>T
g.39685926C>T
-
-
PGAP3_000001
This mutation causes a substitution at a highly conserved residue in a juxtamembrane position on the luminal side. This mutation was absent in the Exome Variant Server, dbSNP (build 137), or 1000 Genomes Project databases, or in 108 ethnically matched controls. CHO cells showed that the mutant G92D protein had almost no or absent enzyme activity. Mutant PGAP3 cDNA bearing G92D did not reduce or reduced only slightly the surface levels of CD59, CD55 and uPAR indicating that the substitution caused a null or nearly null phenotype.
PubMed: Howard et al. 2014
-
rs587777251
Germline
yes
-
-
-
-
DNA
SEQ-NG
-
-
HPMRS4;GPIBD10
-
PubMed: Howard 2014
Three siblings, 17,8 and 4y, with hyperphosphatasia with mental retardation 4.
-
yes
Pakistan
Pakistani
-
-
-
-
1
Philippe Campeau
+/.
3
c.280del
r.(?)
p.(Trp94GlyfsTer27)
Parent #2
-
pathogenic (recessive)
g.37841002del
g.39684749del
NM_033419.3:c.280del
-
PGAP3_000032
-
PubMed: Nambot 2018
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES
?
PED3570.1
PubMed: Nambot 2018
-
-
-
France
-
-
-
-
-
1
Johan den Dunnen
+/.
3
c.314C>A
r.(?)
p.(Pro105Gln)
Both (homozygous)
-
pathogenic
g.37840968G>T
g.39684715G>T
-
-
PGAP3_000022
Missense variant. This mutation was predicted as pathogenic by the in silico software: SIFT=0, PolyPhen2=1, and MutationTaster=disease causing. This new mutation was inherited from both unaffected carrier parents.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
II-1
PubMed: Sakaguchi et al., 2018
Novel homozygous PGAP3 mutation (c.314C>A, p.Pro105Gln) in a Croatian patient. Born to healthy and nonconsanguineous parents (from the same region) after an uneventful pregnancy.
M
no
Croatia (Hrvatska)
Croatian
>08y
-
-
Orthotics at 6 years with no improvements, intensive physical therapy for the marked generalized hypotonia. Phenobarbital and Valproate for seizures. 200 mg of pyridoxine daily for neuronal symptoms.
1
Philippe Campeau
+/.
-
c.314C>G
r.(?)
p.(Pro105Arg)
Both (homozygous)
-
pathogenic
g.37840968G>C
g.39684715G>C
-
-
PGAP3_000004
Substitution at a highly conserved residue in the first transmembrane domain. The mutation was absent in 52 Arabic controls or in the Exome Variant Server database. CHO cells showed that the mutant P105R protein had low residual enzyme activity. Electrophoresis and immunoblotting studies showed that the P105R protein had only immature ER-form N-glycan and did not localize properly to the Golgi, but was retained in the ER.
PubMed: Howard et al. 2014
-
rs371549948
Germline
yes
-
-
-
-
DNA
SEQ-NG
-
-
HPMRS4;GPIBD10
-
PubMed: Howard 2014
Index case.
F
yes
Saudi Arabia
-
-
-
-
-
1
Philippe Campeau
+?/.
-
c.320C>T
r.(?)
p.(Ser107Leu)
Unknown
-
likely pathogenic
g.37840962G>A
g.39684709G>A
-
-
PGAP3_000011
-
PubMed: Knaus et al. 2016
-
-
Unknown
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
A-II-1
Knaus 2016:27120253
-
F
no
-
European American
-
-
-
-
1
Philippe Campeau
+?/.
-
c.320C>T
r.(?)
p.(Ser107Leu)
Paternal (confirmed)
-
likely pathogenic
g.37840962G>A
g.39684709G>A
-
-
PGAP3_000011
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
D-II-2
PubMed: Knaus 2016
-
F
no
-
British
-
-
-
-
1
Philippe Campeau
+?/.
-
c.320C>T
r.(?)
p.(Ser107Leu)
Maternal (confirmed)
-
likely pathogenic
g.37840962G>A
g.39684709G>A
-
-
PGAP3_000011
-
PubMed: Pagnamenta et al. 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG
Blood
WES
DD
257982
PubMed: Pagnamenta 2017
-
F
no
-
white
-
-
-
-
2
Philippe Campeau
+?/.
-
c.320C>T
r.(?)
p.(Ser107Leu)
Maternal (confirmed)
-
likely pathogenic
g.37840962G>A
g.39684709G>A
-
-
PGAP3_000011
-
PubMed: Pagnamenta et al. 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
DD
-
PubMed: Pagnamenta 2017
brother of individual 257982
M
no
-
white
-
-
-
-
1
Philippe Campeau
+/.
2
c.320C>T
r.(?)
p.(Ser107Leu)
Both (homozygous)
-
pathogenic
g.37840962G>A
g.39684709G>A
-
-
PGAP3_000011
Missense mutation. The wild type S107 residue is more hydrophobic and smaller than the mutant residue. This mutation will affect the hydrophobic interactions with the lipid membrane and protein function.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
III-2
PubMed: Balobaid et al., 2018
-
M
yes
Saudi Arabia
Middle Eastern
>03y
-
-
-
1
Philippe Campeau
+/.
2
c.320C>T
r.(?)
p.(Ser107Leu)
Both (homozygous)
-
pathogenic
g.37840962G>A
g.39684709G>A
-
-
PGAP3_000011
Missense mutation. The wild type S107 residue is more hydrophobic and smaller than the mutant residue. This mutation will affect the hydrophobic interactions with the lipid membrane and protein function.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
III-1
PubMed: Balobaid et al., 2018
-
F
yes
Saudi Arabia
Middle Eastern
>09y
-
-
anti-epileptic medications
1
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Paternal (confirmed)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
B-II-2
PubMed: Knaus 2016
-
F
no
-
German
-
-
-
-
1
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_1
PubMed: Abdel-Hamid 2017
-
M
yes
Egypt
-
-
-
-
-
1
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_2
PubMed: Abdel-Hamid 2017
-
F
yes
Egypt
-
-
-
-
-
1
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_3
PubMed: Abdel-Hamid 2017
-
F
yes
Egypt
-
-
-
-
-
1
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_4
PubMed: Abdel-Hamid 2017
-
M
yes
Egypt
-
-
-
-
-
1
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_6
PubMed: Abdel-Hamid 2017
-
F
no
Egypt
-
-
-
-
-
1
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_7
PubMed: Abdel-Hamid 2017
cousin with Patient_8
M
yes
Egypt
-
-
-
-
-
2
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_8
PubMed: Abdel-Hamid 2017
cousin with Patient_7
F
no
Egypt
-
-
-
-
-
1
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_9
PubMed: Abdel-Hamid 2017
-
M
yes
Egypt
-
-
-
-
-
2
Philippe Campeau
+?/.
-
c.402dup
r.(?)
p.(Met135Hisfs*28)
Both (homozygous)
-
likely pathogenic
g.37840884dup
g.39684631dup
-
-
PGAP3_000013
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_10
PubMed: Abdel-Hamid 2017
-
M
yes
Egypt
-
-
-
-
-
1
Philippe Campeau
-?/.
-
c.404T>C
r.(?)
p.(Met135Thr)
Unknown
-
likely benign
g.37840878A>G
g.39684625A>G
PGAP3(NM_033419.3):c.404T>C (p.(Met135Thr))
-
PGAP3_000007
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
-
c.432+1G>A
r.spl
p.?
Both (homozygous)
ACMG
pathogenic (recessive)
g.37840849C>T
g.39684596C>T
-
-
PGAP3_000030
-
PubMed: Hu 2019
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
-
ID
M9000136
PubMed: Hu 2019
family, 2 affected individuals
-
-
Iran
Persia
-
-
-
-
2
Johan den Dunnen
+/.
-
c.439dup
r.(?)
p.(Leu147Profs*16)
Paternal (confirmed)
-
pathogenic
g.37830928dup
g.39674675dup
-
-
PGAP3_000003
In vitro functional expression studies in CHO cells showed that the mutant c.439dupC mutant had no residual enzyme activity, and was likely degraded by nonsense-mediated mRNA decay. Flow cytometric analysis of patient cells showed a reduction in the cell surface levels of GPI-anchored proteins.
PubMed: Howard et al. 2014
-
-
Germline
yes
-
-
-
-
DNA
SEQ-NG
-
-
HPMRS4;GPIBD10
-
PubMed: Howard 2014
Index case.
F
no
United States
white
-
-
-
-
1
Philippe Campeau
+?/.
-
c.449G>A
r.(?)
p.(Trp150*)
Unknown
-
likely pathogenic
g.37830916C>T
-
PGAP3(NM_033419.5):c.449G>A (p.(Trp150*))
-
PGAP3_000034
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.495+10C>T
r.(=)
p.(=)
Unknown
-
likely benign
g.37830860G>A
-
PGAP3(NM_033419.4):c.495+10C>T
-
PGAP3_000029
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.496-9_496-8insCAGAGTA
r.(=)
p.(=)
Unknown
-
VUS
g.37830315_37830316insTACTCTG
g.39674062_39674063insTACTCTG
-
-
PGAP3_000027
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
5
c.507C>A
r.(?)
p.(Tyr169*)
Both (homozygous)
-
pathogenic
g.37830296G>T
g.39674043G>T
-
-
PGAP3_000021
Parents were heterozygous carriers for p.Tyr169Ter. This nonsense alteration was predicted to cause a truncated protein with lacking functionally structural 5 transmembrane domains (TMD)
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES, emulsion PCR
HPMRS4;GPIBD10
Patient 1
PubMed: Akgün Doğan et al., 2018
Second child of the parents (first cousin marriage), born via cesarean delivery at term. Died due to aspiration pneumonia-related respiratory distress.
M
yes
-
-
00y18m
-
-
-
1
Philippe Campeau
+/.
5
c.507C>A
r.(?)
p.(Tyr169*)
Both (homozygous)
-
pathogenic
g.37830296G>T
g.39674043G>T
-
-
PGAP3_000021
Parents were heterozygous carriers for p.Tyr169Ter. This nonsense alteration was predicted to cause a truncated protein with lacking functionally structural 5 transmembrane domains (TMD)
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES, emulsion PCR
HPMRS4;GPIBD10
Patient 2
PubMed: Akgün Doğan et al., 2018
3rd child of parents (first cousin marriage), younger sister of patient 1, born via cesarean delivery at 36 weeks
F
yes
-
-
>00y01m
-
-
-
1
Philippe Campeau
+?/.
-
c.511T>C
r.(?)
p.(Cys171Arg)
Maternal (confirmed)
-
likely pathogenic
g.37830292A>G
g.39674039A>G
-
-
PGAP3_000017
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
F-II-3
PubMed: Knaus 2016
-
M
no
-
Japanese
-
-
-
-
1
Philippe Campeau
+?/.
-
c.558-10G>A
r.(=)
p.(=)
Unknown
-
likely pathogenic
g.37829913C>T
g.39673660C>T
-
-
PGAP3_000012
-
PubMed: Knaus et al. 2016
-
-
Unknown
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
A-II-1
Knaus 2016:27120253
-
F
no
-
European American
-
-
-
-
1
Philippe Campeau
+?/.
-
c.558-10G>A
r.(=)
p.(=)
Maternal (confirmed)
-
likely pathogenic
g.37829913C>T
g.39673660C>T
-
-
PGAP3_000012
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
B-II-2
PubMed: Knaus 2016
-
F
no
-
German
-
-
-
-
1
Philippe Campeau
+?/.
-
c.558-10G>A
r.spl?
p.?
Both (homozygous)
-
likely pathogenic (recessive)
g.37829913C>T
g.39673660C>T
-
-
PGAP3_000012
-
PubMed: Al-Kasbi 2022
VCV000224645.3
rs200598755
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES
ID
10MS6600
PubMed: Al-Kasbi 2022
patient, other affecteds in family
M
-
Oman
-
-
-
-
-
1
Johan den Dunnen
+?/.
-
c.639C>G
r.(?)
p.(Tyr213*)
Unknown
-
likely pathogenic
g.37829822G>C
-
PGAP3(NM_033419.3):c.639C>G (p.(Tyr213*))
-
PGAP3_000035
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
-
c.663T>G
r.(?)
p.(Tyr221Ter)
Unknown
-
pathogenic
g.37829798A>C
g.39673545A>C
PGAP3(NM_033419.5):c.663T>G (p.Y221*)
-
PGAP3_000028
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
-
c.694+1G>A
r.spl?
p.?
Unknown
-
pathogenic
g.37829766C>T
-
PGAP3(NM_033419.5):c.694+1G>A
-
PGAP3_000033
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
-
c.715_717del
r.(?)
p.(Trp239del)
Unknown
-
VUS
g.37829490_37829492del
g.39673237_39673239del
-
-
PGAP3_000009
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.811C>A
r.(?)
p.(Leu271Met)
Unknown
-
likely benign
g.37829392G>T
-
PGAP3(NM_033419.4):c.811C>A (p.L271M)
-
PGAP3_000031
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/.
-
c.817_820del
r.(?)
p.(Asp273Serfs*37)
Both (homozygous)
-
likely pathogenic
g.37829384_37829387del
g.39673131_39673134del
-
-
PGAP3_000019
-
PubMed: Abdel-Hamid et al. 2017
-
-
Germline
yes
-
-
-
-
DNA
SEQ
peripheral blood leukocytes
-
HPMRS1;GPIBD2
Patient_5
PubMed: Abdel-Hamid 2017
-
F
yes
Egypt
-
-
-
-
-
1
Philippe Campeau
?/.
-
c.827C>T
r.(?)
p.(Pro276Leu)
Unknown
-
VUS
g.37829376G>A
g.39673123G>A
PGAP3(NM_033419.5):c.827C>T (p.(Pro276Leu), p.P276L)
-
PGAP3_000006
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/+?
-
c.827C>T
r.(?)
p.(Pro276Leu)
Unknown
-
likely pathogenic
g.37829376G>A
g.39673123G>A
-
-
PGAP3_000006
-
PubMed: Knaus et al. 2018
-
-
Germline/De novo (untested)
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/.
-
c.827C>T
r.(?)
p.(Pro276Leu)
Unknown
-
likely pathogenic
g.37829376G>A
-
PGAP3(NM_033419.5):c.827C>T (p.(Pro276Leu), p.P276L)
-
PGAP3_000006
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/.
-
c.842T>C
r.(?)
p.(Leu281Pro)
Paternal (confirmed)
-
likely pathogenic
g.37829361A>G
g.39673108A>G
-
-
PGAP3_000018
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
F-II-3
PubMed: Knaus 2016
-
M
no
-
Japanese
-
-
-
-
1
Philippe Campeau
+?/.
-
c.845A>G
r.(?)
p.(Asp282Gly)
Both (homozygous)
-
likely pathogenic
g.37829358T>C
g.39673105T>C
-
-
PGAP3_000016
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
E-II-2
PubMed: Knaus 2016
-
F
yes
-
Palestinian
-
-
-
-
2
Philippe Campeau
+?/.
-
c.845A>G
r.(?)
p.(Asp282Gly)
Both (homozygous)
-
likely pathogenic
g.37829358T>C
g.39673105T>C
-
-
PGAP3_000016
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
E-II-4
PubMed: Knaus 2016
-
F
yes
-
Palestinian
-
-
-
-
1
Philippe Campeau
+/.
7
c.845A>G
r.(?)
p.(Asp282Gly)
Parent #1
-
pathogenic (recessive)
g.37829358T>C
g.39673105T>C
-
-
PGAP3_000016
-
PubMed: Nambot 2018
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES
?
PED3570.1
PubMed: Nambot 2018
-
-
-
France
-
-
-
-
-
1
Johan den Dunnen
?/.
-
c.850C>T
r.(?)
p.(His284Tyr)
Unknown
-
VUS
g.37829353G>A
g.39673100G>A
-
-
PGAP3_000008
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
-
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic
g.37829353G>A
g.39673100G>A
-
-
PGAP3_000008
Mutation is heterozygous in the available parents. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
I-1
PubMed: Balobaid et al., 2018
-
F
yes
Saudi Arabia
Middle Eastern
>09y
-
-
anti-epileptic medications
1
Philippe Campeau
+/.
7
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic
g.37829353G>A
g.39673100G>A
-
-
PGAP3_000008
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
II-2
PubMed: Balobaid et al., 2018
-
M
yes
Saudi Arabia
Middle Eastern
>03y
-
-
-
1
Philippe Campeau
+/.
7
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic
g.37829353G>A
g.39673100G>A
-
-
PGAP3_000008
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
II-1
PubMed: Balobaid et al., 2018
-
M
yes
Saudi Arabia
Middle Eastern
>08y
-
-
anti-epileptic medications
1
Philippe Campeau
+/.
7
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic
g.37829353G>A
g.39673100G>A
-
-
PGAP3_000008
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
I-2
PubMed: Balobaid et al., 2018
-
F
yes
Saudi Arabia
Middle Eastern
>06y
-
-
-
1
Philippe Campeau
+/.
-
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic (recessive)
g.37829353G>A
g.39673100G>A
NM_033419.3:c.850C>T:p.(His284Tyr)
-
PGAP3_000008
-
PubMed: Maddirevula 2018
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES
skeletal dysplasia
17DG0809
PubMed: Maddirevula 2018
family
M
yes
-
Arab
-
-
-
-
1
LOVD
+/.
-
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic (recessive)
g.37829353G>A
g.39673100G>A
NM_033419.3:c.850C>T:p.(His284Tyr)
-
PGAP3_000008
-
PubMed: Maddirevula 2018
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES
skeletal dysplasia
14DG0578
PubMed: Maddirevula 2018
family
F
yes
-
Arab
-
-
-
-
1
LOVD
+/.
-
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic (recessive)
g.37829353G>A
g.39673100G>A
NM_033419.3:c.850C>T:p.(His284Tyr)
-
PGAP3_000008
-
PubMed: Maddirevula 2018
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES
skeletal dysplasia
12DG2300 , 12DG2301
PubMed: Maddirevula 2018
family, 2 affected (F, M)
F;M
yes
-
Arab
-
-
-
-
2
LOVD
+/.
-
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic (recessive)
g.37829353G>A
g.39673100G>A
NM_033419.3:c.850C>T:p.(His284Tyr)
-
PGAP3_000008
-
PubMed: Maddirevula 2018
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES
skeletal dysplasia
14DG0816 , 16DG0111
PubMed: Maddirevula 2018
family, 2 affected (2F)
F
yes
-
Arab
-
-
-
-
2
LOVD
+/.
-
c.850C>T
r.(?)
p.(His284Tyr)
Both (homozygous)
-
pathogenic (recessive)
g.37829353G>A
g.39673100G>A
NM_033419.3:c.850C>T:p.(His284Tyr)
-
PGAP3_000008
-
PubMed: Maddirevula 2018
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES
skeletal dysplasia
14DG2083 , 14DG2084, 14DG2085
PubMed: Maddirevula 2018
family, 3 affected (F, 2M)
F;M
yes
-
Arab
-
-
-
-
3
LOVD
+?/.
7
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
likely pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
-
PubMed: Nampoothiri et al. 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG
-
WES
DD
IV-1
PubMed: Nampoothiri 2017
-
M
yes
Oman
-
-
-
-
-
2
Philippe Campeau
+?/.
7
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
likely pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
-
PubMed: Nampoothiri et al. 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG
-
WES
DD, HPMRS6;GPIBD12
IV-2
PubMed: Nampoothiri 2017
-
F
yes
Oman
-
-
-
-
-
1
Philippe Campeau
+/.
-
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES, Homozygosity mapping
HPMRS4;GPIBD10
VIII-2
PubMed: Balobaid et al., 2018
-
F
yes
Oman
Middle Eastern
>04y
-
-
anti-epileptic medications
1
Philippe Campeau
+/.
-
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES, homozygosity by descent
HPMRS4;GPIBD10
VIII-1
PubMed: Balobaid et al., 2018
-
M
yes
Oman
Middle Eastern
>07y
-
-
anti-epileptic medications
1
Philippe Campeau
+/.
-
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
WES, homozygosity by descent
HPMRS4;GPIBD10
VII-2
PubMed: Balobaid et al., 2018
-
F
yes
Oman
Middle Eastern
>05y
-
-
-
1
Philippe Campeau
+/.
-
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES, homozygosity by descent
HPMRS4;GPIBD10
VII-1
PubMed: Balobaid et al., 2018
-
F
yes
Oman
Middle Eastern
>09y
-
-
-
1
Philippe Campeau
+/.
-
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral Blood
WES
HPMRS4;GPIBD10
VI-1
PubMed: Balobaid 2018
-
F
no
Qatar
Middle Eastern
>06y
-
-
-
1
Philippe Campeau
+/.
7
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral Blood
WES, Targeted mutation analysis
HPMRS4;GPIBD10
V-1
PubMed: Balobaid 2018
-
F
yes
Qatar
Middle Eastern
>02y03m
-
-
-
1
Philippe Campeau
+/.
7
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
IV-2
PubMed: Balobaid 2018
-
F
yes
Qatar
Middle Eastern
>10y
-
-
-
1
Philippe Campeau
+/.
7
c.851A>G
r.(?)
p.(His284Arg)
Both (homozygous)
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane.
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
WES
HPMRS4;GPIBD10
IV-1
PubMed: Balobaid 2018
-
F
yes
Qatar
Middle Eastern
>13y
-
-
-
1
Philippe Campeau
+/.
-
c.851A>G
r.(?)
p.(His284Arg)
Unknown
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
-
-
-
-
De novo
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
Clinical Exome sequencing
HPMRS4;GPIBD10
PGAP3 (2x)_individual 1
PubMed: Yavarna et al., 2015
Paper presents a compilation of many genes. No detailed information on specific PGAP3 patients.
-
-
-
Middle Eastern
-
-
-
-
1
Philippe Campeau
+/.
-
c.851A>G
r.(?)
p.(His284Arg)
Unknown
-
pathogenic
g.37829352T>C
g.39673099T>C
-
-
PGAP3_000020
-
-
-
-
De novo
-
-
-
-
-
DNA
SEQ, SEQ-NG
Peripheral blood
Clinical Exome Sequencing
HPMRS4;GPIBD10
PGAP3 (2x)_individual 2
PubMed: Yavarna et al., 2015
Paper presents a compilation of many genes. No detailed information on patient.
-
-
-
Middle Eastern
-
-
-
-
1
Philippe Campeau
+?/.
-
c.861G>T
r.(?)
p.(Trp287Cys)
Paternal (confirmed)
-
likely pathogenic
g.37829342C>A
g.39673089C>A
-
-
PGAP3_000014
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
C-II-1
PubMed: Knaus 2016
-
M
no
-
French
-
-
-
-
2
Philippe Campeau
+?/.
-
c.861G>T
r.(?)
p.(Trp287Cys)
Paternal (confirmed)
-
likely pathogenic
g.37829342C>A
g.39673089C>A
-
-
PGAP3_000014
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
C-II-2
PubMed: Knaus 2016
-
F
no
-
French
-
-
-
-
1
Philippe Campeau
+/.
8
c.914A>G
r.(?)
p.(Asp305Gly)
Maternal (confirmed)
-
pathogenic
g.37829105T>C
g.39672852T>C
-
-
PGAP3_000002
CHO cell line defective in both PGAP3 have GPI-APs at mildly reduced levels because of a lack of GPI fatty acid remodelling. When wild-type PGAP3 cDNA was transfected, the first step in the fatty acid remodelling was restored, whereas the second step remained defective, leading to the release of lyso-GPI intermediates and resulting in a severe reduction in the surface levels of GPI-APs. Mutant PGAP3 cDNA bearing the mutation p.Asp305Gly significantly reduced levels of all three GPI-APs, indicating some residual activity. The p.Asp305Gly protein was readily detectable but had immature N-glycan and was mislocalized in the ER by immunoblot.
PubMed: Howard et al. 2014
-
rs587777252
Germline
yes
-
-
-
-
DNA
SEQ-NG
-
-
HPMRS4;GPIBD10
-
PubMed: Howard 2014
Index case.
F
no
United States
white
-
-
-
-
1
Philippe Campeau
+?/.
-
c.914A>G
r.(?)
p.(Asp305Gly)
Maternal (confirmed)
-
likely pathogenic
g.37829105T>C
g.39672852T>C
-
-
PGAP3_000002
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
D-II-2
PubMed: Knaus 2016
-
F
no
-
British
-
-
-
-
1
Philippe Campeau
+?/.
-
c.914A>G
r.(?)
p.(Asp305Gly)
Paternal (confirmed)
-
likely pathogenic
g.37829105T>C
g.39672852T>C
-
-
PGAP3_000002
-
PubMed: Pagnamenta et al. 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ-NG
Blood
WES
DD
257982
PubMed: Pagnamenta 2017
-
F
no
-
white
-
-
-
-
2
Philippe Campeau
+?/.
-
c.914A>G
r.(?)
p.(Asp305Gly)
Paternal (confirmed)
-
likely pathogenic
g.37829105T>C
g.39672852T>C
-
-
PGAP3_000002
-
PubMed: Pagnamenta et al. 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ
-
-
DD
-
PubMed: Pagnamenta 2017
brother of individual 257982
M
no
-
white
-
-
-
-
1
Philippe Campeau
+?/.
-
c.924C>A
r.(?)
p.(Tyr308*)
Both (homozygous)
ACMG
likely pathogenic
g.37829095G>T
g.39672842G>T
-
-
PGAP3_000005
-
PubMed: Trujillano 2017
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
-
-
HPMRS4;GPIBD10
-
PubMed: Trujillano 2017
unaffected parents
-
-
-
-
-
-
-
-
1
Daniel Trujillano
+?/.
-
c.*559C>T
r.(=)
p.(=)
Maternal (confirmed)
-
likely pathogenic
g.37828497G>A
g.39672244G>A
-
-
PGAP3_000015
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
C-II-1
PubMed: Knaus 2016
-
M
no
-
French
-
-
-
-
2
Philippe Campeau
+?/.
-
c.*559C>T
r.(=)
p.(=)
Maternal (confirmed)
-
likely pathogenic
g.37828497G>A
g.39672244G>A
-
-
PGAP3_000015
-
PubMed: Knaus et al. 2016
-
-
Germline
-
-
-
-
-
DNA, RNA
SEQ-NG
fibroblasts or blood
exome sequencing
HPMRS1;GPIBD2
C-II-2
PubMed: Knaus 2016
-
F
no
-
French
-
-
-
-
1
Philippe Campeau
?/.
-
c.*559C>T
r.(=)
p.(=)
Unknown
-
VUS
g.37828497G>A
-
PGAP3(NM_033419.3):c.*559C>T (p.?)
-
PGAP3_000015
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.*6299G>T
r.(=)
p.(=)
Unknown
-
benign
g.37822757C>A
g.39666504C>A
-
-
PGAP3_000024
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.*6317C>G
r.(=)
p.(=)
Unknown
-
likely benign
g.37822739G>C
g.39666486G>C
-
-
TCAP_000021
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.*6495C>A
r.(=)
p.(=)
Unknown
-
likely benign
g.37822561G>T
g.39666308G>T
-
-
TCAP_000015
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.*6616A>C
r.(=)
p.(=)
Unknown
-
benign
g.37822440T>G
g.39666187T>G
-
-
PGAP3_000023
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.*6618C>A
r.(=)
p.(=)
Unknown
-
likely benign
g.37822438G>T
g.39666185G>T
TCAP(NM_003673.3):c.*76G>T
-
TCAP_000027
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
-
c.*6618C>A
r.(=)
p.(=)
Unknown
-
likely benign
g.37822438G>T
g.39666185G>T
TCAP(NM_003673.3):c.*76G>T
-
TCAP_000027
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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