Global Variome shared LOVD
PGAP2 (post-GPI attachment to proteins 2)
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Curator:
Philippe Campeau
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All individuals with variants in gene PGAP2
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.
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
Variants in genes
: The individual has variants for this gene.
Panel size
: Number of individuals this entry represents; e.g. 1 for an individual, 5 for a family with 5 affected members.
How to query this table
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Operator
Column type
Example
Matches
Text
Arg
all entries containing 'Arg'
space
Text
Arg Ser
all entries containing 'Arg' and 'Ser'
|
Text
Arg|Ser
all entries containing 'Arg' or 'Ser'
!
Text
!fs
all entries not containing 'fs'
^
Text
^p.(Arg
all entries beginning with 'p.(Arg'
$
Text
Ser)$
all entries ending with 'Ser)'
=""
Text
=""
all entries with this field empty
=""
Text
="p.0"
all entries exactly matching 'p.0'
!=""
Text
!=""
all entries with this field not empty
!=""
Text
!="p.0"
all entries not exactly matching 'p.0?'
combination
Text
*|Ter !fs
all entries containing '*' or 'Ter' but not containing 'fs'
Date
2020
all entries matching the year 2020
|
Date
2020-03|2020-04
all entries matching March or April, 2020
!
Date
!2020-03
all entries not matching March, 2020
<
Date
<2020
all entries before the year 2020
<=
Date
<=2020-06
all entries in or before June, 2020
>
Date
>2020-06
all entries after June, 2020
>=
Date
>=2020-06-15
all entries on or after June 15th, 2020
combination
Date
2019|2020 <2020-03
all entries in 2019 or 2020, and before March, 2020
Numeric
23
all entries exactly matching 23
|
Numeric
23|24
all entries exactly matching 23 or 24
!
Numeric
!23
all entries not exactly matching 23
<
Numeric
<23
all entries lower than 23
<=
Numeric
<=23
all entries lower than, or equal to, 23
>
Numeric
>23
all entries higher than 23
>=
Numeric
>=23
all entries higher than, or equal to, 23
combination
Numeric
>=20 <30 !23
all entries with values from 20 to 29, but not equal to 23
Some more advanced examples:
Example
Matches
Asian
all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian
all entries containing 'Asian' but not containing 'Caucasian'
Asian|African !Caucasian
all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"
all entries containing 'South Asian', but not containing 'South East Asian'
To sort on a certain column, click on the column header or on the arrows. If that column is already selected to sort on, the sort order will be swapped. The column currently sorted on has a darker blue background color than the other columns. The up and down arrows next to the column name indicate the current sorting direction. When sorting on any field other than the default, LOVD will sort secondarily on the default sort column.
16 entries on 1 page. Showing entries 1 - 16.
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Legend
How to query
Individual ID
ID_report
Reference
Remarks
Gender
Consanguinity
Country
Population
Age at death
VIP
Data_av
Treatment
Disease
Phenotype details
Variants
Panel size
Owner
00025130
-
PubMed: Hansen 2013
Family with three girls with autosomal recessive hyperphosphatasia with mental retardation-3.
F
yes
Syria
African
-
-
-
-
HPMRS3;GPIBD8
The sisters of the first branch had an IQ below 35. Their motor development was severely delayed, and they had pronounced muscular weakness, hypotonia, and strabismus. Sleep patterns of both girls were disordered. Serum ALP activity was elevated. CT showed atrophy and increased gyration in both girls. Elder sister showed signs of Dandy-Walker malformation. Both girls had stature and head circumference belos the 5th percentile. Parents had also HC below the 5th percentile. The third girl, of the second branch, had hypotonia at birth. Motor development and language were severely delayed. Brain CT showed atrophy. Muscle atrophy was found by biopsy.
1
1
Philippe Campeau
00025486
-
PubMed: Krawitz 2013
Index case
F
no
Finland
white
-
-
-
-
HPMRS3;GPIBD8
Mild intellectual disability and seizures. Facial features included broad nasal bridge and tented upper lip vermilion. Elevated ALP.
2
1
Philippe Campeau
00028965
-
PubMed: Hansen et al 2013
PubMed: Rehman et al 2011
Family with 4 affected siblings. (2 males and 2 females)
-
yes
Pakistan
-
-
-
-
-
HPMRS3;GPIBD8
Average IQ 22, None had epilepsy. Clinical examination was normal. No data about ALP values.
1
1
Philippe Campeau
00028966
-
PubMed: Krawitz et al 2013
Index case
M
yes
Turkey
-
-
-
-
-
HPMRS3;GPIBD8
OFC at birt below 2 SD, cleft palate and Hirschprung at birth, atrial septal defect, hypoplasia of corpus callosum. Intellectual impairment, hypotonia, myoclonic and tonic-clonic seizures, sensorineural hearing loss. Scoliosis, wide palpebral fissures, wide mouth. Hypoplasic fingernails. ALP elevated.
1
1
Philippe Campeau
00154948
-
PubMed: Jezela-Stanek 2016
-
F
no
-
-
-
-
-
-
?
-
2
1
Philippe Campeau
00154977
patient_1
PubMed: Naseer 2016
-
M
yes
Saudi Arabia
-
-
-
-
-
HPMRS3;GPIBD8
-
1
2
Philippe Campeau
00154978
patient_2
PubMed: Naseer 2016
-
F
yes
Saudi Arabia
-
-
-
-
-
HPMRS3;GPIBD8
-
1
1
Philippe Campeau
00207490
IV-3
PubMed: Perez et al., 2017
Consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase.
M
yes
Saudi Arabia
Bedouin
>25y
-
-
-
HPMRS3;GPIBD8
Mild mental retardation, mood problems, depression, speech difficulties, past history of febrile convulsions, Elevated alkaline phosphatase (499 IU/L)
1
1
Philippe Campeau
00207491
IV-5
PubMed: Perez et al., 2017
consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase.
M
yes
Saudi Arabia
Bedouin
>18y
-
-
-
HPMRS3;GPIBD8
Developmental delay, Moderate mental retardation, Behavioral problems- aggression, Past history of seizures without fever, Elevated alkaline phosphatase (673 IU/L), generalized interictal spike and slow epileptiform discharges in EEG. No organ anomaly, No signs of dysmorphism, Normal cranial, motor, sensory, gait, and cerebellar exam, normal brain MRI
1
1
Philippe Campeau
00207493
IV-6
PubMed: Perez et al., 2017
consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase.
F
yes
Saudi Arabia
Bedouin
>15y
-
-
-
HPMRS3;GPIBD8
Mild mental retardation, Mood problems- depression Speech difficulaties, Elevated alkaline phosphatase (>1000 IU/L). No organ anomaly, no signs of dysmorphism.
1
1
Philippe Campeau
00207494
IV-7
PubMed: Perez et al., 2017
consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase.
F
yes
Saudi Arabia
Bedouin
>11y
-
-
-
HPMRS3;GPIBD8
Developmental delay, Mild mental retardation, Speech difficulties, Enuresis, Elevated alkaline phosphatase (1318 IU/L). No organ anomaly, No signs of dysmorphism, Normal cranial, motor, sensory, gait, and cerebellar exam, normal spine MRI.
1
1
Philippe Campeau
00207496
U6
PubMed: Reid et al., 2016
Found in a gene panel targeting (614) genes causing inborn errors of metabolism
M
-
-
-
>02y03m
-
-
-
HPMRS3;GPIBD8
Global severe developmental delay, tonic seizures. Multiorgan malformations including VSD, Hirschprung’s. Dysmorphism. Recurrent hypoglycaemia; hypogammaglobulinaemia, hyperphosphatasia. Dandy-Walker malformation, reduced white matter bulk.
1
1
Philippe Campeau
00269874
-
-
-
?
-
-
-
-
-
-
-
?
Nystagmus (HP:0000639); Global developmental delay (HP:0001263)
1
1
IMGAG
00274197
Pat73
PubMed: Pronicka 2016
-
F
-
Poland
-
-
-
-
-
?
neonatal onset; mitochondrial disease criteria score 3; muscle biopsy
2
1
Johan den Dunnen
00331542
14DG0688
PubMed: Maddirevula 2018
family
M
yes
-
Arab
-
-
-
-
skeletal dysplasia
Global developmental delay, Seizures, Hyperphosphatemia, Elevated alkaline phosphataseNo
1
1
LOVD
00403850
TF001
PubMed: Froukh 2020
analysis 103 families with neurodevelopmental disorders
-
-
Jordan
-
-
-
-
-
NDD
-
1
1
Johan den Dunnen
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