### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = PGAP1) # charset = UTF-8 ## Genes ## Do not remove or alter this header ## ## Count = 1 "{{id}}" "{{name}}" "{{chromosome}}" "{{chrom_band}}" "{{imprinting}}" "{{refseq_genomic}}" "{{refseq_UD}}" "{{reference}}" "{{url_homepage}}" "{{url_external}}" "{{allow_download}}" "{{id_hgnc}}" "{{id_entrez}}" "{{id_omim}}" "{{show_hgmd}}" "{{show_genecards}}" "{{show_genetests}}" "{{show_orphanet}}" "{{note_index}}" "{{note_listing}}" "{{refseq}}" "{{refseq_url}}" "{{disclaimer}}" "{{disclaimer_text}}" "{{header}}" "{{header_align}}" "{{footer}}" "{{footer_align}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{updated_by}}" "{{updated_date}}" "PGAP1" "post-GPI attachment to proteins 1" "2" "q33.1" "unknown" "NC_000002.11" "UD_134712225099" "" "http://www.LOVD.nl/PGAP1" "" "1" "25712" "80055" "611655" "1" "1" "1" "1" "Establishment of this gene variant database (LSDB) was performed by Johan den Dunnen, supported by Global Variome." "" "g" "http://databases.lovd.nl/shared/refseq/PGAP1_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2019-11-05 22:48:48" "00000" "2025-05-05 21:14:00" ## Transcripts ## Do not remove or alter this header ## ## Count = 1 "{{id}}" "{{geneid}}" "{{name}}" "{{id_mutalyzer}}" "{{id_ncbi}}" "{{id_ensembl}}" "{{id_protein_ncbi}}" "{{id_protein_ensembl}}" "{{id_protein_uniprot}}" "{{remarks}}" "{{position_c_mrna_start}}" "{{position_c_mrna_end}}" "{{position_c_cds_end}}" "{{position_g_mrna_start}}" "{{position_g_mrna_end}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "00016026" "PGAP1" "post-GPI attachment to proteins 1" "001" "NM_024989.3" "" "NP_079265.2" "" "" "" "-114" "10999" "2769" "197791454" "197697728" "" "0000-00-00 00:00:00" "" "" ## Diseases ## Do not remove or alter this header ## ## Count = 5 "{{id}}" "{{symbol}}" "{{name}}" "{{inheritance}}" "{{id_omim}}" "{{tissues}}" "{{features}}" "{{remarks}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "00139" "ID" "intellectual disability (ID)" "" "" "" "" "" "00084" "2013-06-04 18:18:07" "00006" "2015-02-09 10:02:49" "00198" "?" "unclassified / mixed" "" "" "" "" "" "00006" "2013-09-13 14:21:47" "00006" "2024-11-23 09:38:12" "04087" "NEDDSBA;MRT42;GPIBD9" "neurodevelopmental disorder with dysmorphic features, spasticity, and brain abnormalities (MRT-42, GPIBD-9)" "AR" "615802" "" "autosomal recessive" "" "00006" "2014-09-25 23:29:40" "00006" "2024-01-16 15:12:18" "04147" "MRT" "mental retardation, autosomal recessive (MRT, intellectual disability (IDT))" "" "" "" "autosomal recessive" "" "00006" "2014-10-11 12:21:35" "00006" "2018-12-18 09:25:11" "04282" "CVI" "cerebral visual impairment (CVI)" "" "" "" "" "" "00006" "2015-06-15 15:37:52" "00006" "2015-06-15 15:38:26" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 2 "{{geneid}}" "{{diseaseid}}" "PGAP1" "04087" "PGAP1" "04147" ## Individuals ## Do not remove or alter this header ## ## Count = 16 "{{id}}" "{{fatherid}}" "{{motherid}}" "{{panelid}}" "{{panel_size}}" "{{license}}" "{{owned_by}}" "{{Individual/Reference}}" "{{Individual/Remarks}}" "{{Individual/Gender}}" "{{Individual/Consanguinity}}" "{{Individual/Origin/Geographic}}" "{{Individual/Age_of_death}}" "{{Individual/VIP}}" "{{Individual/Data_av}}" "{{Individual/Treatment}}" "{{Individual/Origin/Population}}" "{{Individual/Individual_ID}}" "00025011" "" "" "" "1" "" "01158" "{PMID:Bosch 2015:25804403}, {DOI:Bosch 2015:10.1038/ejhg.2015.42}, {PMID:Bosch 2016:26350515}, {DOI:Bosch 2016:10.1038/ejhg.2015.186}" "" "M" "?" "Netherlands" "" "0" "" "" "white" "26350515-Pat12" "00025127" "" "" "" "2" "" "00081" "{PMID:Novarino 2014:24482476}" "4-generation family, 2 affected siblings (9m, 6y) with spastic paraplegia, unaffected heterozygous carrier parents" "M" "yes" "" "" "0" "" "" "Middle East" "" "00025128" "" "" "" "1" "" "00081" "{PMID:Murakami 2014: 24784135}" "Two siblings,4 and 2-year-old, with mental retardation." "" "yes" "Syria" "" "0" "" "" "African" "" "00081033" "" "" "" "1" "" "01758" "{PMID:Trujillano 2017:27848944}" "unaffected parents" "" "" "" "" "0" "" "" "" "" "00155047" "" "" "" "2" "" "00081" "{PMID:Kettwig 2016:27206732}" "" "M" "no" "" "" "0" "" "" "white" "II-1" "00155048" "" "" "00155047" "1" "" "00081" "{PMID:Kettwig 2016:27206732}" "dizygotic twins with ID00155047" "M" "no" "" "" "0" "" "" "white" "II-2" "00155049" "" "" "" "2" "" "00081" "{PMID:Granzow 2015:26050939}" "" "F" "yes" "Turkey" "" "0" "" "" "" "Patient_1" "00155050" "" "" "00155049" "1" "" "00081" "{PMID:Granzow 2015:26050939}" "" "M" "yes" "Turkey" "" "0" "" "" "" "Patient_2" "00155200" "" "" "" "1" "" "00081" "{PMID:Williams 2015:25823418}" "" "M" "no" "" "" "0" "" "" "" "" "00229653" "" "" "" "1" "" "01807" "" "" "F" "" "" "" "0" "" "" "" "" "00267238" "" "" "" "2" "" "02575" "" "" "M" "yes" "Turkey" "" "0" "" "" "Kurdish" "" "00267239" "" "" "00267238" "1" "" "02575" "" "" "F" "yes" "Turkey" "" "0" "" "" "Kurdish" "" "00317999" "" "" "" "1" "" "00006" "{PMID:Riazuddin 2017:27457812}" "" "" "yes" "Pakistan" "" "0" "" "" "" "PKMR119" "00361506" "" "" "" "1" "" "00006" "{PMID:Anazi 2017:27431290}" "simplex case" "F" "yes" "Saudi Arabia" "" "0" "" "" "" "13DG1641" "00427979" "" "" "" "1" "" "00006" "{PMID:Bournazos 2022:34906502}" "family, 1 affected" "" "" "Australia" "" "0" "" "" "" "A031" "00446376" "" "" "" "1" "" "04630" "patient" "" "F" "yes" "Sri Lanka" "" "0" "" "" "" "23_2381" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 13 "{{individualid}}" "{{diseaseid}}" "00025011" "00139" "00025011" "04282" "00025127" "04087" "00025128" "04087" "00081033" "04087" "00155047" "00198" "00229653" "00198" "00267238" "04147" "00267239" "04147" "00317999" "00139" "00361506" "00139" "00427979" "00198" "00446376" "00198" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00139, 00198, 04087, 04147, 04282 ## Count = 11 "{{id}}" "{{diseaseid}}" "{{individualid}}" "{{owned_by}}" "{{Phenotype/Inheritance}}" "{{Phenotype/Age}}" "{{Phenotype/Additional}}" "{{Phenotype/Age/Onset}}" "{{Phenotype/Age/Diagnosis}}" "{{Phenotype/Onset}}" "{{Phenotype/Protein}}" "{{Phenotype/Tumor/MSI}}" "{{Phenotype/Enzyme/CPK}}" "{{Phenotype/Heart/Myocardium}}" "{{Phenotype/Lung}}" "{{Phenotype/Diagnosis/Definite}}" "{{Phenotype/Diagnosis/Initial}}" "{{Phenotype/Diagnosis/Criteria}}" "0000021239" "04087" "00025127" "00081" "Familial, autosomal recessive" "" "The patients had global developmental delay, hand and foot tremors, and spasticity. The older brother could walk with support. Both had increased deep tendon reflexes. The older brother had prominent cortical sulci and widened sylvian fissures; the younger brother had agenesis of the corpus callosum, cerebellar vermis hypoplasia, and defective myelination. The older brother had borderline intelligence." "" "" "" "" "" "" "" "" "" "" "" "0000021240" "04087" "00025128" "00081" "Familial, autosomal recessive" "" "At birth, the older sister was hypotonic and his borther was a floppy baby. Both children have a developmental delay and severe intellectual disability with an estimated IQ below 35. The girl had major and absence epilepsy. They showed some stereotypic movements. Brain CT scan of the girl at age of one year revealed pronounced brain atrophy. They had microcephaly. Both children have large ears and a flattened nasal root. Their parents had head circumferences in the lower percentiles." "" "" "" "" "" "" "" "" "" "" "" "0000060602" "04087" "00081033" "01758" "Familial, autosomal recessive" "" "Mental retardation, autosomal recessive 42 (OMIM:615802)" "" "" "" "" "" "" "" "" "" "" "" "0000078841" "04282" "00025011" "00006" "Unknown" "" "see paper; ..." "" "" "" "" "" "" "" "" "" "" "" "0000172878" "00198" "00229653" "01807" "Unknown" "" "Global developmental delay (HP:0001263); Epileptic spasms (HP:0011097)" "" "" "" "" "" "" "" "" "" "" "" "0000206955" "04147" "00267238" "02575" "Familial, autosomal recessive" "" "" "" "" "" "" "" "" "" "" "MRT42" "intellectual disability" "" "0000206956" "04147" "00267239" "02575" "Familial, autosomal recessive" "" "" "" "" "" "" "" "" "" "" "MRT42" "intellectual disability" "" "0000241783" "00139" "00317999" "00006" "Familial, autosomal recessive" "" "Non syndromic" "" "" "" "" "" "" "" "" "" "intellectual disability" "" "0000256911" "00139" "00361506" "00006" "Familial, autosomal recessive" "3y10m" "not syndromic; intellectual disability and strabismus" "" "" "" "" "" "" "" "" "" "intellectual disability" "" "0000318925" "00198" "00427979" "00006" "Familial, autosomal recessive" "7y" "" "" "" "" "" "" "" "" "" "Mental retardation, autosomal recessive 42" "" "" "0000335611" "00198" "00446376" "04630" "Familial, autosomal recessive" "" "spastic tetraparesis (HP:0001285)" "" "13y" "" "" "" "" "" "" "NEDDSBA" "neurodevelopmental disorder" "" ## Screenings ## Do not remove or alter this header ## ## Count = 16 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000025012" "00025011" "1" "01158" "01158" "2014-12-02 15:58:57" "" "" "PCR;SEQ;SEQ-NG" "DNA" "" "" "0000025129" "00025127" "1" "00081" "00081" "2014-12-05 17:20:16" "" "" "SEQ-NG" "DNA" "" "" "0000025130" "00025128" "1" "00081" "00081" "2014-12-05 18:38:11" "" "" "SEQ-NG" "DNA" "" "" "0000081145" "00081033" "1" "01758" "00006" "2016-09-07 13:24:08" "" "" "SEQ;SEQ-NG" "DNA" "" "" "0000155911" "00155047" "1" "00081" "00081" "2018-03-13 22:22:44" "" "" "SEQ-NG" "DNA" "" "WES" "0000155912" "00155048" "1" "00081" "00081" "2018-03-13 22:30:38" "" "" "SEQ-NG" "DNA" "" "WES" "0000155913" "00155049" "1" "00081" "00081" "2018-03-13 22:48:16" "" "" "SEQ-NG" "DNA" "peripheral blood" "WES" "0000155914" "00155050" "1" "00081" "00081" "2018-03-13 22:53:42" "" "" "SEQ-NG" "DNA" "peripheral blood" "WES" "0000156064" "00155200" "1" "00081" "00081" "2018-03-14 16:26:34" "" "" "SEQ-NG" "DNA" "" "WES" "0000230746" "00229653" "1" "01807" "01807" "2019-04-08 10:01:34" "" "" "SEQ" "DNA" "" "" "0000268367" "00267238" "1" "02575" "02575" "2019-11-03 19:04:01" "" "" "SEQ-NG" "DNA" "lymphocytes" "confimed by Sanger" "0000268368" "00267239" "1" "02575" "02575" "2019-11-03 19:18:51" "" "" "SEQ-NG" "DNA" "lymphocytes" "confimed by Sanger" "0000319181" "00317999" "1" "00006" "00006" "2020-11-05 17:52:36" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000362734" "00361506" "1" "00006" "00006" "2021-04-07 19:07:03" "" "" "SEQ-NG" "DNA" "" "WES" "0000429392" "00427979" "1" "00006" "00006" "2022-12-19 13:11:26" "" "" "RT-PCR;SEQ;SEQ-NG-RNA" "DNA;RNA" "whole blood, fibroblasts" "duo WES" "0000447950" "00446376" "1" "04630" "04630" "2024-01-15 19:06:09" "00006" "2024-01-16 15:17:14" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "WES" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 7 "{{screeningid}}" "{{geneid}}" "0000025129" "PGAP1" "0000025130" "PGAP1" "0000081145" "PGAP1" "0000268367" "PGAP1" "0000319181" "PGAP1" "0000362734" "PGAP1" "0000447950" "PGAP1" ## Variants_On_Genome ## Do not remove or alter this header ## ## Please note that not necessarily all variants found in the given individuals are shown. This output is restricted to variants in the selected gene. ## Count = 47 "{{id}}" "{{allele}}" "{{effectid}}" "{{chromosome}}" "{{position_g_start}}" "{{position_g_end}}" "{{type}}" "{{average_frequency}}" "{{owned_by}}" "{{VariantOnGenome/DBID}}" "{{VariantOnGenome/DNA}}" "{{VariantOnGenome/Frequency}}" "{{VariantOnGenome/Reference}}" "{{VariantOnGenome/Restriction_site}}" "{{VariantOnGenome/Published_as}}" "{{VariantOnGenome/Remarks}}" "{{VariantOnGenome/Genetic_origin}}" "{{VariantOnGenome/Segregation}}" "{{VariantOnGenome/dbSNP}}" "{{VariantOnGenome/VIP}}" "{{VariantOnGenome/Methylation}}" "{{VariantOnGenome/ISCN}}" "{{VariantOnGenome/DNA/hg38}}" "{{VariantOnGenome/ClinVar}}" "{{VariantOnGenome/ClinicalClassification}}" "{{VariantOnGenome/ClinicalClassification/Method}}" "0000047866" "11" "90" "2" "197784747" "197784749" "del" "0" "01158" "PGAP1_000001" "g.197784747_197784749del" "" "{PMID:Bosch 2015:25804403}, {DOI:Bosch 2015:10.1038/ejhg.2015.42}, dear8LOV" "" "" "variant heterozygous in sister" "Germline" "" "" "0" "" "" "g.196920023_196920025del" "" "pathogenic" "" "0000047867" "21" "90" "2" "197761859" "197761863" "del" "0" "01158" "PGAP1_000003" "g.197761859_197761863del" "" "{PMID:Bosch 2015:25804403}, {DOI:Bosch 2015:10.1038/ejhg.2015.42}, {PMID:Bosch 2016:26350515}, {DOI:Bosch 2016:10.1038/ejhg.2015.186}" "" "" "variant not present in sister" "Germline" "" "" "0" "" "" "g.196897135_196897139del" "" "pathogenic" "" "0000047868" "21" "30" "2" "197761868" "197761868" "subst" "0" "01158" "PGAP1_000002" "g.197761868G>A" "" "{PMID:Bosch 2015:25804403}, {DOI:Bosch 2015:10.1038/ejhg.2015.42}" "" "" "" "Germline" "" "" "0" "" "" "g.196897144G>A" "" "likely benign" "" "0000048005" "3" "90" "2" "197712670" "197712670" "subst" "0" "00081" "PGAP1_000004" "g.197712670C>A" "" "{PMID:Novarino et al. :24482476}" "" "" "Functional validation in a knockdown model in zebrafish was performed. Morphants were phenotyped for touch-induced and spontaneous locomotion behavior. Average touch-response distance was blunted in 72-hpf larvae. Immediate touch-response trajectory was reduced. Representative kymographs recording fish position over 30-min recording showed reduced movements per recording." "Germline" "yes" "rs587777202" "0" "" "" "g.196847946C>A" "" "pathogenic" "" "0000048006" "3" "99" "2" "197777668" "197777670" "del" "0" "00081" "PGAP1_000005" "g.197777668_197777670del" "" "{PMID:Murakami et al. 2014:24784135}" "" "" "The mutation was not found in in 372 healthy Syrian adults using Sanger sequencing. Molecular modeling showed that this mutation disrupts the packing of the hydrophobic core and consequently of the entire β-sheet topology, thus leading to a loss of tertiary structure and enzymatic activity. Surface expression of GPI-APs on B-lymphoblastoid cell lines derived from an affected person, parents and controls showed no significant difference. Structural abnormality of GPI-anchors was tested. All GPI-APs on the affected LCLs had abnormal GPI anchors resistant to PI-PLC. This is an indication that the p.Leu197del mutation causes null or almost null activity of the PGAP1 enzyme. GPI-APs on LCLs from heterozygous parents were only partially sensitive to PI-PLC indicating haploinsufficiency. These defective sensitivities were restored by wt-PGAP1 cDNA transfection." "Germline" "yes" "rs587777378" "0" "" "" "g.196912944_196912946del" "" "pathogenic" "" "0000130231" "3" "70" "2" "197708788" "197708788" "delins" "0" "01758" "PGAP1_000006" "g.197708788delinsTTGTTTGGGATTAT" "" "{PMID:Trujillano 2017:27848944}" "" "" "" "Germline" "" "" "0" "" "" "g.196844064delinsTTGTTTGGGATTAT" "" "likely pathogenic" "ACMG" "0000300730" "0" "30" "2" "197761868" "197761868" "subst" "0" "02326" "PGAP1_000002" "g.197761868G>A" "" "" "" "PGAP1(NM_024989.4):c.914C>T (p.A305V)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.196897144G>A" "" "likely benign" "" "0000328034" "0" "50" "2" "197709250" "197709250" "subst" "0" "01804" "PGAP1_000007" "g.197709250C>T" "" "" "" "PGAP1(NM_024989.3):c.2335G>A (p.(Val779Met))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.196844526C>T" "" "VUS" "" "0000328035" "0" "50" "2" "197710703" "197710703" "subst" "0" "01804" "PGAP1_000008" "g.197710703G>A" "" "" "" "PGAP1(NM_024989.3):c.2189C>T (p.(Pro730Leu))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.196845979G>A" "" "VUS" "" "0000347566" "0" "90" "2" "197750149" "197750149" "subst" "0" "02327" "PGAP1_000009" "g.197750149T>C" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.196885425T>C" "" "pathogenic" "" "0000357754" "21" "70" "2" "197781284" "197781285" "ins" "0" "00081" "PGAP1_000010" "g.197781284_197781285insT" "" "{PMID:Kettwig et al. 2016:27206732}" "" "" "" "Germline" "" "" "0" "" "" "g.196916560_196916561insT" "" "likely pathogenic" "" "0000357755" "11" "70" "2" "197755552" "197755552" "subst" "0" "00081" "PGAP1_000011" "g.197755552C>G" "" "{PMID:Kettwig et al. 2016:27206732}" "" "" "" "Germline" "" "" "0" "" "" "g.196890828C>G" "" "likely pathogenic" "" "0000357756" "21" "70" "2" "197781284" "197781285" "ins" "0" "00081" "PGAP1_000010" "g.197781284_197781285insT" "" "{PMID:Kettwig et al. 2016:27206732}" "" "" "" "Germline" "" "" "0" "" "" "g.196916560_196916561insT" "" "likely pathogenic" "" "0000357757" "11" "70" "2" "197755552" "197755552" "subst" "0" "00081" "PGAP1_000011" "g.197755552C>G" "" "{PMID:Kettwig et al. 2016:27206732}" "" "" "" "Germline" "" "" "0" "" "" "g.196890828C>G" "" "likely pathogenic" "" "0000357758" "3" "70" "2" "197755637" "197755637" "subst" "0" "00081" "PGAP1_000012" "g.197755637T>C" "" "{PMID:Granzow et al. 2015:26050939}" "" "" "" "Germline" "" "" "0" "" "" "g.196890913T>C" "" "likely pathogenic" "" "0000357759" "3" "70" "2" "197755637" "197755637" "subst" "0" "00081" "PGAP1_000012" "g.197755637T>C" "" "{PMID:Granzow et al. 2015:26050939}" "" "" "" "Germline" "" "" "0" "" "" "g.196890913T>C" "" "likely pathogenic" "" "0000357911" "11" "70" "2" "197737731" "197737731" "subst" "0" "00081" "PGAP1_000013" "g.197737731A>T" "" "{PMID:Williams et al. 2015:25823418}" "" "" "" "Germline" "" "" "0" "" "" "g.196873007A>T" "" "likely pathogenic" "" "0000357912" "21" "70" "2" "197740500" "197740500" "subst" "1.24639E-5" "00081" "PGAP1_000014" "g.197740500G>A" "" "{PMID:Williams et al. 2015:25823418}" "" "" "" "Germline" "" "" "0" "" "" "g.196875776G>A" "" "likely pathogenic" "" "0000472364" "0" "50" "2" "197757065" "197757065" "del" "0" "01807" "PGAP1_000015" "g.197757065del" "" "" "" "1089+5delG" "" "Unknown" "" "" "0" "" "" "g.196892341del" "" "VUS" "" "0000472365" "0" "50" "2" "197757069" "197757069" "subst" "0" "01807" "PGAP1_000016" "g.197757069C>T" "" "" "" "" "" "Unknown" "" "" "0" "" "" "g.196892345C>T" "" "VUS" "" "0000513829" "0" "50" "2" "197708729" "197708729" "subst" "4.07388E-5" "01804" "PGAP1_000018" "g.197708729C>T" "" "" "" "PGAP1(NM_024989.3):c.2408G>A (p.(Arg803His))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196844005C>T" "" "VUS" "" "0000513830" "0" "30" "2" "197709279" "197709279" "subst" "0" "01943" "PGAP1_000019" "g.197709279C>T" "" "" "" "PGAP1(NM_001321099.1):c.1784G>A (p.S595N)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196844555C>T" "" "likely benign" "" "0000513831" "0" "30" "2" "197729785" "197729785" "subst" "0" "01804" "PGAP1_000020" "g.197729785C>A" "" "" "" "PGAP1(NM_024989.3):c.1787G>T (p.(Gly596Val))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196865061C>A" "" "likely benign" "" "0000513832" "0" "30" "2" "197735679" "197735679" "subst" "0.00437749" "01804" "PGAP1_000021" "g.197735679G>C" "" "" "" "PGAP1(NM_024989.3):c.1753C>G (p.(Gln585Glu))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196870955G>C" "" "likely benign" "" "0000513833" "0" "50" "2" "197735707" "197735707" "subst" "3.29029E-5" "02327" "PGAP1_000022" "g.197735707G>A" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196870983G>A" "" "VUS" "" "0000513834" "0" "30" "2" "197761876" "197761876" "subst" "0.00221983" "02326" "PGAP1_000023" "g.197761876A>G" "" "" "" "PGAP1(NM_001321099.2):c.384T>C (p.L128=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196897152A>G" "" "likely benign" "" "0000513835" "0" "90" "2" "197781192" "197781192" "subst" "4.07554E-6" "02327" "PGAP1_000024" "g.197781192G>A" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196916468G>A" "" "pathogenic" "" "0000513836" "0" "50" "2" "197781288" "197781288" "subst" "0.000833155" "02327" "PGAP1_000025" "g.197781288T>C" "" "" "" "PGAP1(NM_024989.3):c.331A>G (p.K111E), PGAP1(NM_024989.4):c.331A>G (p.(Lys111Glu))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196916564T>C" "" "VUS" "" "0000601057" "3" "70" "2" "197740526" "197740526" "subst" "0" "02575" "PGAP1_000026" "g.197740526A>C" "" "" "" "" "" "Germline" "yes" "" "0" "" "" "g.196875802A>C" "" "likely pathogenic" "" "0000601058" "3" "70" "2" "197740526" "197740526" "subst" "0" "02575" "PGAP1_000026" "g.197740526A>C" "" "" "" "" "" "Germline" "yes" "" "0" "" "" "g.196875802A>C" "" "likely pathogenic" "" "0000654483" "0" "30" "2" "197711819" "197711819" "subst" "0" "01943" "PGAP1_000027" "g.197711819G>A" "" "" "" "PGAP1(NM_001321099.1):c.1536C>T (p.L512=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196847095G>A" "" "likely benign" "" "0000654484" "0" "30" "2" "197761936" "197761939" "del" "0" "02326" "PGAP1_000028" "g.197761936_197761939del" "" "" "" "PGAP1(NM_001321099.2):c.339-14_339-11delACTT" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.196897212_196897215del" "" "likely benign" "" "0000676433" "0" "30" "2" "197777763" "197777763" "subst" "4.14948E-6" "01943" "PGAP1_000029" "g.197777763A>C" "" "" "" "PGAP1(NM_024989.3):c.492T>G (p.A164=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000688593" "0" "50" "2" "197784874" "197784874" "subst" "4.30615E-6" "01943" "PGAP1_000030" "g.197784874T>C" "" "" "" "PGAP1(NM_024989.3):c.148A>G (p.K50E)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000701845" "3" "50" "2" "197710616" "197710616" "subst" "1.22716E-5" "00006" "PGAP1_000031" "g.197710616T>C" "" "{PMID:Riazuddin 2017:27457812}" "" "" "" "Germline" "" "" "0" "" "" "g.196845892T>C" "" "VUS" "" "0000763108" "3" "70" "2" "197761923" "197761923" "subst" "0" "00006" "PGAP1_000032" "g.197761923T>C" "" "{PMID:Anazi 2017:27431290}" "" "" "ACMG PVS1, PM2" "Germline" "" "" "0" "" "" "g.196897199T>C" "" "likely pathogenic" "ACMG" "0000800254" "0" "30" "2" "197706066" "197706066" "subst" "4.07332E-6" "01943" "PGAP1_000033" "g.197706066T>C" "" "" "" "PGAP1(NM_001321099.1):c.2139A>G (p.P713=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000849634" "0" "50" "2" "197755620" "197755620" "subst" "0" "01943" "PGAP1_000035" "g.197755620A>G" "" "" "" "PGAP1(NM_001321099.1):c.583T>C (p.Y195H)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000849635" "0" "50" "2" "197781288" "197781288" "subst" "0.000833155" "01943" "PGAP1_000025" "g.197781288T>C" "" "" "" "PGAP1(NM_024989.3):c.331A>G (p.K111E), PGAP1(NM_024989.4):c.331A>G (p.(Lys111Glu))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000858225" "0" "30" "2" "197729765" "197729765" "subst" "0" "01943" "PGAP1_000034" "g.197729765C>T" "" "" "" "PGAP1(NM_001321099.1):c.1285G>A (p.V429I)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000884664" "0" "50" "2" "197791286" "197791286" "subst" "7.30905E-5" "02329" "PGAP1_000036" "g.197791286A>G" "" "" "" "PGAP1(NM_024989.4):c.55T>C (p.F19L)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000908865" "3" "90" "2" "197750202" "197750202" "subst" "0" "00006" "PGAP1_000037" "g.197750202T>C" "" "{PMID:Bournazos 2022:34906502}" "" "" "cryptic splice acceptor; transcripts cycloheximide sensitive" "Germline" "" "" "0" "" "" "g.196885478T>C" "" "pathogenic (recessive)" "" "0000957322" "3" "90" "2" "197750148" "197750148" "subst" "0" "04630" "PGAP1_000038" "g.197750148C>T" "0" "" "" "" "cDNA sequencing shows skipping of exon 12" "Germline" "yes" "" "0" "" "" "g.196885424C>T" "" "likely pathogenic" "ACMG" "0000974846" "0" "70" "2" "197705957" "197705963" "del" "0" "01804" "PGAP1_000039" "g.197705957_197705963del" "" "" "" "PGAP1(NM_024989.4):c.2766_*3del (p.(Met922IlefsTer6))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely pathogenic" "" "0000974847" "0" "30" "2" "197781288" "197781288" "subst" "0.000833155" "01804" "PGAP1_000025" "g.197781288T>C" "" "" "" "PGAP1(NM_024989.3):c.331A>G (p.K111E), PGAP1(NM_024989.4):c.331A>G (p.(Lys111Glu))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0001032881" "0" "50" "2" "197710616" "197710616" "subst" "1.22716E-5" "01804" "PGAP1_000031" "g.197710616T>C" "" "" "" "PGAP1(NM_024989.4):c.2276A>G (p.(Tyr759Cys))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001032882" "0" "30" "2" "197763105" "197763109" "del" "0" "01804" "PGAP1_000040" "g.197763105_197763109del" "" "" "" "PGAP1(NM_024989.4):c.808-7_808-3del" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" ## Variants_On_Transcripts ## Do not remove or alter this header ## ## Please note that not necessarily all variants found in the given individuals are shown. This output is restricted to variants in the selected gene. ## Note: Only showing Variants_On_Transcript columns active for Genes PGAP1 ## Count = 47 "{{id}}" "{{transcriptid}}" "{{effectid}}" "{{position_c_start}}" "{{position_c_start_intron}}" "{{position_c_end}}" "{{position_c_end_intron}}" "{{VariantOnTranscript/DNA}}" "{{VariantOnTranscript/RNA}}" "{{VariantOnTranscript/Protein}}" "{{VariantOnTranscript/Exon}}" "0000047866" "00016026" "90" "274" "0" "276" "0" "c.274_276del" "r.(?)" "p.(Pro92del)" "2" "0000047867" "00016026" "90" "921" "0" "925" "0" "c.921_925del" "r.(?)" "p.(Lys308Asnfs*25)" "7" "0000047868" "00016026" "30" "914" "0" "914" "0" "c.914C>T" "r.(?)" "p.(Ala305Val)" "7" "0000048005" "00016026" "90" "1952" "1" "1952" "1" "c.1952+1G>T" "r.spl?" "p.?" "" "0000048006" "00016026" "99" "589" "0" "591" "0" "c.589_591del" "r.(?)" "p.(Leu197del)" "" "0000130231" "00016026" "70" "2349" "0" "2349" "0" "c.2349delinsATAATCCCAAACAA" "r.(?)" "p.(His783Glnfs*2)" "" "0000300730" "00016026" "30" "914" "0" "914" "0" "c.914C>T" "r.(?)" "p.(Ala305Val)" "" "0000328034" "00016026" "50" "2335" "0" "2335" "0" "c.2335G>A" "r.(?)" "p.(Val779Met)" "" "0000328035" "00016026" "50" "2189" "0" "2189" "0" "c.2189C>T" "r.(?)" "p.(Pro730Leu)" "" "0000347566" "00016026" "90" "1271" "0" "1271" "0" "c.1271A>G" "r.(?)" "p.(Lys424Arg)" "" "0000357754" "00016026" "70" "334" "0" "335" "0" "c.334_335insA" "r.(?)" "p.(Ala112Aspfs*5)" "" "0000357755" "00016026" "70" "1173" "0" "1173" "0" "c.1173G>C" "r.(=)" "p.(=)" "" "0000357756" "00016026" "70" "334" "0" "335" "0" "c.334_335insA" "r.(?)" "p.(Ala112Aspfs*5)" "" "0000357757" "00016026" "70" "1173" "0" "1173" "0" "c.1173G>C" "r.(=)" "p.(=)" "" "0000357758" "00016026" "70" "1090" "-2" "1090" "-2" "c.1090-2A>G" "r.spl?" "p.?" "" "0000357759" "00016026" "70" "1090" "-2" "1090" "-2" "c.1090-2A>G" "r.spl?" "p.?" "" "0000357911" "00016026" "70" "1572" "0" "1572" "0" "c.1572T>A" "r.(?)" "p.(Tyr524*)" "" "0000357912" "00016026" "70" "1396" "0" "1396" "0" "c.1396C>T" "r.(?)" "p.(Gln466*)" "" "0000472364" "00016026" "50" "1089" "5" "1089" "5" "c.1089+5del" "r.(?)" "p.()" "" "0000472365" "00016026" "50" "1089" "1" "1089" "1" "c.1089+1G>A" "r.(?)" "p.()" "" "0000513829" "00016026" "50" "2408" "0" "2408" "0" "c.2408G>A" "r.(?)" "p.(Arg803His)" "" "0000513830" "00016026" "30" "2306" "0" "2306" "0" "c.2306G>A" "r.(?)" "p.(Ser769Asn)" "" "0000513831" "00016026" "30" "1787" "0" "1787" "0" "c.1787G>T" "r.(?)" "p.(Gly596Val)" "" "0000513832" "00016026" "30" "1753" "0" "1753" "0" "c.1753C>G" "r.(?)" "p.(Gln585Glu)" "" "0000513833" "00016026" "50" "1729" "-4" "1729" "-4" "c.1729-4C>T" "r.spl?" "p.?" "" "0000513834" "00016026" "30" "906" "0" "906" "0" "c.906T>C" "r.(?)" "p.(Leu302=)" "" "0000513835" "00016026" "90" "427" "0" "427" "0" "c.427C>T" "r.(?)" "p.(Gln143Ter)" "" "0000513836" "00016026" "50" "331" "0" "331" "0" "c.331A>G" "r.(?)" "p.(Lys111Glu)" "" "0000601057" "00016026" "70" "1370" "0" "1370" "0" "c.1370T>G" "r.(?)" "p.(Phe457Cys)" "14" "0000601058" "00016026" "70" "1370" "0" "1370" "0" "c.1370T>G" "r.(1370u>g)" "p.(Phe457Cys)" "14" "0000654483" "00016026" "30" "2058" "0" "2058" "0" "c.2058C>T" "r.(?)" "p.(Leu686=)" "" "0000654484" "00016026" "30" "861" "-14" "861" "-11" "c.861-14_861-11del" "r.(=)" "p.(=)" "" "0000676433" "00016026" "30" "492" "0" "492" "0" "c.492T>G" "r.(?)" "p.(Ala164=)" "" "0000688593" "00016026" "50" "148" "0" "148" "0" "c.148A>G" "r.(?)" "p.(Lys50Glu)" "" "0000701845" "00016026" "50" "2276" "0" "2276" "0" "c.2276A>G" "r.(?)" "p.(Tyr759Cys)" "" "0000763108" "00016026" "70" "861" "-2" "861" "-2" "c.861-2A>G" "r.spl" "p.?" "" "0000800254" "00016026" "30" "2661" "0" "2661" "0" "c.2661A>G" "r.(?)" "p.(Pro887=)" "" "0000849634" "00016026" "50" "1105" "0" "1105" "0" "c.1105T>C" "r.(?)" "p.(Tyr369His)" "" "0000849635" "00016026" "50" "331" "0" "331" "0" "c.331A>G" "r.(?)" "p.(Lys111Glu)" "" "0000858225" "00016026" "30" "1807" "0" "1807" "0" "c.1807G>A" "r.(?)" "p.(Val603Ile)" "" "0000884664" "00016026" "50" "55" "0" "55" "0" "c.55T>C" "r.(?)" "p.(Phe19Leu)" "" "0000908865" "00016026" "90" "1221" "-3" "1221" "-3" "c.1221-3A>G" "r.1220_1221ins[1221-2_1221-1]" "p.Cys407*" "" "0000957322" "00016026" "90" "1272" "0" "1272" "0" "c.1272G>A" "r.[1272g>a,1221_1272del]" "p.[Lys424=,Gln409*]" "12" "0000974846" "00016026" "70" "2766" "0" "2772" "0" "c.2766_*3del" "r.(?)" "p.(Met922Ilefs*6)" "" "0000974847" "00016026" "30" "331" "0" "331" "0" "c.331A>G" "r.(?)" "p.(Lys111Glu)" "" "0001032881" "00016026" "50" "2276" "0" "2276" "0" "c.2276A>G" "r.(?)" "p.(Tyr759Cys)" "" "0001032882" "00016026" "30" "808" "-7" "808" "-3" "c.808-7_808-3del" "r.spl?" "p.?" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 22 "{{screeningid}}" "{{variantid}}" "0000025012" "0000047866" "0000025012" "0000047867" "0000025012" "0000047868" "0000025129" "0000048005" "0000025130" "0000048006" "0000081145" "0000130231" "0000155911" "0000357754" "0000155911" "0000357755" "0000155912" "0000357756" "0000155912" "0000357757" "0000155913" "0000357758" "0000155914" "0000357759" "0000156064" "0000357911" "0000156064" "0000357912" "0000230746" "0000472364" "0000230746" "0000472365" "0000268367" "0000601057" "0000268368" "0000601058" "0000319181" "0000701845" "0000362734" "0000763108" "0000429392" "0000908865" "0000447950" "0000957322"