### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = PGAP2) # 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}}" "PGAP2" "post-GPI attachment to proteins 2" "11" "p15.4" "unknown" "NC_000011.9" "UD_136090074022" "" "http://www.LOVD.nl/PGAP2" "" "1" "17893" "27315" "615187" "1" "1" "1" "1" "" "" "g" "http://databases.lovd.nl/shared/refseq/PGAP2_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00081" "2018-12-31 00:36:23" "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}}" "00023992" "PGAP2" "transcript variant 12" "013" "NM_001256240.1" "" "NP_001243169.1" "" "" "" "-126" "1678" "765" "3829766" "3847601" "00081" "2014-12-18 20:34:20" "" "" ## Diseases ## Do not remove or alter this header ## ## Count = 4 "{{id}}" "{{symbol}}" "{{name}}" "{{inheritance}}" "{{id_omim}}" "{{tissues}}" "{{features}}" "{{remarks}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "00198" "?" "unclassified / mixed" "" "" "" "" "" "00006" "2013-09-13 14:21:47" "00006" "2024-11-23 09:38:12" "03582" "HPMRS3;GPIBD8" "hyperphosphatasia, with mental retardation syndrome, type 3 (HPMRS-3, glycosylphosphatidylinositol deficiency, type 8 (GPIBD-8))" "AR" "614207" "" "autosomal recessive" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "05517" "skeletal dysplasia" "dysplasia, skeletal" "" "" "" "" "" "00006" "2018-11-16 16:43:21" "" "" "05611" "NDD" "neurodevelopmental disorder (NDD)" "" "" "" "" "" "00006" "2019-06-19 12:27:20" "00006" "2024-12-13 11:12:21" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "PGAP2" "03582" ## 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}}" "00025130" "" "" "" "1" "" "00081" "{PMID:Hansen 2013: 23561846}" "Family with three girls with autosomal recessive hyperphosphatasia with mental retardation-3." "F" "yes" "Syria" "" "0" "" "" "African" "" "00025486" "" "" "" "1" "" "00081" "{PMID:Krawitz 2013:23561847}" "Index case" "F" "no" "Finland" "" "0" "" "" "white" "" "00028965" "" "" "" "1" "" "00081" "{PMID:Hansen et al 2013:23561846} {PMID:Rehman et al 2011: 21643797}" "Family with 4 affected siblings. (2 males and 2 females)" "" "yes" "Pakistan" "" "0" "" "" "" "" "00028966" "" "" "" "1" "" "00081" "{PMID: Krawitz et al 2013: 23561847}" "Index case" "M" "yes" "Turkey" "" "0" "" "" "" "" "00154948" "" "" "" "1" "" "00081" "{PMID:Jezela-Stanek 2016:26879448}" "" "F" "no" "" "" "0" "" "" "" "" "00154977" "" "" "" "2" "" "00081" "{PMID:Naseer 2016:27871432}" "" "M" "yes" "Saudi Arabia" "" "0" "" "" "" "patient_1" "00154978" "" "" "00154977" "1" "" "00081" "{PMID:Naseer 2016:27871432}" "" "F" "yes" "Saudi Arabia" "" "0" "" "" "" "patient_2" "00207490" "" "" "" "1" "" "00081" "{PMID:Perez et al., 2017:29119105}" "Consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase. " "M" "yes" "Saudi Arabia" ">25y" "0" "" "" "Bedouin" "IV-3" "00207491" "" "" "" "1" "" "00081" "{PMID:Perez et al., 2017:29119105}" "consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase. " "M" "yes" "Saudi Arabia" ">18y" "0" "" "" "Bedouin" "IV-5" "00207493" "" "" "" "1" "" "00081" "{PMID:Perez et al., 2017:29119105}" "consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase. " "F" "yes" "Saudi Arabia" ">15y" "0" "" "" "Bedouin" "IV-6" "00207494" "" "" "" "1" "" "00081" "{PMID:Perez et al., 2017:29119105}" "consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase. " "F" "yes" "Saudi Arabia" ">11y" "0" "" "" "Bedouin" "IV-7" "00207496" "" "" "" "1" "" "00081" "{PMID:Reid et al., 2016:27604308}" "Found in a gene panel targeting (614) genes causing inborn errors of metabolism" "M" "" "" ">02y03m" "0" "" "" "" "U6" "00269874" "" "" "" "1" "" "01807" "" "" "?" "" "" "" "0" "" "" "" "" "00274197" "" "" "" "1" "" "00006" "{PMID:Pronicka 2016:27290639}" "" "F" "" "Poland" "" "0" "" "" "" "Pat73" "00331542" "" "" "" "1" "" "00000" "{PMID:Maddirevula 2018:29620724}" "family" "M" "yes" "" "" "0" "" "" "Arab" "14DG0688" "00403850" "" "" "" "1" "" "00006" "{PMID:Froukh 2020:32056211}" "analysis 103 families with neurodevelopmental disorders" "" "" "Jordan" "" "0" "" "" "" "TF001" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 16 "{{individualid}}" "{{diseaseid}}" "00025130" "03582" "00025486" "03582" "00028965" "03582" "00028966" "03582" "00154948" "00198" "00154977" "03582" "00154978" "03582" "00207490" "03582" "00207491" "03582" "00207493" "03582" "00207494" "03582" "00207496" "03582" "00269874" "00198" "00274197" "00198" "00331542" "05517" "00403850" "05611" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00198, 03582, 05517, 05611 ## Count = 15 "{{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}}" "0000021241" "03582" "00025130" "00081" "Familial, autosomal recessive" "" "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." "" "" "" "" "" "" "" "" "" "" "" "0000021598" "03582" "00025486" "00081" "Familial, autosomal recessive" "28y" "Mild intellectual disability and seizures. Facial features included broad nasal bridge and tented upper lip vermilion. Elevated ALP." "" "" "" "" "" "" "" "" "" "" "" "0000024991" "03582" "00028965" "00081" "Familial, autosomal recessive" "" "Average IQ 22, None had epilepsy. Clinical examination was normal. No data about ALP values." "" "" "" "" "" "" "" "" "" "" "" "0000024992" "03582" "00028966" "00081" "Familial, autosomal recessive" "" "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." "" "" "" "" "" "" "" "" "" "" "" "0000127710" "03582" "00154977" "00081" "Familial, autosomal recessive" "" "" "" "" "" "" "" "" "" "" "" "" "" "0000127711" "03582" "00154978" "00081" "Familial, autosomal recessive" "" "" "" "" "" "" "" "" "" "" "" "" "" "0000155267" "03582" "00207490" "00081" "Familial, autosomal recessive" "23y" "Mild mental retardation, mood problems, depression, speech difficulties, past history of febrile convulsions, Elevated alkaline phosphatase (499 IU/L)" "" "" "" "" "" "" "" "" "HPMRS3" "" "" "0000155268" "03582" "00207491" "00081" "Familial, autosomal recessive" "17y" "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" "" "" "" "" "" "" "" "" "HPMRS3" "" "" "0000155270" "03582" "00207493" "00081" "Familial, autosomal recessive" "10y" "Mild mental retardation, Mood problems- depression Speech difficulaties, Elevated alkaline phosphatase (>1000 IU/L). No organ anomaly, no signs of dysmorphism." "" "" "" "" "" "" "" "" "HPMRS3" "" "" "0000155271" "03582" "00207494" "00081" "Familial, autosomal recessive" "10y" "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." "" "" "" "" "" "" "" "" "HPMRS3" "" "" "0000155274" "03582" "00207496" "00081" "Familial, autosomal recessive" "02y" "Global severe developmental delay, tonic seizures. Multiorgan malformations including VSD, Hirschprung’s. Dysmorphism. Recurrent hypoglycaemia; hypogammaglobulinaemia, hyperphosphatasia. Dandy-Walker malformation, reduced white matter bulk." "" "" "" "" "" "" "" "" "" "" "" "0000207670" "00198" "00269874" "01807" "Unknown" "" "Nystagmus (HP:0000639); Global developmental delay (HP:0001263)" "" "" "" "" "" "" "" "" "" "" "" "0000209142" "00198" "00274197" "00006" "Familial, autosomal recessive" "" "neonatal onset; mitochondrial disease criteria score 3; muscle biopsy" "0d" "" "" "" "" "" "" "" "" "expected mitochondrial disorder" "" "0000249734" "05517" "00331542" "00000" "Familial, autosomal recessive" "" "Global developmental delay, Seizures, Hyperphosphatemia, Elevated alkaline phosphataseNo" "" "" "" "" "" "" "" "" "" "skeletal dysplasia" "" "0000296530" "05611" "00403850" "00006" "Familial, autosomal recessive" "" "" "" "" "" "" "" "" "" "" "" "neurodevelopmental delay" "" ## 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}}" "0000025131" "00025130" "1" "00081" "00081" "2014-12-05 20:23:15" "" "" "SEQ-NG" "DNA" "" "" "0000025490" "00025486" "1" "00081" "00081" "2014-12-11 17:08:25" "" "" "SEQ-NG" "DNA" "" "" "0000028999" "00028965" "1" "00081" "00081" "2015-01-09 22:39:20" "" "" "SEQ-NG" "DNA" "" "" "0000029000" "00028966" "1" "00081" "00081" "2015-01-09 23:54:44" "" "" "SEQ-NG" "DNA" "" "" "0000155808" "00154948" "1" "00081" "00081" "2018-03-06 23:32:19" "" "" "SEQ-NG" "DNA" "peripheral blood" "WES" "0000155840" "00154977" "1" "00081" "00081" "2018-03-07 17:17:46" "" "" "SEQ-NG" "DNA" "Blood" "WES" "0000155841" "00154978" "1" "00081" "00081" "2018-03-07 18:10:01" "" "" "SEQ-NG" "DNA" "Blood" "WES" "0000208526" "00207490" "1" "00081" "00081" "2018-11-23 16:20:04" "" "" "PCRq;SEQ;SEQ-NG" "DNA" "" "WES, Homozygosity mapping" "0000208527" "00207491" "1" "00081" "00081" "2018-11-23 16:25:49" "" "" "PCRq;SEQ;SEQ-NG" "DNA" "" "WES, Homozygosity mapping" "0000208529" "00207493" "1" "00081" "00081" "2018-11-23 16:31:03" "" "" "PCRq;SEQ;SEQ-NG" "DNA" "" "" "0000208531" "00207494" "1" "00081" "00081" "2018-11-23 16:34:40" "" "" "PCRq;SEQ;SEQ-NG" "DNA" "" "WES, Homozygosity mapping" "0000208533" "00207496" "1" "00081" "00081" "2018-11-23 16:38:15" "" "" "SEQ" "DNA" "" "Gene panel, Sanger seq" "0000271027" "00269874" "1" "01807" "01807" "2019-12-10 12:31:13" "" "" "SEQ" "DNA" "" "" "0000275352" "00274197" "1" "00006" "00006" "2019-12-24 17:05:37" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000332761" "00331542" "1" "00000" "00006" "2021-02-11 15:29:38" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000405088" "00403850" "1" "00006" "00006" "2022-02-24 16:43:58" "" "" "SEQ;SEQ-NG" "DNA" "" "" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 11 "{{screeningid}}" "{{geneid}}" "0000025131" "PGAP2" "0000025490" "PGAP2" "0000028999" "PGAP2" "0000029000" "PGAP2" "0000208526" "PGAP2" "0000208527" "PGAP2" "0000208529" "PGAP2" "0000208531" "PGAP2" "0000208533" "PGAP2" "0000275352" "PGAP2" "0000332761" "PGAP2" ## 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 = 38 "{{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}}" "0000048877" "3" "90" "11" "3845243" "3845243" "subst" "0" "00081" "PGAP2_000001" "g.3845243A>G" "" "{PMID:Hansen et al. 2013:23561846}" "" "" "Rescue experiments with the altered proteins in PGAP2-deficient Chinese hamster ovary cell lines showed less expression of cell-surface GPI-anchored proteins DAF and CD59 than of the wild-type protein. atient lymphoblastoid cells showed essentially normal expression of the GPI-anchored proteins supporting a hypomorphic effect of this mutation." "Germline" "yes" "" "0" "" "" "g.3824013A>G" "" "pathogenic" "" "0000048878" "10" "90" "11" "3832535" "3832535" "subst" "5.28275E-5" "00081" "PGAP2_000003" "g.3832535C>T" "" "{PMID:Krawitz et al 2013: 23561847}" "" "" "Substitution in a highly conserved residue. Transfection with protein construct showed partial restoration of GPI-anchored marker proteins. Higer residual activity with this mutation." "Germline" "yes" "" "0" "" "" "g.3811305C>T" "" "pathogenic" "" "0000052316" "3" "90" "11" "3846254" "3846254" "subst" "3.65545E-5" "00081" "PGAP2_000002" "g.3846254G>C" "" "{PMID: Hansen et al 2013 :23561846}" "" "" "Substitution between transmembrane segments 3 and 4 in the Golgi lumen. Predicted to be pathogenic. In vitro CHO cells study showed that the mutant protein was expressed but had significantly decreased activity compared to wildtype. Lymphoblastoid cells of patient showed normal levels of DAF and CD59, which suggest a hypomorphic effect." "Germline" "yes" "" "0" "" "" "g.3825024G>C" "" "pathogenic" "" "0000052317" "21" "90" "11" "3845560" "3845560" "subst" "2.43633E-5" "00081" "PGAP2_000004" "g.3845560C>T" "" "{PMID:Krawitz et al 2013: 23561847}" "" "" "Sustitution at highly conserved residue. Transfection of altered protein construct showed partial restoration of GPI-anchored marker proteins." "Germline" "yes" "" "0" "" "" "g.3824330C>T" "" "pathogenic" "" "0000052318" "3" "90" "11" "3845327" "3845327" "subst" "0" "00081" "PGAP2_000005" "g.3845327T>C" "" "{PMID:Krawitz et al 2013: 23561847}" "" "" "Substitution at highly conserved residue. Transfection of the altered protein constructsinto PGAP2-null cells showed only partial restoration of GPI-anchored marker proteins, CD55 and CD59, on the cell surface." "Germline" "yes" "" "0" "" "" "g.3824097T>C" "" "pathogenic" "" "0000296931" "0" "50" "11" "3846558" "3846558" "subst" "8.15036E-6" "02325" "PGAP2_000009" "g.3846558T>C" "" "" "" "PGAP2(NM_001256236.1):c.989T>C (p.V330A)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.3825328T>C" "" "VUS" "" "0000356887" "21" "70" "11" "3832491" "3832491" "subst" "0" "00081" "PGAP2_000010" "g.3832491T>G" "" "{PMID:Jezela-Stanek et al. 2016:26879448}" "" "" "" "Germline" "" "" "0" "" "" "g.3811261T>G" "" "likely pathogenic" "" "0000356888" "11" "70" "11" "3845168" "3845168" "subst" "1.25971E-5" "00081" "PGAP2_000011" "g.3845168G>A" "" "{PMID:Jezela-Stanek et al. 2016:26879448}" "" "" "" "Germline" "" "" "0" "" "" "g.3823938G>A" "" "likely pathogenic" "" "0000356927" "3" "70" "11" "3845138" "3845138" "subst" "0" "00081" "PGAP2_000012" "g.3845138C>T" "" "{PMID:Naseer et al. 2016:27871432}" "" "c.191C>T" "Variant Error [EREF/EREF]: This genomic variant does not match the reference sequence; the transcript variant does not match the reference sequence either. Please fix this entry and then remove this message." "Germline" "" "" "0" "" "" "" "" "likely pathogenic" "" "0000356928" "0" "70" "11" "3845138" "3845138" "subst" "0" "00081" "PGAP2_000012" "g.3845138C>T" "" "{PMID:Naseer et al. 2016:27871432}" "" "c.191C>T" "Variant Error [EREF/EREF]: This genomic variant does not match the reference sequence; the transcript variant does not match the reference sequence either. Please fix this entry and then remove this message." "Germline" "" "" "0" "" "" "" "" "likely pathogenic" "" "0000438403" "3" "90" "11" "3846278" "3846278" "subst" "8.12156E-6" "00081" "PGAP2_000013" "g.3846278G>A" "0.00000824 in dbSNP. In ExAC database: allele frequency of 0.000008122" "" "" "NM_001256240.1:c.554G>A, p.(Arg185Gln)" "The mutation replaces a highly conserved arginine residue with glutamine within the Frag1 (FGF receptor activating) domain of PGAP2. The mutation was also found to be possibly damaging by Polyphen-2 predictions with a score of 0.942." "Germline" "" "rs745521288" "0" "" "" "g.3825048G>A" "" "pathogenic" "" "0000438405" "3" "90" "11" "3846278" "3846278" "subst" "8.12156E-6" "00081" "PGAP2_000013" "g.3846278G>A" "0.00000824 in dbSNP. In ExAC database: allele frequency of 0.000008122" "" "" "NM_001256240.1:c.554G>A, p.(Arg185Gln)" "The mutation replaces a highly conserved arginine residue with glutamine within the Frag1 (FGF receptor activating) domain of PGAP2. The mutation was also found to be possibly damaging by Polyphen-2 predictions with a score of 0.942." "Germline" "" "rs745521288" "0" "" "" "g.3825048G>A" "" "pathogenic" "" "0000438406" "3" "90" "11" "3846278" "3846278" "subst" "8.12156E-6" "00081" "PGAP2_000013" "g.3846278G>A" "0.00000824 in dbSNP. In ExAC database: allele frequency of 0.000008122" "" "" "NM_001256240.1:c.554G>A, p.(Arg185Gln)" "The mutation replaces a highly conserved arginine residue with glutamine within the Frag1 (FGF receptor activating) domain of PGAP2. The mutation was also found to be possibly damaging by Polyphen-2 predictions with a score of 0.942." "Germline" "" "rs745521288" "0" "" "" "g.3825048G>A" "" "pathogenic" "" "0000438409" "3" "90" "11" "3846278" "3846278" "subst" "8.12156E-6" "00081" "PGAP2_000013" "g.3846278G>A" "0.00000824 in dbSNP. In ExAC database: allele frequency of 0.000008122" "" "" "NM_001256240.1:c.554G>A, p.(Arg185Gln)" "The mutation replaces a highly conserved arginine residue with glutamine within the Frag1 (FGF receptor activating) domain of PGAP2. The mutation was also found to be possibly damaging by Polyphen-2 predictions with a score of 0.942." "Germline" "" "rs745521288" "0" "" "" "g.3825048G>A" "" "pathogenic" "" "0000438410" "3" "90" "11" "3846284" "3846284" "subst" "0" "00081" "PGAP2_000014" "g.3846284C>T" "" "" "" "" "SIFT=deleterious, Polyphen-2=Probably damaging , CADD score=23.3\r\nVariant Error [EREF/EREF]: This genomic variant does not match the reference sequence; the transcript variant does not match the reference sequence either. Please fix this entry and then remove this message." "Germline" "" "" "0" "" "" "" "" "pathogenic" "" "0000543887" "0" "50" "11" "3832542" "3832542" "subst" "2.0315E-5" "01943" "NUP98_000005" "g.3832542G>A" "" "" "" "PGAP2(NM_001256236.1):c.224G>A (p.R75H)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.3811312G>A" "" "VUS" "" "0000543888" "0" "50" "11" "3846291" "3846291" "subst" "1.62431E-5" "01943" "NUP98_000006" "g.3846291C>T" "" "" "" "PGAP2(NM_001256237.1):c.817C>T (p.Q273*)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.3825061C>T" "" "VUS" "" "0000543889" "0" "50" "11" "3846355" "3846355" "subst" "0" "02327" "NUP98_000007" "g.3846355G>C" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.3825125G>C" "" "VUS" "" "0000624873" "3" "70" "11" "3845167" "3845167" "subst" "0" "01807" "PGAP2_000015" "g.3845167C>T" "" "" "" "" "" "Unknown" "" "" "0" "" "" "g.3823937C>T" "" "likely pathogenic" "" "0000629316" "21" "90" "11" "3832491" "3832491" "subst" "0" "00006" "PGAP2_000010" "g.3832491T>G" "1/113 cases" "{PMID:Pronicka 2016:27290639}" "" "" "" "Germline" "" "" "0" "" "" "g.3811261T>G" "" "pathogenic" "" "0000629354" "11" "90" "11" "3845168" "3845168" "subst" "1.25971E-5" "00006" "PGAP2_000011" "g.3845168G>A" "1/113 cases" "{PMID:Pronicka 2016:27290639}" "" "" "" "Germline" "" "" "0" "" "" "g.3823938G>A" "" "pathogenic" "" "0000679182" "0" "50" "11" "3838630" "3838630" "dup" "0" "01943" "NUP98_000008" "g.3838630dup" "" "" "" "PGAP2(NM_001256236.1):c.384dupC (p.D129Rfs*37)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000723441" "0" "50" "11" "3838599" "3838599" "subst" "0.000146649" "02329" "PGAP2_000006" "g.3838599T>C" "" "" "" "PGAP2(NM_001256236.1):c.353T>C (p.M118T)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000723442" "0" "50" "11" "3838766" "3838766" "subst" "0" "02329" "PGAP2_000007" "g.3838766G>A" "" "" "" "PGAP2(NM_001256236.1):c.519+1G>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000723443" "0" "50" "11" "3845245" "3845245" "subst" "0.000365524" "01943" "NUP98_000009" "g.3845245C>T" "" "" "" "PGAP2(NM_001346401.1):c.308C>T (p.P103L)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000723444" "0" "50" "11" "3845677" "3845677" "subst" "3.28745E-5" "02329" "PGAP2_000008" "g.3845677C>T" "" "" "" "PGAP2(NM_001256237.1):c.767C>T (p.S256L)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000730043" "3" "90" "11" "3845595" "3845595" "subst" "0" "00000" "PGAP2_000016" "g.3845595G>A" "" "{PMID:Maddirevula 2018:29620724}" "" "NM_014489.3:c.697G>A:p.(Val233Ile)" "" "Germline" "" "" "0" "" "" "g.3824365G>A" "" "likely pathogenic (recessive)" "" "0000805114" "0" "50" "11" "3829526" "3829526" "subst" "0" "02327" "NUP98_000010" "g.3829526A>G" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000841149" "3" "90" "11" "3845167" "3845167" "subst" "0" "00006" "PGAP2_000015" "g.3845167C>T" "" "{PMID:Froukh 2020:32056211}" "" "" "" "Germline" "" "" "0" "" "" "g.3823937C>T" "" "pathogenic (recessive)" "" "0000852896" "0" "30" "11" "3848892" "3848892" "subst" "4.07067E-6" "01943" "NUP98_000013" "g.3848892G>A" "" "" "" "RHOG(NM_001665.4):c.477C>T (p.A159=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000862526" "0" "90" "11" "3819074" "3819074" "subst" "0" "01943" "NUP98_000011" "g.3819074A>C" "" "" "" "PGAP2(NM_001256236.1):c.1A>C (p.M1?)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "pathogenic" "" "0000862527" "0" "50" "11" "3846253" "3846253" "subst" "0.000426448" "01943" "NUP98_000012" "g.3846253C>T" "" "" "" "PGAP2(NM_001346401.1):c.527C>T (p.S176L)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000925381" "0" "30" "11" "3849224" "3849224" "subst" "0.00010152" "02326" "NUP98_000015" "g.3849224G>A" "" "" "" "RHOG(NM_001665.4):c.145C>T (p.R49C)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000929860" "0" "30" "11" "3848859" "3848859" "subst" "0.000473481" "02326" "NUP98_000016" "g.3848859G>A" "" "" "" "RHOG(NM_001665.4):c.510C>T (p.A170=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000949652" "0" "30" "11" "3848826" "3848826" "subst" "6.61693E-5" "02326" "NUP98_000017" "g.3848826C>T" "" "" "" "RHOG(NM_001665.4):c.543G>A (p.P181=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000949653" "0" "30" "11" "3849236" "3849236" "subst" "0.00116951" "02326" "NUP98_000018" "g.3849236C>T" "" "" "" "RHOG(NM_001665.4):c.133G>A (p.A45T)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000966350" "0" "50" "11" "3849232" "3849232" "subst" "0" "02325" "NUP98_000019" "g.3849232A>G" "" "" "" "RHOG(NM_001665.4):c.137T>C (p.V46A)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001038436" "0" "50" "11" "3838668" "3838668" "del" "0.000296432" "01804" "NUP98_000024" "g.3838668del" "" "" "" "PGAP2(NM_014489.4):c.251del (p.(Val84Alafs*41))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" ## 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 PGAP2 ## Count = 38 "{{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}}" "0000048877" "00023992" "00" "296" "0" "296" "0" "c.296A>G" "r.(?)" "p.(Tyr99Cys)" "" "0000048878" "00023992" "90" "46" "0" "46" "0" "c.46C>T" "r.(?)" "p.(Arg16Trp)" "" "0000052316" "00023992" "90" "530" "0" "530" "0" "c.530G>C" "r.(?)" "p.(Arg177Pro)" "" "0000052317" "00023992" "90" "479" "0" "479" "0" "c.479C>T" "r.(?)" "p.(Thr160Ile)" "" "0000052318" "00023992" "90" "380" "0" "380" "0" "c.380T>C" "r.(?)" "p.(Leu127Ser)" "" "0000296931" "00023992" "50" "635" "0" "635" "0" "c.635T>C" "r.(?)" "p.(Val212Ala)" "" "0000356887" "00023992" "70" "2" "0" "2" "0" "c.2T>G" "r.(?)" "p.(Met1?)" "2" "0000356888" "00023992" "70" "221" "0" "221" "0" "c.221G>A" "r.(?)" "p.(Arg74His)" "3" "0000356927" "00023992" "70" "191" "0" "191" "0" "c.191C>T" "r.?" "p.(Ala64Val)" "" "0000356928" "00023992" "70" "191" "0" "191" "0" "c.191C>T" "r.?" "p.(Ala64Val)" "" "0000438403" "00023992" "90" "554" "0" "554" "0" "c.554G>A" "r.(?)" "p.(Arg185Gln)" "" "0000438405" "00023992" "90" "554" "0" "554" "0" "c.554G>A" "r.(?)" "p.(Arg185Gln)" "" "0000438406" "00023992" "90" "554" "0" "554" "0" "c.554G>A" "r.(?)" "p.(Arg185Gln)" "" "0000438409" "00023992" "90" "554" "0" "554" "0" "c.554G>A" "r.(?)" "p.(Arg185Gln)" "" "0000438410" "00023992" "90" "560" "0" "560" "0" "c.560C>T" "r.(?)" "p.Ala187Val" "" "0000543887" "00023992" "50" "53" "0" "53" "0" "c.53G>A" "r.(?)" "p.(Arg18His)" "" "0000543888" "00023992" "50" "567" "0" "567" "0" "c.567C>T" "r.(?)" "p.(Ile189=)" "" "0000543889" "00023992" "50" "631" "0" "631" "0" "c.631G>C" "r.(?)" "p.(Gly211Arg)" "" "0000624873" "00023992" "70" "220" "0" "220" "0" "c.220C>T" "r.(?)" "p.(Arg74Cys)" "" "0000629316" "00023992" "90" "2" "0" "2" "0" "c.2T>G" "r.(?)" "p.(Met1?)" "" "0000629354" "00023992" "90" "221" "0" "221" "0" "c.221G>A" "r.(?)" "p.(Arg74His)" "" "0000679182" "00023992" "50" "165" "5976" "165" "5976" "c.165+5976dup" "r.(=)" "p.(=)" "" "0000723441" "00023992" "50" "165" "5945" "165" "5945" "c.165+5945T>C" "r.(=)" "p.(=)" "" "0000723442" "00023992" "50" "165" "6112" "165" "6112" "c.165+6112G>A" "r.(=)" "p.(=)" "" "0000723443" "00023992" "50" "298" "0" "298" "0" "c.298C>T" "r.(?)" "p.(Leu100Phe)" "" "0000723444" "00023992" "50" "525" "71" "525" "71" "c.525+71C>T" "r.(=)" "p.(=)" "" "0000730043" "00023992" "90" "514" "0" "514" "0" "c.514G>A" "" "" "" "0000805114" "00023992" "50" "-366" "0" "-366" "0" "c.-366A>G" "r.(?)" "p.(=)" "" "0000841149" "00023992" "90" "220" "0" "220" "0" "c.220C>T" "r.(?)" "p.(Arg74Cys)" "" "0000852896" "00023992" "30" "2969" "0" "2969" "0" "c.*2204G>A" "r.(=)" "p.(=)" "" "0000862526" "00023992" "90" "-10818" "0" "-10818" "0" "c.-10818A>C" "r.(?)" "p.(=)" "" "0000862527" "00023992" "50" "529" "0" "529" "0" "c.529C>T" "r.(?)" "p.(Arg177Cys)" "" "0000925381" "00023992" "30" "3301" "0" "3301" "0" "c.*2536G>A" "r.(=)" "p.(=)" "" "0000929860" "00023992" "30" "2936" "0" "2936" "0" "c.*2171G>A" "r.(=)" "p.(=)" "" "0000949652" "00023992" "30" "2903" "0" "2903" "0" "c.*2138C>T" "r.(=)" "p.(=)" "" "0000949653" "00023992" "30" "3313" "0" "3313" "0" "c.*2548C>T" "r.(=)" "p.(=)" "" "0000966350" "00023992" "50" "3309" "0" "3309" "0" "c.*2544A>G" "r.(=)" "p.(=)" "" "0001038436" "00023992" "50" "165" "6014" "165" "6014" "c.165+6014del" "r.(=)" "p.(=)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 19 "{{screeningid}}" "{{variantid}}" "0000025131" "0000048877" "0000025490" "0000048878" "0000025490" "0000052317" "0000028999" "0000052316" "0000029000" "0000052318" "0000155808" "0000356887" "0000155808" "0000356888" "0000155840" "0000356927" "0000155841" "0000356928" "0000208526" "0000438403" "0000208527" "0000438405" "0000208529" "0000438406" "0000208531" "0000438409" "0000208533" "0000438410" "0000271027" "0000624873" "0000275352" "0000629316" "0000275352" "0000629354" "0000332761" "0000730043" "0000405088" "0000841149"