### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = PIGW) # 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}}" "PIGW" "phosphatidylinositol glycan anchor biosynthesis, class W" "17" "q21.1" "unknown" "NC_000017.10" "UD_136090115920" "" "http://www.LOVD.nl/PIGW" "" "1" "23213" "284098" "610275" "1" "1" "1" "1" "" "" "g" "http://databases.lovd.nl/shared/refseq/PIGW_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2014-12-19 17:08:58" "00000" "2021-02-08 18:36:18" ## 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}}" "00016162" "PIGW" "phosphatidylinositol glycan anchor biosynthesis, class W" "001" "NM_178517.3" "" "NP_848612.2" "" "" "" "-55" "2200" "1515" "34891403" "34895150" "" "0000-00-00 00:00:00" "" "" ## 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}}" "00937" "HPMRS2;GPIBD6" "hyperphosphatasia, with mental retardation syndrome, type 2 (HPMRS-2, glycosylphosphatidylinositol deficiency, type 6 (GPIBD-6))" "AR" "614749" "" "autosomal recessive" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "04270" "epilepsy" "epilepsy" "" "" "" "" "" "00006" "2015-05-14 16:00:06" "00006" "2017-09-07 14:25:59" "04612" "HPMRS5;GPIBD11" "hyperphosphatasia with mental retardation syndrome, type 5 (HPMRS-5, glycosylphosphatidylinositol deficiency, type 11 (GPIBD-11))" "AR" "616025" "" "autosomal recessive" "" "00000" "2015-09-23 10:25:23" "00006" "2021-12-10 21:51:32" "05161" "FRNS" "Fryns syndrome (FRNS)" "" "229850" "" "" "" "00006" "2016-04-29 17:42:03" "" "" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "PIGW" "04612" ## Individuals ## Do not remove or alter this header ## ## Count = 7 "{{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}}" "00025483" "" "" "" "1" "" "00081" "{PMID:Chiyonobu 2014: 24367057}" "Index case with hyperphosphatasia with mental retardation 5 . OMIM 610275." "M" "no" "Japan" "" "0" "" "" "" "" "00155020" "" "" "" "2" "" "00081" "{PMID:Hogrebe 2016:27626616}" "" "M" "yes" "" "" "0" "" "" "" "Patient_1" "00155021" "" "" "00155020" "1" "" "00081" "{PMID:Hogrebe 2016:27626616}" "" "F" "" "" "" "0" "" "" "" "Patient_2" "00181144" "" "" "" "2" "" "02575" "" "" "M" "?" "" "" "0" "" "" "" "" "00181145" "" "" "00181144" "1" "" "02575" "" "" "F" "?" "" "" "0" "" "" "" "" "00207532" "" "" "" "1" "" "00081" "{PMID:Foskett et al., 2018:30078644}" "" "F" "no" "Mexico" ">00y08m" "0" "" "" "Mexican" "Patient" "00207792" "" "" "" "1" "" "01164" "" "" "M" "" "Germany" "" "0" "" "" "" "" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 4 "{{individualid}}" "{{diseaseid}}" "00025483" "00937" "00181144" "05161" "00181145" "05161" "00207532" "04270" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00937, 04270, 04612, 05161 ## Count = 5 "{{id}}" "{{diseaseid}}" "{{individualid}}" "{{owned_by}}" "{{Phenotype/Inheritance}}" "{{Phenotype/Age}}" "{{Phenotype/Additional}}" "{{Phenotype/Age/Onset}}" "{{Phenotype/Age/Diagnosis}}" "{{Phenotype/Onset}}" "{{Phenotype/Protein}}" "{{Phenotype/Enzyme/CPK}}" "{{Phenotype/Heart/Myocardium}}" "{{Phenotype/Lung}}" "{{Phenotype/Diagnosis/Definite}}" "{{Phenotype/Diagnosis/Initial}}" "0000021594" "00937" "00025483" "00081" "Familial, autosomal recessive" "" "Development was profoundly delayed from early infancy. Dysmorphic facial features included broad nasal bridge and tented upper lip. Inguinal hernia was noted. The patient developed clusters of tonic spasms and was diagnosed as having West syndrome based on a high-amplitude hypsarrhythmic pattern on interictal EEG. ALP level were elevated." "" "" "" "" "" "" "" "" "" "0000143366" "00253" "00181144" "02575" "Familial, autosomal recessive" "" "Dandy Walker malformation (HP:0001305), Hydronephrosis (HP:0000126), External genital hypoplasia (HP:0003241)" "" "" "" "" "" "" "" "" "" "0000143367" "05161" "00181145" "02575" "Familial, autosomal recessive" "" "Dandy Walker malformation (HP:0001305), Renal dysplasia (HP:0000110), Hydronephrosis (HP:0000126), Diaphragmatic hernia (HP:0000776)" "" "" "" "" "" "" "" "" "" "0000155310" "04270" "00207532" "00081" "Familial, autosomal recessive" "00y08m" "Infantile spasms, myoclonic seizures, cortical visual impairment, developmental delay, and minor dysmorphic features (Anteverted nares, tented upper lip), pectus excavatum, and mild flexion contractures of all fingers bilaterally. Alkaline phosphatase levels ranged from normal to mildly elevated. No evidence of metabolic bone disease." "" "" "" "" "" "" "" "" "" "0000155575" "00198" "00207792" "01164" "Unknown" "" "HP:0000098 (Tall stature); HP:0100022 (Abnormality of movement); HP:0012758 (Neurodevelopmental delay); HP:0001679 (Abnormality of the aorta); HP:0000365 (Hearing impairment); HP:0000717 (Autism)" "" "" "" "" "" "" "" "" "" ## Screenings ## Do not remove or alter this header ## ## Count = 7 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000025487" "00025483" "1" "00081" "00081" "2014-12-10 23:44:15" "" "" "SEQ" "DNA" "" "" "0000155884" "00155020" "1" "00081" "00081" "2018-03-09 21:47:02" "" "" "SEQ-NG" "DNA" "" "" "0000155885" "00155021" "1" "00081" "00081" "2018-03-09 21:51:56" "" "" "SEQ-NG" "DNA" "" "" "0000182101" "00181144" "1" "02575" "02575" "2018-10-01 18:31:40" "" "" "SEQ-NG" "DNA" "" "" "0000182103" "00181145" "1" "02575" "02575" "2018-10-01 18:47:39" "" "" "SEQ-NG" "DNA" "" "" "0000208571" "00207532" "1" "00081" "00081" "2018-11-23 19:54:41" "" "" "arraySNP" "DNA" "" "SNP microarray (Reveal), Epilepsy panel (EpiXpanded Panel, GeneDx)" "0000208833" "00207792" "1" "01164" "01164" "2018-11-30 14:41:29" "" "" "SEQ-NG" "DNA" "" "" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 4 "{{screeningid}}" "{{geneid}}" "0000025487" "PIGW" "0000182101" "PIGW" "0000182103" "PIGW" "0000208571" "PIGW" ## 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 = 15 "{{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}}" "0000048377" "0" "90" "17" "34893161" "34893161" "subst" "0" "00081" "PIGW_000001" "g.34893161A>C" "" "{PMID:Chiyonobu et al. 2014:24367057}" "" "" "This mutation affects the second transmembrane domain. PIGW deficient CHO cells were transfected with Thr71Pro cDNA partiallly restored C59, DAF and uPAR levels whereas wild-type cDNA completely restored it. Protein expression of the Thr71Pro mutant was decreased to one-third of the wild-type level. Frequency of the variant c.211A>C is 0.004." "Germline" "yes" "rs587777733" "0" "" "" "g.36537312A>C" "" "pathogenic" "" "0000048378" "0" "90" "17" "34893449" "34893449" "subst" "0" "00081" "PIGW_000002" "g.34893449A>G" "" "{PMID:Chiyonobu et al. 2014:24367057}" "" "" "Transfection of the mutation M167V into PIGW-deficient CHO cells did not restore at all CD59, DAR et uPAR levels." "Germline" "yes" "rs200024253" "0" "" "" "g.36537600A>G" "" "pathogenic" "" "0000325342" "0" "50" "17" "34894191" "34894191" "subst" "0.000113793" "01804" "PIGW_000003" "g.34894191T>C" "" "" "" "PIGW(NM_178517.3):c.1241T>C (p.(Ile414Thr))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.36538342T>C" "" "VUS" "" "0000357716" "3" "70" "17" "34893410" "34893410" "subst" "0" "00081" "PIGW_000004" "g.34893410A>G" "" "{PMID:Hogrebe et al. 2016:27626616}" "" "" "" "Germline" "" "" "0" "" "" "g.36537561A>G" "" "likely pathogenic" "" "0000357717" "3" "70" "17" "34893410" "34893410" "subst" "0" "00081" "PIGW_000004" "g.34893410A>G" "" "{PMID:Hogrebe et al. 2016:27626616}" "" "" "" "Germline" "" "" "0" "" "" "g.36537561A>G" "" "likely pathogenic" "" "0000405925" "3" "70" "17" "34893056" "34893056" "subst" "0.000215223" "02575" "PIGW_000005" "g.34893056A>G" "" "" "" "" "" "Germline" "yes" "" "0" "" "" "g.36537207A>G" "" "likely pathogenic" "" "0000405926" "3" "70" "17" "34893056" "34893056" "subst" "0.000215223" "02575" "PIGW_000005" "g.34893056A>G" "" "" "" "" "" "Germline" "yes" "" "0" "" "" "g.36537207A>G" "" "likely pathogenic" "" "0000438453" "3" "90" "17" "34893149" "34893149" "subst" "0" "00081" "PIGW_000006" "g.34893149C>G" "" "" "" "" "Parents were heterozygous for the variant. This variant was reported to result in a semiconservative amino acid substitution that alters a conserved position within the protein. MutationTaster and PolyPhen-2 predicted the variant to be damaging while SIFT predicted the variant to be benign." "Germline" "" "" "0" "" "" "g.36537300C>G" "" "pathogenic" "" "0000438454" "3" "90" "17" "34893149" "34893149" "subst" "0" "00081" "PIGW_000006" "g.34893149C>G" "" "" "" "" "Parents were heterozygous for the variant. This variant was reported to result in a semiconservative amino acid substitution that alters a conserved position within the protein. MutationTaster and PolyPhen-2 predicted the variant to be damaging while SIFT predicted the variant to be benign." "Germline" "" "" "0" "" "" "g.36537300C>G" "" "pathogenic" "" "0000438815" "0" "50" "17" "34893462" "34893462" "dup" "0" "01164" "PIGW_000007" "g.34893462dup" "" "" "" "" "ACMG grading: PM2; so far only missense variants described as pathogenic / no second variant in PIGW detected in our patient" "Germline" "" "" "0" "" "" "g.36537613dup" "" "VUS" "ACMG" "0000561085" "0" "50" "17" "34893567" "34893570" "del" "0" "01943" "MYO19_000008" "g.34893567_34893570del" "" "" "" "PIGW(NM_178517.4):c.617_620delTTTG (p.V206Gfs*3)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.36537718_36537721del" "" "VUS" "" "0000561086" "0" "30" "17" "34894018" "34894018" "subst" "2.43988E-5" "01943" "MYO19_000009" "g.34894018A>G" "" "" "" "PIGW(NM_178517.4):c.1068A>G (p.V356=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.36538169A>G" "" "likely benign" "" "0000658088" "0" "30" "17" "34894360" "34894360" "subst" "5.28228E-5" "01943" "MYO19_000011" "g.34894360C>T" "" "" "" "PIGW(NM_178517.4):c.1410C>T (p.H470=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.36538511C>T" "" "likely benign" "" "0000692317" "0" "30" "17" "34894082" "34894082" "subst" "0.00070584" "01943" "MYO19_000012" "g.34894082G>C" "" "" "" "PIGW(NM_178517.4):c.1132G>C (p.V378L)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000726312" "0" "50" "17" "34893558" "34893558" "subst" "8.12176E-6" "02329" "MYO19_000007" "g.34893558T>G" "" "" "" "PIGW(NM_178517.4):c.608T>G (p.L203W)" "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 PIGW ## Count = 15 "{{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}}" "0000048377" "00016162" "90" "211" "0" "211" "0" "c.211A>C" "r.(?)" "p.(Thr71Pro)" "" "0000048378" "00016162" "90" "499" "0" "499" "0" "c.499A>G" "r.(?)" "p.(Met167Val)" "" "0000325342" "00016162" "50" "1241" "0" "1241" "0" "c.1241T>C" "r.(?)" "p.(Ile414Thr)" "" "0000357716" "00016162" "70" "460" "0" "460" "0" "c.460A>G" "r.(?)" "p.(Arg154Gly)" "" "0000357717" "00016162" "70" "460" "0" "460" "0" "c.460A>G" "r.(?)" "p.(Arg154Gly)" "" "0000405925" "00016162" "70" "106" "0" "106" "0" "c.106A>G" "r.(?)" "p.(Arg36Gly)" "" "0000405926" "00016162" "70" "106" "0" "106" "0" "c.106A>G" "r.(?)" "p.(Arg36Gly)" "" "0000438453" "00016162" "90" "199" "0" "199" "0" "c.199C>G" "r.(?)" "p.(Pro67Ala)" "2" "0000438454" "00016162" "90" "199" "0" "199" "0" "c.199C>G" "r.(?)" "p.(Pro67Ala)" "2" "0000438815" "00016162" "50" "512" "0" "512" "0" "c.512dup" "r.(?)" "p.Gly172Argfs*89" "" "0000561085" "00016162" "50" "617" "0" "620" "0" "c.617_620del" "r.(?)" "p.(Val206GlyfsTer3)" "" "0000561086" "00016162" "30" "1068" "0" "1068" "0" "c.1068A>G" "r.(?)" "p.(Val356=)" "" "0000658088" "00016162" "30" "1410" "0" "1410" "0" "c.1410C>T" "r.(?)" "p.(His470=)" "" "0000692317" "00016162" "30" "1132" "0" "1132" "0" "c.1132G>C" "r.(?)" "p.(Val378Leu)" "" "0000726312" "00016162" "50" "608" "0" "608" "0" "c.608T>G" "r.(?)" "p.(Leu203Trp)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 9 "{{screeningid}}" "{{variantid}}" "0000025487" "0000048377" "0000025487" "0000048378" "0000155884" "0000357716" "0000155885" "0000357717" "0000182101" "0000405925" "0000182103" "0000405926" "0000208571" "0000438453" "0000208571" "0000438454" "0000208833" "0000438815"