### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = PIGY) # 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}}" "PIGY" "phosphatidylinositol glycan anchor biosynthesis, class Y" "4" "q22.1" "unknown" "NG_046719.1" "UD_136090116365" "" "http://www.LOVD.nl/PIGY" "" "1" "28213" "84992" "610662" "1" "1" "1" "1" "Establishment of this gene variant database (LSDB) was supported by the Leiden University Medical Center (LUMC), Leiden, Nederland." "" "g" "http://databases.lovd.nl/shared/refseq/PIGY_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2018-03-09 09:01:24" "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}}" "00016164" "PIGY" "phosphatidylinositol glycan anchor biosynthesis, class Y" "001" "NM_001042616.2" "" "NP_001036081.1" "" "" "" "-544" "812" "216" "89444952" "89442129" "" "0000-00-00 00:00:00" "" "" ## Diseases ## Do not remove or alter this header ## ## Count = 3 "{{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" "00360" "MDC" "dystrophy, muscular, congenital (MDC)" "" "" "" "" "" "00006" "2014-03-21 23:02:36" "00006" "2018-07-03 16:30:02" "05402" "HPMRS6;GPIBD12" "hyperphosphatasia with mental retardation syndrome, type 6 (HPMRS-6, glycosylphosphatidylinositol deficiency, type 12 (GPIBD-12))" "AR" "616809" "" "autosomal recessive" "" "00006" "2018-03-09 09:00:33" "00006" "2021-12-10 21:51:32" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "PIGY" "05402" ## Individuals ## Do not remove or alter this header ## ## Count = 5 "{{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}}" "00054658" "" "" "" "2" "" "00006" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "2-generation family, 2 affected sisters, unaffected heterozygous carrier parents" "F" "no" "Australia" "02y" "0" "" "" "white" "" "00054659" "" "" "00054658" "1" "" "00006" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "2-generation family, 2 affected sisters, unaffected heterozygous carrier parents" "F" "no" "Australia" "" "0" "" "" "" "" "00054660" "" "" "" "2" "" "00006" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "2-generation family, 2 affecteds (brother/sister), unaffected heterozygous carrier parents/brother" "" "yes" "Pakistan" ">05y" "0" "" "" "" "" "00054661" "" "" "00054660" "1" "" "00006" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "2-generation family, 2 affecteds (brother/sister), unaffected heterozygous carrier parents/brother" "F" "yes" "Pakistan" ">03y" "0" "" "" "" "" "00054668" "" "" "" "1" "" "01399" "{PMID:O\'Grady 2016:27159402}" "2-generation family, unaffected heterozygous carrier parents" "F" "" "Australia" "2y" "0" "" "" "" "" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 5 "{{individualid}}" "{{diseaseid}}" "00054658" "00198" "00054659" "00198" "00054660" "00198" "00054661" "00198" "00054668" "00360" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00198, 00360, 05402 ## Count = 5 "{{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}}" "0000041337" "00198" "00054658" "00006" "Familial, autosomal recessive" "" "see paper; born 32w, necrotizing enterocolitis, chronic lung disease, dysmorphic, brachyphalangy, 2–3 toe syndactyly, elbow/knee flexion contractures, severe bilateral hip dysplasia; 5m intractable seizure disorder with multifocal spike and slow wave activity on EEG followed by developmental regression; 2y died of respiratory infection; congenital cataracts, intermittent episodes abdominal distress, vomiting, growth failure normal OFC, normal growth; MRI brain normal in neonates, 9m loss of white matter and cerebral volume, ..." "" "" "" "" "" "" "" "" "" "" "" "0000041338" "00198" "00054659" "00006" "Familial, autosomal recessive" "" "see paper; 25w gestation abnormal antenatal scans, enlarged echogenic kidneys/bowel, long-bone growth failure; born 28w due to polyhydramnios; dysmorphic features, brachyphalangy, proximal limb shortening, contractures, left hip dysplasia; bilateral inguinal hernias, bilateral dilatation renal collecting systems, markedly increased echogenicity renal parenchyma; 6w intractable seizures, development regressed; 5m mostly unresponsive, poor vision; 7m died secondary to aspiration; congenital cataracts, intermittent episodes abdominal distress, vomiting, growth failure normal OFC, normal growth; MRI brain normal in neonates, ..." "" "" "" "" "" "" "" "" "" "" "" "0000041339" "00198" "00054660" "00006" "Familial, autosomal recessive" "" "see paper; uncomplicated pregnancy/delivery; 6w microcephaly, 5y OFC 46 cm (-3-4 SD); delayed developmental milestones, sat_support-15m, walk-3y, speech delayed (5y only short 2-3 word sentences), short-sighted, strabismus, behavioural difficulties (aggressive outbursts), no seizures, mild facial dysmorphism, long palpebral fissures, bulbous nose tip, wide mouth, no brachytelephalangy" "" "" "global developmental delay, micro-cephaly" "" "" "" "" "" "" "" "" "0000041340" "00198" "00054661" "00006" "Familial, autosomal recessive" "" "see paper; born following uncomplicated pregnancy/de-livery; 2w-microcephaly (2y OFC 42.1 cm (−4-5SD)); delayed development, sat_support-18, not_walk-3y, speech delayed (3y 10-15 single word sentences), poor concentration, hyperactive, no seizures, mild facial dysmorphism, long palpebral fissures, bulbous nose tip, wide mouth, no brachytelephalangy" "" "" "global developmental delay, microcephaly" "" "" "" "" "" "" "" "" "0000041347" "00360" "00054668" "01399" "Familial, autosomal recessive" "2y" "infantile hypotonia, profound global delay, arthrogryposis, seizures; died at 2y; CPK mild elevation (323-554); histology dystrophic" "" "" "" "" "" "" "" "" "" "" "" ## Screenings ## Do not remove or alter this header ## ## Count = 5 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000054607" "00054658" "1" "00006" "00006" "2015-11-07 17:46:05" "" "" "SEQ;SEQ-NG" "DNA" "" "" "0000054608" "00054659" "1" "00006" "00006" "2015-11-07 18:51:56" "" "" "SEQ;SEQ-NG" "DNA" "" "" "0000054609" "00054660" "1" "00006" "00006" "2015-11-07 19:11:30" "00006" "2015-11-07 19:26:01" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "blood" "" "0000054610" "00054661" "1" "00006" "00006" "2015-11-07 19:20:15" "" "" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "" "0000054617" "00054668" "1" "01399" "01399" "2015-11-08 12:06:11" "" "" "SEQ;SEQ-NG" "DNA" "" "" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 5 "{{screeningid}}" "{{geneid}}" "0000054607" "PIGY" "0000054608" "PIGY" "0000054609" "PIGY" "0000054610" "PIGY" "0000054617" "PIGY" ## 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 = 9 "{{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}}" "0000084554" "3" "90" "4" "89442804" "89442804" "subst" "0" "00006" "PIGY_000002" "g.89442804A>G" "" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "" "" "variant in 10 Mb homozygous segment, parents may be distantly related" "Germline" "yes" "" "0" "" "" "g.88521653A>G" "" "pathogenic" "" "0000084555" "3" "90" "4" "89442804" "89442804" "subst" "0" "00006" "PIGY_000002" "g.89442804A>G" "" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "" "" "variant in 10 Mb homozygous segment, parents may be distantly related" "Germline" "yes" "" "0" "" "" "g.88521653A>G" "" "pathogenic" "" "0000084556" "0" "90" "4" "89442804" "89442804" "subst" "0" "00006" "PIGY_000002" "g.89442804A>G" "" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "" "" "expression cloning (human cells) shows reduced PIGY protein stability, yielding lower protein levels and reduced capacity to synthesize GPI anchors for correct protein targeting to the cell surface" "In vitro (cloned)" "-" "" "0" "" "" "g.88521653A>G" "" "NA" "" "0000084557" "3" "90" "4" "89444948" "89444948" "subst" "0" "00006" "PIGY_000003" "g.89444948C>T" "" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "" "" "exome sequencing, 7 Mb homozygous region; reduced mRNA expression (0.10)" "Germline" "yes" "" "0" "" "" "g.88523797C>T" "" "pathogenic" "" "0000084558" "3" "90" "4" "89444948" "89444948" "subst" "0" "00006" "PIGY_000003" "g.89444948C>T" "" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "" "" "exome sequencing, 7 Mb homozygous region; reduced mRNA expression (0.05)" "Germline" "yes" "" "0" "" "" "g.88523797C>T" "" "pathogenic" "" "0000084559" "3" "30" "4" "89443162" "89443162" "subst" "0.138069" "00006" "PIGY_000004" "g.89443162G>A" "" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "" "" "reduced mRNA expression (0.05)" "Germline" "" "rs3177413" "0" "" "" "g.88522011G>A" "" "likely benign" "" "0000084560" "3" "30" "4" "89443162" "89443162" "subst" "0.138069" "00006" "PIGY_000004" "g.89443162G>A" "" "{PMID:Ilkovski 2015:26293662}, {DOI:Ilkovski 2015:10.1093/hmg/ddv331}" "" "" "reduced mRNA expression (0.10)" "Germline" "" "rs3177413" "0" "" "" "g.88522011G>A" "" "likely benign" "" "0000084567" "3" "90" "4" "89442804" "89442804" "subst" "0" "01399" "PIGY_000001" "g.89442804A>G" "" "{PMID:O\'Grady 2016:27159402}" "" "" "" "Germline" "yes" "" "0" "" "" "g.88521653A>G" "" "pathogenic" "" "0000720044" "0" "50" "4" "89442924" "89442924" "subst" "0.00281376" "01943" "PIGY_000005" "g.89442924G>C" "" "" "" "PIGY(NM_001042616.2):c.17C>G (p.P6R)" "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 PIGY ## Count = 9 "{{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}}" "0000084554" "00016164" "90" "137" "0" "137" "0" "c.137T>C" "r.(?)" "p.(Leu46Pro)" "2" "0000084555" "00016164" "90" "137" "0" "137" "0" "c.137T>C" "r.(?)" "p.(Leu46Pro)" "2" "0000084556" "00016164" "90" "137" "0" "137" "0" "c.137T>C" "r.(?)" "p.Leu46Pro" "2" "0000084557" "00016164" "90" "-540" "0" "-540" "0" "c.-540G>A" "r.-540g>a" "p.=" "1" "0000084558" "00016164" "90" "-540" "0" "-540" "0" "c.-540G>A" "r.-540g>a" "p.=" "1" "0000084559" "00016164" "30" "-222" "0" "-222" "0" "c.-222C>T" "r.-222c>u" "p.=" "1" "0000084560" "00016164" "30" "-222" "0" "-222" "0" "c.-222C>T" "r.-222c>u" "p.=" "1" "0000084567" "00016164" "90" "137" "0" "137" "0" "c.137T>C" "r.(?)" "p.(Leu46Pro)" "" "0000720044" "00016164" "50" "17" "0" "17" "0" "c.17C>G" "r.(?)" "p.(Pro6Arg)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 7 "{{screeningid}}" "{{variantid}}" "0000054607" "0000084554" "0000054608" "0000084555" "0000054609" "0000084557" "0000054609" "0000084560" "0000054610" "0000084558" "0000054610" "0000084559" "0000054617" "0000084567"