### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = PIGL) # 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}}" "PIGL" "phosphatidylinositol glycan anchor biosynthesis, class L" "17" "p12-p11.2" "no" "NG_032651.1" "UD_132439412158" "" "http://www.LOVD.nl/PIGL" "" "1" "8966" "9487" "605947" "1" "1" "1" "1" "Establishment of this gene variant database (LSDB) was supported by the European Community\'s Seventh Framework Programme (FP7/2007-2013) under grant agreement No 200754 - the GEN2PHEN project." "" "g" "http://databases.lovd.nl/shared/refseq/PIGL_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2012-04-18 00:00:00" "00081" "2018-12-31 00:38:40" "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}}" "00016151" "PIGL" "phosphatidylinositol glycan anchor biosynthesis, class L" "001" "NM_004278.3" "" "NP_004269.1" "" "" "" "-32" "1120" "759" "16120509" "16229573" "" "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" "00541" "HPMRS1;GPIBD2" "hyperphosphatasia, with mental retardation syndrome, type 1 (HPMRS-1, glycosylphosphatidylinositol deficiency, type 2 (GPIBD-2))" "AR" "239300" "" "autosomal recessive" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "01001" "CHIME;GPIBD5" "CHIME syndrome (Zunich neuroectodermal syndrome, glycosylphosphatidylinositol deficiency, type 5 (GPIBD-5))" "AR" "280000" "" "autosomal recessive" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "05365" "NEDHCAS" "neurodevelopmental disorder with hypotonia and cerebellar atrophy, with or without seizures" "AR" "618879" "" "" "" "00006" "2017-12-29 14:39:52" "00006" "2024-07-24 10:12:34" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 2 "{{geneid}}" "{{diseaseid}}" "PIGL" "00139" "PIGL" "01001" ## Individuals ## Do not remove or alter this header ## ## Count = 18 "{{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}}" "00025915" "" "" "" "2" "" "00081" "{PMID:Ng 2012 : 22444671}" "Two siblings with Zunich neuroectodermal syndrome." "?" "no" "" "" "0" "" "" "" "22444671-Fam" "00025916" "" "" "" "1" "" "00081" "{PMID:Ng 2012: 22444671}" "Index case with CHIME syndrome." "" "" "" "" "0" "" "" "" "" "00025917" "" "" "" "1" "" "00081" "{PMID:Ng 2012:22444671}" "Index case with CHIME syndrome, one mutation in PIGL found." "" "" "" "" "0" "" "" "" "" "00025918" "" "" "" "1" "" "00081" "{PMID:Ng 2012:22444671}" "Index case with CHIME syndrome" "M" "no" "" "" "0" "" "" "" "" "00025919" "" "" "" "1" "" "00081" "{PMID:Ng 2012:22444671}, case described in {PMID:Tinschert 1996:8893234}" "Index case with CHIME syndrome who carries one mutation in PIGL and a deletion on chromosome 17." "F" "no" "Germany" "" "0" "" "" "" "22444671-Pat33300" "00155017" "" "" "" "1" "" "00081" "{PMID:Fujiwara 2015:25706356}" "" "F" "no" "Japan" "" "0" "" "" "" "" "00155018" "" "" "" "1" "" "00081" "{PMID:Johnson 2017:28371479}" "" "M" "no" "" "" "0" "" "" "" "" "00155019" "" "" "" "1" "" "00081" "{PMID:Pagnamenta 2017:28327575}" "" "F" "no" "" "" "0" "" "" "white" "277013" "00163760" "" "" "" "1" "" "00081" "{PMID:Ceroni 2018:29473937}" "" "M" "no" "Brazil" "" "0" "" "" "" "" "00207524" "" "" "" "1" "" "00081" "{PMID:Altassan et al., 2018:30023290}" "Individual presented with the main features of HPMRS; developmental delay, cognitive impairment, seizure disorder, skeletal deformities, and high alkaline phosphatase. " "M" "no" "" ">10y" "0" "" "Anti-epileptic medications" "" "Patient 1" "00207525" "" "" "" "1" "" "00081" "{PMID:Altassan et al., 2018:30023290}" "Patient 1\'s younger brother" "M" "no" "" ">04y" "0" "" "Anti-epileptic medications. Surgical correction of strabismus." "" "Patient 2" "00207526" "" "" "" "1" "" "00081" "{PMID:Mogami et al., 2018:29444765}" "3 siblings with mutations in the PIGL gene. They lacked three symptoms of CHIME syndrome (eye colobomas, heart defects, and ear anomalies). These patients are the first published cases of inherited GPI anchor deficiency with stimulation- induced epileptic myoclonic seizures, confirmed by ictal EEG." "F" "no" "Japan" ">02y02m" "0" "" "Antiepileptic medications. Vitamin B6 but not effective." "Japanese" "Case 1" "00207527" "" "" "" "1" "" "00081" "{PMID:Mogami et al., 2018:29444765}" "Elder brother of Case 1" "M" "no" "" ">09y04m" "0" "" "Antiepileptic medications. Vitamin B6 but not effective." "" "Case 2" "00207528" "" "" "" "1" "" "00081" "{PMID:Mogami et al., 2018:29444765}" "Eldest brother of Case 1 and 2" "M" "no" "" ">13y03m" "0" "" "Antiepileptic medications" "" "Case 3" "00291641" "" "" "" "4" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00291642" "" "" "" "1" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00291643" "" "" "" "7" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00304566" "" "" "" "1" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 17 "{{individualid}}" "{{diseaseid}}" "00025915" "01001" "00025916" "01001" "00025917" "01001" "00025918" "01001" "00025919" "01001" "00155017" "00541" "00155018" "01001" "00163760" "01001" "00207524" "00541" "00207525" "00541" "00207526" "05365" "00207527" "05365" "00207528" "05365" "00291641" "00198" "00291642" "00198" "00291643" "00198" "00304566" "00198" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00139, 00198, 00541, 01001, 05365 ## Count = 10 "{{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}}" "0000021985" "01001" "00025915" "00081" "Familial, autosomal recessive" "" "FEatures included ocular colobomas, congenital heart disease, early onset migratory ichthyosiform dermatosis, mental retardation, conductive hearing loss, seizures, and typical facial features." "" "" "" "" "" "" "" "" "" "" "" "0000021986" "01001" "00025916" "00081" "Familial, autosomal recessive" "" "Clinical features included ocular colobomas, congenital heart disease, early onset migratory ichthyosiform dermatosis, mental retardation, conductive hearing loss, seizures, and typical facial features." "" "" "" "" "" "" "" "" "" "" "" "0000021987" "01001" "00025917" "00081" "Familial, autosomal recessive" "" "Phenotype included a migratory ichthyosiform dermatosis, multiple skin infections and infestations, bilateral retinal coloboma, developmental delay, seizures, infantile macrosomia, facial anomalies, a duplicated renal collecting system, and conductive hearing loss. Histologic examination of the skin findings of an epidermal nevus with deep rete pegs, hyperkeratosis, and a markedly increased granular layer. The patient developped acute lymphoblastic leukemia at age 4 1/2 years." "" "" "" "" "" "" "" "" "" "" "" "0000021988" "01001" "00025918" "00081" "Isolated (sporadic)" "" "Clinical features included bilateral retinal colobomas, subaortic stenosis, and hydronephrosis. Facial dysmorphic features were frontal bossing, a broad nasal root, a flat midface with an elongated philtrum, and slightly lowset, posteriorly angulated ears. He showed delayed psychomotor skills including speech and had conductive hearing loss and a seizure disorder. At 10 years, his skin showed mild erythema, with lamellated, ichthyosiform changes." "" "" "" "" "" "" "" "" "" "" "" "0000021989" "01001" "00025919" "00081" "Isolated (sporadic)" "" "She presented craniofacial dysmorphism, bilateral colobomas of the retina, sparse and fine hair, hearing loss, ichthyosiform erythroderma, mental retardation, ear anomalies, brachydactyly, and broad second toes. Light microscopic and ultrastructural investigations of the affected skin showed characteristic but nonspecific changes." "" "" "" "" "" "" "" "" "" "" "" "0000155302" "00541" "00207524" "00081" "Familial, autosomal recessive" "00y06m" "Myoclonic seizures. Inguinal herna, hydrocele, strabismus. Global DD. Dysmorphic features (prominent forehead, high arched eyebrows and sparse on the outer third, nystagmus, mild telecanthus, uplifted ear lobes, open mouth with intermittent drooling). Pectus excavatum, clinodactyly involving the fifth digits, 4th and 5th toes bilaterally. reducible umbilical hernia, mild hepatomegaly, and ataxic gait. Brain MRI showed symmetrical bilateral patchy signal abnormalities in the periventricular zones in the parietal, occipital and frontal regions, white matter loss, and thin corpus callosum. Elevated ALP (968 U/L). No skin abnormalities. Normal hearing and heart evaluations. Normal Vitamin E and alpha-fetoprotein." "" "" "" "" "" "" "" "" "" "" "" "0000155303" "00541" "00207525" "00081" "Familial, autosomal recessive" "00y04m" "Global DD. Tonic-clonic seizures. Strabismus (was surgically corrected). Coarse facial features (high hairlines, hypertelorism, epicanthal folds, horizontal nystagmus, depressed nasal bridge, delayed teeth eruption, everted and partially bifid lower lip, folded ears, and irregular hypopigmented skin margins surrounding the eyes and the nose.) Spastic lower limbs, bilateral brachydactyly, severe clinodactyly of both fifth fingers and toes and dry eczematous skin. High ALP level (454 U/L). No chest deformity or organomegaly." "" "" "" "" "" "" "" "" "" "" "" "0000155304" "05365" "00207526" "00081" "Familial, autosomal recessive" "02y" "Ichthyosiform dermatosis at birth. Dysmorphic facial features (hypertelorism, brachycephaly, epicanthal folds, flat broad nasal root, full lips, widely spaced teeth, overfolded helices, thickened palms and soles. Myoclonic jerks evoked by sudden unexpected acoustic or tactile stimuli. Focal seizures. DD. Severe ID. Ear anomalies. Transient apnea. Normal serum ALP. No retinal coloboma, congenital heart defects or hearing loss. No renal abnormalities. Normal brain MRI." "" "" "" "" "" "" "" "" "" "" "" "0000155305" "05365" "00207527" "00081" "Unknown" "09y" "Ichthyosiform dermatosis at birth. Dysmorphic facial features (hypertelorism, brachycephaly, epicanthal folds, flat broad nasal root, full lips, widely spaced teeth, overfolded helices, thickened palms and soles. DD. Severe ID. Ear anomalies. Myoclonic and focal seizures. Transient apnea. Normal serum ALP. No retinal coloboma, congenital heart defects or hearing loss. No renal abnormalities. Normal brain MRI." "" "" "" "" "" "" "" "" "" "" "" "0000155306" "05365" "00207528" "00081" "Unknown" "13y" "During pregnancy: foetal ultrasound shows congenital hydronephrosis. Ichthyosiform dermatosis at birth. Dysmorphic facial features (hypertelorism, brachycephaly, epicanthal folds, flat broad nasal root, full lips, widely spaced teeth, overfolded helices, thickened palms and soles. DD. Severe ID. Ear anomalies. Seizures: myoclonic, focal, absence, atonic. Transient apnea. Normal serum ALP. No retinal coloboma, congenital heart defects or hearing loss." "" "" "2d" "" "" "" "" "" "" "" "" ## Screenings ## Do not remove or alter this header ## ## Count = 19 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000025917" "00025915" "1" "00081" "00081" "2014-12-04 21:38:45" "" "" "SEQ-NG" "DNA" "" "" "0000025918" "00025916" "1" "00081" "00081" "2014-12-04 22:17:34" "" "" "SEQ-NG" "DNA" "" "" "0000025919" "00025917" "1" "00081" "00081" "2014-12-04 22:46:50" "" "" "SEQ-NG" "DNA" "" "" "0000025920" "00025918" "1" "00081" "00081" "2014-12-04 23:05:50" "" "" "SEQ-NG" "DNA" "" "" "0000025921" "00025919" "1" "00081" "00081" "2014-12-04 23:24:16" "" "" "SEQ-NG" "DNA" "" "" "0000155881" "00155017" "1" "00081" "00081" "2018-03-09 17:12:24" "" "" "SEQ-NG" "DNA" "Blood" "WES" "0000155882" "00155018" "1" "00081" "00081" "2018-03-09 18:14:55" "" "" "PCR" "DNA" "peripheral blood" "" "0000155883" "00155019" "1" "00081" "00081" "2018-03-09 20:26:04" "" "" "SEQ-NG" "DNA" "Blood" "WES" "0000164622" "00163760" "1" "00081" "00081" "2018-04-09 23:30:32" "" "" "SEQ-NG" "DNA" "" "WES" "0000164677" "00025919" "1" "00081" "00006" "2018-04-16 08:11:22" "" "" "arrayCGH" "DNA" "" "" "0000208562" "00207524" "1" "00081" "00081" "2018-11-23 18:32:39" "" "" "SEQ" "DNA" "" "Commercially available multigene panel for intellectual disability (GeneDx), Sanger sequencing " "0000208563" "00207525" "1" "00081" "00081" "2018-11-23 18:45:28" "" "" "SEQ" "DNA" "" "Commercially available multigene panel for intellectual disability (GeneDx), Sanger sequencing " "0000208564" "00207526" "1" "00081" "00081" "2018-11-23 18:53:17" "" "" "PCRq;SEQ-NG" "DNA" "" "Exome analysis" "0000208565" "00207527" "1" "00081" "00081" "2018-11-23 18:57:38" "" "" "PCRq;SEQ-NG" "DNA" "" "" "0000208566" "00207528" "1" "00081" "00081" "2018-11-23 19:03:30" "" "" "PCRq;SEQ-NG" "DNA" "" "Exome analysis" "0000292809" "00291641" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000292810" "00291642" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000292811" "00291643" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000305695" "00304566" "1" "03575" "00006" "2020-06-24 11:55:42" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 12 "{{screeningid}}" "{{geneid}}" "0000025917" "PIGL" "0000025918" "PIGL" "0000025919" "PIGL" "0000025920" "PIGL" "0000025921" "PIGL" "0000155882" "PIGL" "0000164677" "PIGL" "0000208562" "PIGL" "0000208563" "PIGL" "0000208564" "PIGL" "0000208565" "PIGL" "0000208566" "PIGL" ## 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 = 42 "{{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}}" "0000048940" "0" "99" "17" "16220000" "16220000" "subst" "0.000418332" "00081" "PIGL_000002" "g.16220000T>C" "" "{PMID:Ng et al. 2012: 22444671}" "" "" "Heterozygous missense mutation c.500T>C in eight out of nearly 13,000 alleles. In (NHLBI) Exome Sequencing Project, this mutation appears at a frequency of 6:10,752 alleles. (NHLBI) Exome Sequencing Project, the c.500T>C mutation appears at a frequency of 6:10,752 alleles. Cells available from CHIME syndrome cases werr deficient for GPI anchor markers (C59 and FLAER)" "Germline" "yes" "rs145303331" "0" "" "" "g.16316686T>C" "" "pathogenic" "" "0000048941" "0" "90" "17" "16137323" "16137323" "del" "4.06256E-6" "00081" "PIGL_000001" "g.16137323del" "" "{PMID:Ng et al. 2012:22444671}" "" "274delC" "cell lines derived from these cases had significantly reduced levels of the two GPI anchor markers, CD59 and a GPI-binding toxin, aerolysin (FLAER), confirming the pathogenicity of the mutations." "Germline" "yes" "" "0" "" "" "g.16234009del" "" "pathogenic" "" "0000048942" "0" "90" "17" "16221214" "16221214" "subst" "8.14412E-6" "00081" "PIGL_000003" "g.16221214C>T" "" "{PMID:Ng et al. 2012: 22444671}" "" "" "cell lines derived from these cases had significantly reduced levels of the two GPI anchor markers, CD59 and a GPI-binding toxin, aerolysin (FLAER), confirming the pathogenicity of the mutations." "Germline" "yes" "rs139004722" "0" "" "" "g.16317900C>T" "" "pathogenic" "" "0000048943" "0" "90" "17" "16220000" "16220000" "subst" "0.000418332" "00081" "PIGL_000002" "g.16220000T>C" "" "{PMID:Ng et al. 2012: 22444671}" "" "" "This mutation found in the patient is at a highly conserved residue located in the catalytic domain and predicted by both PolyPhen and SIFT to be damaging. Utilizing two large public databases, we found the heterozygous missense mutation c.500T>C in eight out of nearly 13,000 alleles. Cell lines derived from these cases had significantly reduced levels of the two GPI anchor markers, CD59 and a GPI-binding toxin, aerolysin (FLAER), confirming the pathogenicity of the mutations." "Germline" "yes" "rs145303331" "0" "" "" "g.16316686T>C" "" "pathogenic" "" "0000048944" "0" "90" "17" "16220000" "16220000" "subst" "0.000418332" "00081" "PIGL_000002" "g.16220000T>C" "" "{PMID:Ng et al. 2012:22444671}" "" "" "This mutation alters a conserved residue in the catalytic domain. It is predicted to be damaging by PolyPhen and SIFT. cell lines derived from these cases had significantly reduced levels of the two GPI anchor markers, CD59 and a GPI-binding toxin, aerolysin (FLAER), confirming the pathogenicity of the mutations." "Germline" "yes" "rs145303331" "0" "" "" "g.16316686T>C" "" "pathogenic" "" "0000048945" "0" "99" "17" "16220000" "16220000" "subst" "0.000418332" "00081" "PIGL_000002" "g.16220000T>C" "" "{PMID:Ng et al 2012:22444671}" "" "" "This mutation alters a conserved residue in the catalytic domain. This is predicted damagind by PolyPhen and SIFT. Utilizing two large public databases, we found the heterozygous missense mutation c.500T>C in eight out of nearly 13,000 alleles. Cell lines derived from these cases had significantly reduced levels of the two GPI anchor markers, CD59 and a GPI-binding toxin, aerolysin (FLAER), confirming the pathogenicity of the mutations." "Germline" "yes" "rs145303331" "0" "" "" "g.16316686T>C" "" "pathogenic" "" "0000048946" "0" "99" "17" "16216860" "16216860" "subst" "8.12137E-6" "00081" "PIGL_000004" "g.16216860G>A" "" "{PMID:Ng et al. 2012:22444671}" "" "" "Cell lines derived from this cas had significantly reduced levels of the two GPI anchor markers, CD59 and a GPI-binding toxin, aerolysin (FLAER), confirming the pathogenicity of the mutations." "Germline" "yes" "" "0" "" "" "g.16313546G>A" "" "pathogenic" "" "0000048947" "0" "99" "17" "16220000" "16220000" "subst" "0.000418332" "00081" "PIGL_000002" "g.16220000T>C" "" "{PMID:Ng et al 2012: 22444671}" "" "" "Mutation alters a conserved residue in the catalytic domain. Predicted to be damaging by PolyPhen and SIFT. cell lines derived from these cases had significantly reduced levels of the two GPI anchor markers, CD59 and a GPI-binding toxin, aerolysin (FLAER), confirming the pathogenicity of the mutations." "Germline" "" "rs145303331" "0" "" "" "g.16316686T>C" "" "pathogenic" "" "0000300760" "0" "90" "17" "16220000" "16220000" "subst" "0.000418332" "02326" "PIGL_000002" "g.16220000T>C" "" "" "" "PIGL(NM_004278.3):c.500T>C (p.L167P, p.(Leu167Pro)), PIGL(NM_004278.4):c.500T>C (p.L167P)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.16316686T>C" "" "pathogenic" "" "0000337313" "0" "10" "17" "16229232" "16229232" "subst" "0.425783" "02327" "PIGL_000006" "g.16229232A>G" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.16325918A>G" "" "benign" "" "0000346936" "0" "90" "17" "16220000" "16220000" "subst" "0.000418332" "02327" "PIGL_000002" "g.16220000T>C" "" "" "" "PIGL(NM_004278.3):c.500T>C (p.L167P, p.(Leu167Pro)), PIGL(NM_004278.4):c.500T>C (p.L167P)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.16316686T>C" "" "pathogenic" "" "0000357711" "11" "70" "17" "16120578" "16120590" "del" "0" "00081" "PIGL_000008" "g.16120578_16120590del" "" "{PMID:Fujiwara et al. 2015:25706356}" "" "" "" "Germline" "" "" "0" "" "" "g.16217264_16217276del" "" "likely pathogenic" "" "0000357712" "21" "70" "17" "16137307" "16137308" "del" "0" "00081" "PIGL_000007" "g.16137307_16137308del" "" "{PMID:Fujiwara et al. 2015:25706356}" "" "" "" "Germline" "" "" "0" "" "" "g.16233993_16233994del" "" "likely pathogenic" "" "0000357713" "0" "50" "17" "16209946" "16224353" "del" "0" "00081" "PIGL_000009" "g.16209946_16224353del" "" "{PMID:Johnson et al. 2017:28371479}" "" "" "" "Unknown" "" "" "0" "" "" "g.16306632_16321039del" "" "VUS" "" "0000357714" "21" "50" "17" "16120588" "16120588" "subst" "8.1217E-6" "00081" "PIGL_000010" "g.16120588G>A" "" "{PMID:Pagnamenta et al. 2017:28327575}" "" "" "" "Germline" "" "" "0" "" "" "g.16217274G>A" "" "VUS" "" "0000357715" "11" "70" "17" "16203200" "16203200" "subst" "4.06141E-5" "00081" "PIGL_000011" "g.16203200A>G" "" "{PMID:Pagnamenta et al. 2017:28327575}" "" "" "" "Germline" "" "" "0" "" "" "g.16299886A>G" "" "likely pathogenic" "" "0000368182" "0" "70" "17" "16220000" "16220000" "subst" "0.000418332" "00081" "PIGL_000002" "g.16220000T>C" "" "{PMID:Ceroni et al. 2018:29473937}" "" "" "" "Germline/De novo (untested)" "" "" "0" "" "" "g.16316686T>C" "" "likely pathogenic" "" "0000368183" "0" "70" "17" "16119889" "16120690" "del" "0" "00081" "PIGL_000013" "g.16119889_16120690del" "" "{PMID:Ceroni et al. 2018:29473937}" "" "chr7: 16,119,889-16,120,690" "" "Germline/De novo (untested)" "" "" "0" "" "" "g.16216575_16217376del" "" "likely pathogenic" "" "0000368249" "21" "70" "17" "15680029" "16757764" "del" "0" "00081" "PIGL_000014" "g.(15000000_15680029)_(16757764_17000000)del" "" "{PMID:Ng et al. 2012:22444671}" "" "hg18 15,620,754–16,698,489del" "" "Germline" "" "" "0" "" "del 17p12-p11.2" "" "" "likely pathogenic" "" "0000438442" "0" "90" "17" "16120600" "16120600" "subst" "4.06075E-6" "00081" "PIGL_000015" "g.16120600G>A" "" "" "" "" "Compound Heterozygous. Two variants in PIGL gene. This is a nonsense (c.60G > A; p.Trp20Ter; W20X) pathogenic variant. It was interpreted as pathogenic as it causes loss of normal protein function through truncation or nonsense-mediated mRNA decay." "Germline/De novo (untested)" "" "" "0" "" "" "g.16217286G>A" "" "pathogenic" "" "0000438443" "0" "90" "17" "16137311" "16137311" "subst" "0" "00081" "PIGL_000016" "g.16137311C>T" "" "" "" "" "Compound heterozygous variants in the PIGL gene. This is a missense (c.262C > T; p.Arg88Cys; R88C) variant. in silico analysis predicted it as likely damaging the protein structure and function." "Germline/De novo (untested)" "" "" "0" "" "" "g.16233997C>T" "" "pathogenic" "" "0000438444" "0" "90" "17" "16137311" "16137311" "subst" "0" "00081" "PIGL_000016" "g.16137311C>T" "" "" "" "" "Compound heterozygous variants in the PIGL gene. This is a missense (c.262C > T; p.Arg88Cys; R88C) variant. in silico analysis predicted it as likely damaging the protein structure and function." "Germline/De novo (untested)" "" "" "0" "" "" "g.16233997C>T" "" "pathogenic" "" "0000438445" "0" "90" "17" "16120600" "16120600" "subst" "4.06075E-6" "00081" "PIGL_000015" "g.16120600G>A" "" "" "" "" "Compound heterozygous. The first variant (c.60G > A; p.Trp20Ter; W20X) is a nonsense variant and was interpreted as pathogenic as it causes loss of normal protein function through truncation or nonsense-mediated mRNA decay." "Germline/De novo (untested)" "" "" "0" "" "" "g.16217286G>A" "" "pathogenic" "" "0000438446" "0" "90" "17" "16137311" "16137311" "subst" "0" "00081" "PIGL_000016" "g.16137311C>T" "" "" "" "" "Compound heterozygous. This second variant is a missense (c.262C > T; p.Arg88Cys; R88C) variant. In silico analysis predicted it as likely damaging the protein structure and function." "Germline/De novo (untested)" "" "" "0" "" "" "g.16233997C>T" "" "pathogenic" "" "0000438447" "11" "90" "17" "16229154" "16229154" "subst" "0" "00081" "PIGL_000017" "g.16229154G>A" "" "" "" "" "" "Germline" "" "" "0" "" "" "g.16325840G>A" "" "pathogenic" "" "0000438448" "11" "90" "17" "16229154" "16229154" "subst" "0" "00081" "PIGL_000017" "g.16229154G>A" "" "" "" "NM_004278.3 c.701G>A p.Arg234His" "" "Germline" "" "" "0" "" "" "g.16325840G>A" "" "pathogenic" "" "0000438449" "11" "90" "17" "16229154" "16229154" "subst" "0" "00081" "PIGL_000017" "g.16229154G>A" "" "" "" "NM_004278.3 c.701G>A p.Arg234His" "" "Germline" "" "" "0" "" "" "g.16325840G>A" "" "pathogenic" "" "0000560370" "0" "30" "17" "16216858" "16216858" "del" "0" "01804" "PIGL_000019" "g.16216858del" "" "" "" "PIGL(NM_004278.3):c.427-3del (p.?)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.16313544del" "" "likely benign" "" "0000560371" "0" "90" "17" "16220000" "16220000" "subst" "0.000418332" "01943" "PIGL_000002" "g.16220000T>C" "" "" "" "PIGL(NM_004278.3):c.500T>C (p.L167P, p.(Leu167Pro)), PIGL(NM_004278.4):c.500T>C (p.L167P)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.16316686T>C" "" "pathogenic" "" "0000560372" "0" "90" "17" "16220000" "16220000" "subst" "0.000418332" "02325" "PIGL_000002" "g.16220000T>C" "" "" "" "PIGL(NM_004278.3):c.500T>C (p.L167P, p.(Leu167Pro)), PIGL(NM_004278.4):c.500T>C (p.L167P)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.16316686T>C" "" "pathogenic" "" "0000560373" "0" "10" "17" "16220036" "16220036" "subst" "0.00118171" "01943" "PIGL_000020" "g.16220036G>A" "" "" "" "PIGL(NM_004278.3):c.526+10G>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.16316722G>A" "" "benign" "" "0000623618" "0" "30" "17" "16229133" "16229133" "subst" "6.50666E-5" "01943" "PIGL_000022" "g.16229133G>A" "" "" "" "PIGL(NM_004278.3):c.680G>A (p.R227H)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.16325819G>A" "" "likely benign" "" "0000649498" "1" "50" "17" "16203290" "16203290" "subst" "0.00506818" "03575" "PIGL_000018" "g.16203290C>A" "4/2794 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "conflicting interpretations of pathogenicity; 4 heterozygous, no homozygous; {DB:CLININrs115958467}" "Germline" "" "rs115958467" "0" "" "" "g.16299976C>A" "" "VUS" "" "0000649499" "3" "50" "17" "16220000" "16220000" "subst" "0.000418332" "03575" "PIGL_000002" "g.16220000T>C" "1/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "conflicting interpretations of pathogenicity; 1 homozygous, no heterozygous ; {DB:CLININrs145303331}" "Germline" "" "rs145303331" "0" "" "" "g.16316686T>C" "" "VUS" "" "0000649500" "1" "50" "17" "16221097" "16221097" "subst" "1.21833E-5" "03575" "PIGL_000023" "g.16221097G>A" "7/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "7 heterozygous; {DB:CLININrs116591352}" "Germline" "" "rs116591352" "0" "" "" "g.16317783G>A" "" "VUS" "" "0000658040" "0" "50" "17" "16120683" "16120683" "subst" "4.06058E-6" "01943" "NCOR1_000013" "g.16120683C>T" "" "" "" "PIGL(NM_004278.3):c.143C>T (p.A48V)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.16217369C>T" "" "VUS" "" "0000658041" "0" "90" "17" "16221214" "16221214" "subst" "8.14412E-6" "01943" "PIGL_000003" "g.16221214C>T" "" "" "" "PIGL(NM_004278.3):c.652C>T (p.Q218*), PIGL(NM_004278.4):c.652C>T (p.(Gln218*))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.16317900C>T" "" "pathogenic" "" "0000669383" "3" "50" "17" "16221097" "16221097" "subst" "1.21833E-5" "03575" "PIGL_000023" "g.16221097G>A" "1/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "1 homozygous; {DB:CLININrs116591352}" "Germline" "" "rs116591352" "0" "" "" "g.16317783G>A" "" "VUS" "" "0000680788" "0" "30" "17" "16229183" "16229183" "subst" "1.62559E-5" "01804" "PIGL_000024" "g.16229183A>C" "" "" "" "PIGL(NM_004278.3):c.730A>C (p.(Met244Leu))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000807819" "0" "30" "17" "16203192" "16203192" "subst" "1.21855E-5" "01943" "PIGL_000025" "g.16203192T>G" "" "" "" "PIGL(NM_004278.3):c.336-10T>G" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000982326" "0" "50" "17" "16220000" "16220000" "subst" "0.000418332" "01804" "PIGL_000002" "g.16220000T>C" "" "" "" "PIGL(NM_004278.3):c.500T>C (p.L167P, p.(Leu167Pro)), PIGL(NM_004278.4):c.500T>C (p.L167P)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001041637" "0" "90" "17" "16221214" "16221214" "subst" "8.14412E-6" "01804" "PIGL_000003" "g.16221214C>T" "" "" "" "PIGL(NM_004278.3):c.652C>T (p.Q218*), PIGL(NM_004278.4):c.652C>T (p.(Gln218*))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "pathogenic" "" ## 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 PIGL ## Count = 42 "{{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}}" "0000048940" "00016151" "99" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "5" "0000048941" "00016151" "90" "274" "0" "274" "0" "c.274del" "r.(?)" "p.(Leu92Phefs*15)" "2" "0000048942" "00016151" "90" "652" "0" "652" "0" "c.652C>T" "r.(?)" "p.(Gln218*)" "6" "0000048943" "00016151" "90" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "5" "0000048944" "00016151" "90" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "5" "0000048945" "00016151" "99" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "5" "0000048946" "00016151" "99" "427" "-1" "427" "-1" "c.427-1G>A" "r.spl?" "p.?" "3i" "0000048947" "00016151" "99" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "5" "0000300760" "00016151" "90" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "" "0000337313" "00016151" "10" "779" "0" "779" "0" "c.*20A>G" "r.(=)" "p.(=)" "" "0000346936" "00016151" "90" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "" "0000357711" "00016151" "70" "38" "0" "50" "0" "c.38_50del" "r.(?)" "p.(Val13AlafsTer12)" "" "0000357712" "00016151" "70" "258" "0" "259" "0" "c.258_259del" "r.(?)" "p.(Glu86AspfsTer3)" "" "0000357713" "00016151" "50" "426" "6654" "660" "3131" "c.426+6654_660+3131del" "r.(?)" "p.(Val143_Lys220del)" "" "0000357714" "00016151" "50" "48" "0" "48" "0" "c.48G>A" "r.(?)" "p.(Trp16*)" "" "0000357715" "00016151" "70" "336" "-2" "336" "-2" "c.336-2A>G" "r.spl?" "p.?" "" "0000368182" "00016151" "70" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "" "0000368183" "00016151" "70" "-652" "0" "150" "0" "c.-652_150del" "r.?" "p.?" "_1_1" "0000368249" "00016151" "70" "0" "0" "0" "0" "c.0" "r.0" "p.0" "_1_7_" "0000438442" "00016151" "90" "60" "0" "60" "0" "c.60G>A" "r.(?)" "p.(Trp20*)" "" "0000438443" "00016151" "90" "262" "0" "262" "0" "c.262C>T" "r.(?)" "p.(Arg88Cys)" "" "0000438444" "00016151" "90" "262" "0" "262" "0" "c.262C>T" "r.(?)" "p.(Arg88Cys)" "" "0000438445" "00016151" "90" "60" "0" "60" "0" "c.60G>A" "r.(?)" "p.(Trp20*)" "" "0000438446" "00016151" "90" "262" "0" "262" "0" "c.262C>T" "r.(?)" "p.(Arg88Cys)" "" "0000438447" "00016151" "90" "701" "0" "701" "0" "c.701G>A" "r.(?)" "p.(Arg234His)" "" "0000438448" "00016151" "90" "701" "0" "701" "0" "c.701G>A" "r.(?)" "p.(Arg234His)" "" "0000438449" "00016151" "90" "701" "0" "701" "0" "c.701G>A" "r.(?)" "p.(Arg234His)" "" "0000560370" "00016151" "30" "427" "-3" "427" "-3" "c.427-3del" "r.spl?" "p.?" "" "0000560371" "00016151" "90" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "" "0000560372" "00016151" "90" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "" "0000560373" "00016151" "10" "526" "10" "526" "10" "c.526+10G>A" "r.(=)" "p.(=)" "" "0000623618" "00016151" "30" "680" "0" "680" "0" "c.680G>A" "r.(?)" "p.(Arg227His)" "" "0000649498" "00016151" "50" "424" "0" "424" "0" "c.424C>A" "r.(?)" "p.(Leu142Met)" "" "0000649499" "00016151" "50" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "" "0000649500" "00016151" "50" "535" "0" "535" "0" "c.535G>A" "r.(?)" "p.(Val179Met)" "" "0000658040" "00016151" "50" "143" "0" "143" "0" "c.143C>T" "r.(?)" "p.(Ala48Val)" "" "0000658041" "00016151" "90" "652" "0" "652" "0" "c.652C>T" "r.(?)" "p.(Gln218Ter)" "" "0000669383" "00016151" "50" "535" "0" "535" "0" "c.535G>A" "r.(?)" "p.(Val179Met)" "" "0000680788" "00016151" "30" "730" "0" "730" "0" "c.730A>C" "r.(?)" "p.(Met244Leu)" "" "0000807819" "00016151" "30" "336" "-10" "336" "-10" "c.336-10T>G" "r.(=)" "p.(=)" "" "0000982326" "00016151" "50" "500" "0" "500" "0" "c.500T>C" "r.(?)" "p.(Leu167Pro)" "" "0001041637" "00016151" "90" "652" "0" "652" "0" "c.652C>T" "r.(?)" "p.(Gln218Ter)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 28 "{{screeningid}}" "{{variantid}}" "0000025917" "0000048940" "0000025917" "0000048941" "0000025918" "0000048942" "0000025918" "0000048943" "0000025919" "0000048944" "0000025920" "0000048945" "0000025920" "0000048946" "0000025921" "0000048947" "0000155881" "0000357711" "0000155881" "0000357712" "0000155882" "0000357713" "0000155883" "0000357714" "0000155883" "0000357715" "0000164622" "0000368182" "0000164622" "0000368183" "0000164677" "0000368249" "0000208562" "0000438442" "0000208562" "0000438443" "0000208562" "0000438444" "0000208563" "0000438445" "0000208563" "0000438446" "0000208564" "0000438447" "0000208565" "0000438448" "0000208566" "0000438449" "0000292809" "0000649498" "0000292810" "0000649499" "0000292811" "0000649500" "0000305695" "0000669383"