### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = VPS53) # 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}}" "VPS53" "vacuolar protein sorting 53 homolog (S. cerevisiae)" "17" "p13.3" "unknown" "NC_000017.10" "UD_132376464073" "" "https://www.LOVD.nl/VPS53" "" "1" "25608" "55275" "615850" "1" "1" "1" "1" "Establishment of this gene variant database (LSDB) was performed by Johan den Dunnen, supported by Global Variome." "" "g" "https://databases.lovd.nl/shared/refseq/VPS53_codingDNA.html" "1" "" "" "-1" "" "-1" "00000" "2012-09-13 00:00:00" "00006" "2021-10-07 11:00:08" "00000" "2026-01-20 18:57:21" ## Transcripts ## Do not remove or alter this header ## ## Count = 2 "{{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}}" "00000642" "VPS53" "transcript variant 2" "002" "NM_018289.3" "" "NP_060759.2" "" "" "" "-147" "2547" "2013" "435533" "618096" "00000" "2012-09-13 12:42:33" "" "" "00025638" "VPS53" "transcript variant 1" "001" "NM_001128159.2" "" "NP_001121631.1" "" "" "" "-147" "12959" "2499" "618096" "411908" "00006" "2021-10-06 16:39:34" "" "" ## 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}}" "00000" "Healthy/Control" "Healthy individual / control" "" "" "" "" "" "00000" "2012-07-26 17:29:43" "" "" "01157" "CHTE" "Hypothyroidism, central, testicular enlargement (CHTE)" "XLR" "300888" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "03381" "cancer, gastric" "cancer, gastric (Neoplasm of stomach)" "" "613659" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2017-07-14 15:28:09" "04106" "PCH2E" "hypoplasia, pontocerebellar, type 2e (PCH2E)" "AR" "615851" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2021-10-06 16:41:13" "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 = 2 "{{geneid}}" "{{diseaseid}}" "VPS53" "04106" "VPS53" "05611" ## Individuals ## Do not remove or alter this header ## ## Count = 11 "{{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}}" "00000208" "" "" "" "1" "" "00037" "{PMID:Sun 2011:23143598}, {DOI:Sun 2011:10.1038/ng.2453}" "" "M" "no" "Netherlands" "" "0" "" "" "" "" "00000209" "" "" "" "1" "" "00037" "{PMID:Sun 2011:23143598}, {DOI:Sun 2011:10.1038/ng.2453}" "" "M" "no" "Netherlands" "" "0" "" "" "" "" "00104037" "" "" "" "1" "" "00587" "{PMID:Vogelaar 2017:28875981}, {DOI:Vogelaar 2017:10.1038/ejhg.2017.138}" "54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type gastric cancer" "" "" "" "" "0" "" "" "" "Vogelaar-760A" "00384987" "" "" "" "1" "" "00006" "{PMID:Hady-Cohen 2018:30100179}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "F" "" "Israel" "" "0" "" "" "Jewish;Morocco" "Fam1" "00384988" "" "" "" "2" "" "00006" "{PMID:Feinstein 2014:24577744}" "2-generation family, 2 affected sisters, unaffected heterozygous carrier parents" "F" "" "Israel" "" "0" "" "" "Jewish;Morocco" "Fam2" "00385096" "" "" "" "2" "" "00006" "{PMID:Feinstein 2014:24577744}" "2-generation family, 2 affected brothers, unaffected heterozygous carrier mother" "M" "" "Israel" "" "0" "" "" "Jewish;Morocco" "Fam3" "00385097" "" "" "" "5" "" "00006" "{PMID:Feinstein 2014:24577744}" "4-generation family, 5 affected (2F, 3M), unaffected heterozygous carrier parents" "F;M" "no" "Israel" "" "0" "" "" "Jewish;Morocco" "Fam4" "00385098" "" "" "" "2" "" "00006" "{PMID:Feinstein 2014:24577744}" "analysis 143 controls" "F" "" "Israel" "" "0" "" "" "Jewish;Morocco" "controls" "00385099" "" "" "" "2" "" "00006" "{PMID:Feinstein 2014:24577744}" "analysis 156 controls" "F" "" "Israel" "" "0" "" "" "Jewish;Morocco" "controls" "00385102" "" "" "" "1" "" "00006" "{PMID:Hady-Cohen 2018:30100179}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "M" "" "Israel" "" "0" "" "" "Jewish;Morocco" "Fam2" "00385103" "" "" "" "2" "" "00006" "{PMID:Hausman-Kedem 2019:31418091}" "3-generation family, 2 affected sisters, unaffected heterozygous carrier parents" "F" "no" "Israel" "" "0" "" "" "Jewish;Morocco" "family" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 11 "{{individualid}}" "{{diseaseid}}" "00000208" "01157" "00000209" "01157" "00104037" "03381" "00384987" "05611" "00384988" "05611" "00385096" "05611" "00385097" "05611" "00385098" "00000" "00385099" "00000" "00385102" "05611" "00385103" "05611" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00000, 01157, 03381, 04106, 05611 ## Count = 9 "{{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}}" "{{Phenotype/Diagnosis/Criteria}}" "0000038983" "01157" "00000208" "00006" "Familial, X-linked recessive" "" "central hypothyroidism (FT4 0.50-0.99of lower limit normal), no prolactin deficiency, age sonographic determination testicular volume 17.64y, testicular volume right/left 21/20 (7.3–16ml)" "" "3w" "" "" "" "" "" "" "" "" "0000038984" "01157" "00000209" "00006" "Familial, X-linked recessive" "" "central hypothyroidism (FT4 0.50-0.99of lower limit normal), prolactin deficiency, age sonographic determination testicular volume 21.36y, testicular volume right/left 30/26 (8.5–18.3ml)" "" "07y04m" "" "" "" "" "" "" "" "" "0000081971" "03381" "00104037" "00587" "Unknown" "" "diffuse-type or intestinal-type gastric cancer" "" "" "" "" "" "" "" "" "" "" "0000278771" "05611" "00384987" "00006" "Familial, autosomal recessive" "12y" "see paper; ..., severe global developmental delay (HP:0001263), profound intellectual disability (HP:0001249), microcephaly (HP:0000252), limb and facila edema (HP:0000969), early-onset epilepsy (HP:0001250), spasticity (HP:0001257), optic atrophy (HP:0001138); abnormal brain morphology (HP:0012443), normal/mild unspecific anomalies early in life followed by cerebellar and cerebral atrophy; no cholestasis (-HP:0001396); failure to thrive (HP:0001508)" "" "" "" "" "" "" "" "PCH2E" "PHEO syndrome" "" "0000278772" "05611" "00384988" "00006" "Familial, autosomal recessive" "" "see paper; ..., severe global developmental delay (HP:0001263), profound intellectual disability (HP:0001249), microcephaly (HP:0000252), early-onset epilepsy (HP:0001250), progressive spastic quadriplegia, opisthotonos (HP:0001257), irritability (HP:0000737), no optic atrophy (-HP:0001138); abnormal brain morphology (HP:0012443), normal early in life followed by cerebellar, cerebral and corpus callosum atrophy; no cholestasis (-HP:0001396)" "" "" "" "" "" "" "" "PCH2E" "neurodevelopmental delay" "" "0000278880" "05611" "00385096" "00006" "Familial, autosomal recessive" "" "see paper; ..., severe global developmental delay (HP:0001263), profound intellectual disability (HP:0001249), microcephaly (HP:0000252), early-onset epilepsy (HP:0001250), progressive spastic quadriplegia, opisthotonos (HP:0001257), irritability (HP:0000737), no optic atrophy (-HP:0001138); abnormal brain morphology (HP:0012443), normal early in life followed by cerebellar, cerebral and corpus callosum atrophy; no cholestasis (-HP:0001396)" "" "" "" "" "" "" "" "PCH2E" "neurodevelopmental delay" "" "0000278882" "05611" "00385097" "00006" "Familial, autosomal recessive" "" "see paper; ..., severe global developmental delay (HP:0001263), profound intellectual disability (HP:0001249), microcephaly (HP:0000252), early-onset epilepsy (HP:0001250), progressive spastic quadriplegia, opisthotonos (HP:0001257), irritability (HP:0000737), no optic atrophy (-HP:0001138); abnormal brain morphology (HP:0012443), normal early in life followed by cerebellar, cerebral and corpus callosum atrophy; no cholestasis (-HP:0001396)" "" "" "" "" "" "" "" "PCH2E" "neurodevelopmental delay" "" "0000278885" "05611" "00385102" "00006" "Familial, autosomal recessive" "11y" "see paper; ..., severe global developmental delay (HP:0001263), profound intellectual disability (HP:0001249), microcephaly (HP:0000252), limb and facila edema (HP:0000969), early-onset epilepsy (HP:0001250), spasticity (HP:0001257), optic atrophy (HP:0001138); abnormal brain morphology (HP:0012443), normal/mild unspecific anomalies early in life followed by cerebellar and cerebral atrophy; no cholestasis (-HP:0001396); failure to thrive (HP:0001508)" "" "" "" "" "" "" "" "PCH2E" "PHEO syndrome" "" "0000278886" "05611" "00385103" "00006" "Familial, autosomal recessive" "" "see paper; ..., moderate global developmental delay (HP:0001263), mild/moderate intellectual disability (HP:0001249), no microcephaly (-HP:0000252), progressive spastic paraparesis (HP:0001257), no irritability (-HP:0000737, no optic atrophy (-HP:0001138); normal brain morphology (-HP:0012443); no cholestasis (-HP:0001396); no failure to thrive (-HP:0001508)" "" "" "" "" "" "" "" "PCH2E" "hereditary spastic paraparesis" "" ## Screenings ## Do not remove or alter this header ## ## Count = 11 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000000209" "00000208" "1" "00037" "00001" "2012-09-13 12:02:03" "" "" "SEQ-NG-I" "DNA" "" "" "0000000210" "00000209" "1" "00037" "00001" "2012-09-13 12:09:36" "" "" "SEQ-NG-I" "DNA" "" "" "0000104508" "00104037" "1" "00587" "00006" "2017-04-28 08:15:46" "" "" "SEQ-NG" "DNA" "" "" "0000386216" "00384987" "1" "00006" "00006" "2021-10-06 16:52:14" "00006" "2021-10-07 09:38:25" "SEQ;SEQ-NG" "DNA" "" "WES" "0000386217" "00384988" "1" "00006" "00006" "2021-10-06 16:52:14" "" "" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "WES" "0000386325" "00385096" "1" "00006" "00006" "2021-10-06 16:52:14" "" "" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "WES" "0000386326" "00385097" "1" "00006" "00006" "2021-10-06 16:52:14" "" "" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "WES" "0000386327" "00385098" "1" "00006" "00006" "2021-10-06 16:52:14" "" "" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "WES" "0000386328" "00385099" "1" "00006" "00006" "2021-10-06 16:52:14" "" "" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "WES" "0000386331" "00385102" "1" "00006" "00006" "2021-10-06 16:52:14" "00006" "2021-10-06 16:58:42" "SEQ;SEQ-NG" "DNA" "" "WES" "0000386332" "00385103" "1" "00006" "00006" "2021-10-07 09:55:06" "00006" "2021-10-07 09:58:21" "SEQ" "DNA" "" "WES" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 8 "{{screeningid}}" "{{geneid}}" "0000386216" "VPS53" "0000386217" "VPS53" "0000386325" "VPS53" "0000386326" "VPS53" "0000386327" "VPS53" "0000386328" "VPS53" "0000386331" "VPS53" "0000386332" "VPS53" ## 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 = 52 "{{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}}" "0000002652" "3" "50" "17" "559940" "559945" "del" "0" "00037" "VPS53_000009" "g.559940_559945del" "" "" "" "" "" "Germline" "" "" "" "" "" "g.656700_656705del" "" "VUS" "" "0000005642" "0" "50" "17" "559888" "559888" "subst" "0" "00037" "VPS53_000007" "g.559888A>T" "" "" "" "" "" "Germline" "" "" "" "" "" "g.656648A>T" "" "VUS" "" "0000005643" "0" "50" "17" "560009" "560009" "subst" "0" "00037" "VPS53_000001" "g.560009T>C" "" "" "" "" "" "Germline" "" "" "" "" "" "g.656769T>C" "" "VUS" "" "0000005644" "0" "50" "17" "560221" "560221" "subst" "0" "00037" "VPS53_000002" "g.560221G>A" "" "" "" "" "" "Germline" "" "" "" "" "" "g.656981G>A" "" "VUS" "" "0000005645" "0" "50" "17" "560604" "560604" "subst" "0" "00037" "VPS53_000003" "g.560604T>C" "" "" "" "" "" "Germline" "" "" "" "" "" "g.657364T>C" "" "VUS" "" "0000005646" "0" "50" "17" "560851" "560851" "subst" "0" "00037" "VPS53_000005" "g.560851T>C" "" "" "" "" "" "Germline" "" "" "" "" "" "g.657611T>C" "" "VUS" "" "0000010658" "0" "50" "17" "559940" "559945" "del" "0" "00037" "VPS53_000009" "g.559940_559945del" "" "" "" "" "" "Germline" "" "" "" "" "" "g.656700_656705del" "" "VUS" "" "0000010659" "0" "50" "17" "559940" "559947" "del" "0" "00037" "VPS53_000011" "g.559940_559947del" "" "" "" "" "" "Germline" "" "" "" "" "" "g.656700_656707del" "" "VUS" "" "0000013619" "3" "50" "17" "559888" "559888" "subst" "0" "00037" "VPS53_000007" "g.559888A>T" "" "" "" "" "" "Germline" "" "" "" "" "" "g.656648A>T" "" "VUS" "" "0000013620" "3" "50" "17" "560604" "560604" "subst" "0" "00037" "VPS53_000003" "g.560604T>C" "" "" "" "" "" "Germline" "" "" "" "" "" "g.657364T>C" "" "VUS" "" "0000013621" "3" "50" "17" "560851" "560851" "subst" "0" "00037" "VPS53_000005" "g.560851T>C" "" "" "" "" "" "Germline" "" "" "" "" "" "g.657611T>C" "" "VUS" "" "0000169433" "0" "70" "17" "526807" "526807" "subst" "0.000121833" "00587" "VPS53_000012" "g.526807C>T" "" "{PMID:Vogelaar 2017:28875981}, {DOI:Vogelaar 2017:10.1038/ejhg.2017.138}" "" "NM_001128159.2(VPS53):c.1082G>A p.(Arg361His)" "variant could not be associated with disease phenotype" "Germline" "" "" "0" "" "" "g.623567C>T" "" "likely pathogenic" "" "0000247458" "0" "10" "17" "600735" "600735" "subst" "0.187402" "02330" "VPS53_000014" "g.600735A>G" "" "" "" "VPS53(NM_001128159.3):c.219-11T>C" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.697495A>G" "" "benign" "" "0000311322" "0" "10" "17" "465775" "465775" "subst" "0.278341" "02330" "VPS53_000015" "g.465775G>A" "" "" "" "VPS53(NM_001128159.3):c.1524C>T (p.Y508=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.562535G>A" "" "benign" "" "0000311323" "0" "10" "17" "423051" "423051" "subst" "0.597773" "02330" "VPS53_000017" "g.423051T>C" "" "" "" "VPS53(NM_001128159.3):c.2328+15A>G" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.519811T>C" "" "benign" "" "0000315356" "0" "90" "17" "600705" "600705" "subst" "8.12156E-6" "02326" "VPS53_000016" "g.600705G>A" "" "" "" "VPS53(NM_001128159.3):c.238C>T (p.R80*)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.697465G>A" "" "pathogenic" "" "0000562106" "0" "10" "17" "466004" "466004" "dup" "0" "02330" "VPS53_000018" "g.466004dup" "" "" "" "VPS53(NM_001128159.3):c.1314-9dupT" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.562764dup" "" "benign" "" "0000562307" "0" "10" "17" "505139" "505139" "subst" "0.0860451" "02325" "VPS53_000019" "g.505139G>A" "" "" "" "VPS53(NM_001128159.3):c.1117-3C>T" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.601899G>A" "" "benign" "" "0000562631" "0" "10" "17" "617869" "617869" "subst" "0.210684" "02330" "VPS53_000020" "g.617869G>A" "" "" "" "VPS53(NM_001128159.3):c.81C>T (p.I27=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.714629G>A" "" "benign" "" "0000623719" "0" "50" "17" "530438" "530438" "subst" "0.000139162" "01943" "VPS53_000021" "g.530438G>A" "" "" "" "VPS53(NM_001128159.2):c.950C>T (p.A317V)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.627198G>A" "" "VUS" "" "0000658166" "0" "30" "17" "455184" "455184" "subst" "0.00064686" "01943" "VPS53_000022" "g.455184G>A" "" "" "" "VPS53(NM_001128159.2):c.1794C>T (p.I598=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.551944G>A" "" "likely benign" "" "0000680927" "0" "50" "17" "526814" "526814" "subst" "1.62443E-5" "01943" "VPS53_000023" "g.526814C>G" "" "" "" "VPS53(NM_001128159.2):c.1075G>C (p.A359P)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000692402" "0" "30" "17" "530420" "530420" "subst" "2.87158E-5" "01943" "VPS53_000024" "g.530420A>G" "" "" "" "VPS53(NM_001128159.2):c.968T>C (p.V323A)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000692429" "0" "50" "17" "600663" "600663" "subst" "0.000113714" "01943" "VPS53_000025" "g.600663G>A" "" "" "" "VPS53(NM_001128159.2):c.280C>T (p.R94W)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000726453" "0" "50" "17" "424905" "424905" "subst" "6.59918E-6" "02325" "VPS53_000026" "g.424905T>G" "" "" "" "VPS53(NM_001128159.3):c.2159A>C (p.K720T)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000726474" "0" "50" "17" "456629" "456629" "subst" "8.93604E-5" "02325" "VPS53_000027" "g.456629G>A" "" "" "" "VPS53(NM_001128159.3):c.1778C>T (p.(Thr593Met), p.T593M)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000808059" "0" "30" "17" "455147" "455147" "subst" "3.42636E-5" "01943" "VPS53_000028" "g.455147C>T" "" "" "" "VPS53(NM_001128159.2):c.1831G>A (p.A611T)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000808060" "0" "30" "17" "463696" "463696" "subst" "0.00064225" "01943" "VPS53_000029" "g.463696C>T" "" "" "" "VPS53(NM_001128159.2):c.1674G>A (p.T558=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000813621" "1" "90" "17" "465738" "465738" "subst" "0" "00006" "VPS53_000030" "g.465738C>T" "" "{PMID:Hady-Cohen 2018:30100179}" "" "" "" "Germline" "" "" "0" "" "" "g.562498C>T" "" "pathogenic (recessive)" "" "0000813622" "2" "90" "17" "436083" "436083" "subst" "0" "00006" "VPS53_000031" "g.436083T>C" "" "{PMID:Hady-Cohen 2018:30100179}" "" "" "" "Germline" "" "" "0" "" "" "g.532843T>C" "" "pathogenic (recessive)" "" "0000813623" "11" "90" "17" "465738" "465738" "subst" "0" "00006" "VPS53_000030" "g.465738C>T" "" "{PMID:Feinstein 2014:24577744}" "" "" "" "Germline" "yes" "" "0" "" "" "g.562498C>T" "" "pathogenic (recessive)" "" "0000813624" "21" "90" "17" "436083" "436083" "subst" "0" "00006" "VPS53_000031" "g.436083T>C" "" "{PMID:Feinstein 2014:24577744}" "" "" "" "Germline" "yes" "" "0" "" "" "g.532843T>C" "" "pathogenic (recessive)" "" "0000813792" "20" "90" "17" "465738" "465738" "subst" "0" "00006" "VPS53_000030" "g.465738C>T" "" "{PMID:Feinstein 2014:24577744}" "" "" "" "Germline" "yes" "" "0" "" "" "g.562498C>T" "" "pathogenic (recessive)" "" "0000813793" "21" "90" "17" "436083" "436083" "subst" "0" "00006" "VPS53_000031" "g.436083T>C" "" "{PMID:Feinstein 2014:24577744}" "" "" "" "Germline" "yes" "" "0" "" "" "g.532843T>C" "" "pathogenic (recessive)" "" "0000813794" "1" "90" "17" "465738" "465738" "subst" "0" "00006" "VPS53_000030" "g.465738C>T" "" "{PMID:Feinstein 2014:24577744}" "" "" "" "Germline" "yes" "" "0" "" "" "g.562498C>T" "" "pathogenic (recessive)" "" "0000813795" "2" "90" "17" "436083" "436083" "subst" "0" "00006" "VPS53_000031" "g.436083T>C" "" "{PMID:Feinstein 2014:24577744}" "" "" "" "Germline" "yes" "" "0" "" "" "g.532843T>C" "" "pathogenic (recessive)" "" "0000813796" "0" "90" "17" "436083" "436083" "subst" "0" "00006" "VPS53_000031" "g.436083T>C" "2/143 control individuals" "{PMID:Feinstein 2014:24577744}" "" "" "" "Germline" "" "" "0" "" "" "g.532843T>C" "" "pathogenic (recessive)" "" "0000813797" "1" "90" "17" "465738" "465738" "subst" "0" "00006" "VPS53_000030" "g.465738C>T" "2/156 control individuals" "{PMID:Feinstein 2014:24577744}" "" "" "" "Germline" "" "" "0" "" "" "g.562498C>T" "" "pathogenic (recessive)" "" "0000813804" "1" "90" "17" "465738" "465738" "subst" "0" "00006" "VPS53_000030" "g.465738C>T" "" "{PMID:Hady-Cohen 2018:30100179}" "" "" "" "Germline" "" "" "0" "" "" "g.562498C>T" "" "pathogenic (recessive)" "" "0000813805" "2" "90" "17" "436083" "436083" "subst" "0" "00006" "VPS53_000031" "g.436083T>C" "" "{PMID:Hady-Cohen 2018:30100179}" "" "" "" "Germline" "" "" "0" "" "" "g.532843T>C" "" "pathogenic (recessive)" "" "0000813806" "3" "90" "17" "436083" "436083" "subst" "0" "00006" "VPS53_000031" "g.436083T>C" "" "{PMID:Hausman-Kedem 2019:31418091}" "" "" "" "Germline" "yes" "" "0" "" "" "g.532843T>C" "" "pathogenic (recessive)" "" "0000854940" "0" "30" "17" "423141" "423141" "subst" "0.00127706" "01943" "VPS53_000033" "g.423141C>T" "" "" "" "VPS53(NM_001128159.2):c.2253G>A (p.V751=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000854963" "0" "30" "17" "436121" "436121" "subst" "0.00536163" "01943" "VPS53_000034" "g.436121G>A" "" "" "" "VPS53(NM_001128159.2):c.2046C>T (p.L682=), VPS53(NM_001128159.3):c.2046C>T (p.(Leu682=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000865306" "0" "50" "17" "422409" "422409" "subst" "6.88952E-6" "01943" "VPS53_000032" "g.422409G>A" "" "" "" "VPS53(NM_001128159.2):c.2458C>T (p.R820C)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000865336" "0" "30" "17" "456673" "456673" "subst" "4.06213E-6" "01943" "VPS53_000035" "g.456673A>G" "" "" "" "VPS53(NM_001128159.2):c.1734T>C (p.D578=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000982559" "0" "30" "17" "436121" "436121" "subst" "0.00536163" "01804" "VPS53_000034" "g.436121G>A" "" "" "" "VPS53(NM_001128159.2):c.2046C>T (p.L682=), VPS53(NM_001128159.3):c.2046C>T (p.(Leu682=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0001041938" "0" "50" "17" "465845" "465845" "subst" "0" "01804" "VPS53_000037" "g.465845C>A" "" "" "" "VPS53(NM_001128159.3):c.1454G>T (p.(Cys485Phe))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001041986" "0" "50" "17" "489576" "489576" "subst" "6.90518E-5" "01804" "VPS53_000038" "g.489576G>T" "" "" "" "VPS53(NM_001128159.3):c.1247C>A (p.(Pro416Gln))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001041991" "0" "30" "17" "535990" "535990" "subst" "0" "01804" "VPS53_000039" "g.535990G>A" "" "" "" "VPS53(NM_001366254.2):c.8C>T (p.(Ser3Leu))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0001055759" "0" "50" "17" "423155" "423155" "subst" "0" "01804" "VPS53_000040" "g.423155G>C" "" "" "" "VPS53(NM_001128159.3):c.2239C>G (p.(His747Asp))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001055760" "0" "50" "17" "456629" "456629" "subst" "8.93604E-5" "01804" "VPS53_000027" "g.456629G>A" "" "" "" "VPS53(NM_001128159.3):c.1778C>T (p.(Thr593Met), p.T593M)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001066588" "0" "50" "17" "440338" "440338" "subst" "0" "02325" "VPS53_000041" "g.440338C>A" "" "" "" "" "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 VPS53 ## Count = 104 "{{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}}" "0000002652" "00025638" "50" "373" "-752" "373" "-747" "c.373-752_373-747del" "r.(=)" "p.(=)" "" "0000002652" "00000642" "50" "286" "-752" "286" "-747" "c.286-752_286-747del" "r.(=)" "p.(=)" "" "0000005642" "00025638" "50" "373" "-695" "373" "-695" "c.373-695T>A" "r.(=)" "p.(=)" "" "0000005642" "00000642" "50" "286" "-695" "286" "-695" "c.286-695T>A" "r.(=)" "p.(=)" "" "0000005643" "00025638" "50" "373" "-816" "373" "-816" "c.373-816A>G" "r.(=)" "p.(=)" "" "0000005643" "00000642" "50" "286" "-816" "286" "-816" "c.286-816A>G" "r.(=)" "p.(=)" "" "0000005644" "00025638" "50" "373" "-1028" "373" "-1028" "c.373-1028C>T" "r.(=)" "p.(=)" "" "0000005644" "00000642" "50" "286" "-1028" "286" "-1028" "c.286-1028C>T" "r.(=)" "p.(=)" "" "0000005645" "00025638" "50" "373" "-1411" "373" "-1411" "c.373-1411A>G" "r.(=)" "p.(=)" "" "0000005645" "00000642" "50" "286" "-1411" "286" "-1411" "c.286-1411A>G" "r.(=)" "p.(=)" "" "0000005646" "00025638" "50" "373" "-1658" "373" "-1658" "c.373-1658A>G" "r.(=)" "p.(=)" "" "0000005646" "00000642" "50" "286" "-1658" "286" "-1658" "c.286-1658A>G" "r.(=)" "p.(=)" "" "0000010658" "00025638" "50" "373" "-752" "373" "-747" "c.373-752_373-747del" "r.(=)" "p.(=)" "" "0000010658" "00000642" "50" "286" "-752" "286" "-747" "c.286-752_286-747del" "r.(=)" "p.(=)" "" "0000010659" "00025638" "50" "373" "-754" "373" "-747" "c.373-754_373-747del" "r.(=)" "p.(=)" "" "0000010659" "00000642" "50" "286" "-754" "286" "-747" "c.286-754_286-747del" "r.(=)" "p.(=)" "" "0000013619" "00025638" "50" "373" "-695" "373" "-695" "c.373-695T>A" "r.(=)" "p.(=)" "" "0000013619" "00000642" "50" "286" "-695" "286" "-695" "c.286-695T>A" "r.(=)" "p.(=)" "" "0000013620" "00025638" "50" "373" "-1411" "373" "-1411" "c.373-1411A>G" "r.(=)" "p.(=)" "" "0000013620" "00000642" "50" "286" "-1411" "286" "-1411" "c.286-1411A>G" "r.(=)" "p.(=)" "" "0000013621" "00025638" "50" "373" "-1658" "373" "-1658" "c.373-1658A>G" "r.(=)" "p.(=)" "" "0000013621" "00000642" "50" "286" "-1658" "286" "-1658" "c.286-1658A>G" "r.(=)" "p.(=)" "" "0000169433" "00025638" "70" "1082" "0" "1082" "0" "c.1082G>A" "r.(?)" "p.(Arg361His)" "" "0000169433" "00000642" "00" "995" "0" "995" "0" "c.995G>A" "r.(?)" "p.(Arg332His)" "" "0000247458" "00025638" "10" "219" "-11" "219" "-11" "c.219-11T>C" "r.(=)" "p.(=)" "" "0000247458" "00000642" "10" "219" "-11" "219" "-11" "c.219-11T>C" "r.(=)" "p.(=)" "" "0000311322" "00025638" "10" "1524" "0" "1524" "0" "c.1524C>T" "r.(?)" "p.(Tyr508=)" "" "0000311322" "00000642" "10" "1437" "0" "1437" "0" "c.1437C>T" "r.(?)" "p.(Tyr479=)" "" "0000311323" "00025638" "10" "2328" "15" "2328" "15" "c.2328+15A>G" "r.(=)" "p.(=)" "" "0000311323" "00000642" "10" "15029" "0" "15029" "0" "c.*13016A>G" "r.(=)" "p.(=)" "" "0000315356" "00025638" "90" "238" "0" "238" "0" "c.238C>T" "r.(?)" "p.(Arg80Ter)" "" "0000315356" "00000642" "90" "238" "0" "238" "0" "c.238C>T" "r.(?)" "p.(Arg80Ter)" "" "0000562106" "00025638" "10" "1314" "-9" "1314" "-9" "c.1314-9dup" "r.(=)" "p.(=)" "" "0000562106" "00000642" "10" "1227" "-9" "1227" "-9" "c.1227-9dup" "r.(=)" "p.(=)" "" "0000562307" "00025638" "10" "1117" "-3" "1117" "-3" "c.1117-3C>T" "r.spl?" "p.?" "" "0000562307" "00000642" "10" "1030" "-3" "1030" "-3" "c.1030-3C>T" "r.spl?" "p.?" "" "0000562631" "00025638" "10" "81" "0" "81" "0" "c.81C>T" "r.(?)" "p.(Ile27=)" "" "0000562631" "00000642" "10" "81" "0" "81" "0" "c.81C>T" "r.(?)" "p.(Ile27=)" "" "0000623719" "00025638" "50" "950" "0" "950" "0" "c.950C>T" "r.(?)" "p.(Ala317Val)" "" "0000623719" "00000642" "50" "863" "0" "863" "0" "c.863C>T" "r.(?)" "p.(Ala288Val)" "" "0000658166" "00025638" "30" "1794" "0" "1794" "0" "c.1794C>T" "r.(?)" "p.(Ile598=)" "" "0000658166" "00000642" "30" "1707" "0" "1707" "0" "c.1707C>T" "r.(?)" "p.(Ile569=)" "" "0000680927" "00025638" "50" "1075" "0" "1075" "0" "c.1075G>C" "r.(?)" "p.(Ala359Pro)" "" "0000680927" "00000642" "50" "988" "0" "988" "0" "c.988G>C" "r.(?)" "p.(Ala330Pro)" "" "0000692402" "00025638" "30" "968" "0" "968" "0" "c.968T>C" "r.(?)" "p.(Val323Ala)" "" "0000692402" "00000642" "30" "881" "0" "881" "0" "c.881T>C" "r.(?)" "p.(Val294Ala)" "" "0000692429" "00025638" "50" "280" "0" "280" "0" "c.280C>T" "r.(?)" "p.(Arg94Trp)" "" "0000692429" "00000642" "50" "280" "0" "280" "0" "c.280C>T" "r.(?)" "p.(Arg94Trp)" "" "0000726453" "00025638" "50" "2159" "0" "2159" "0" "c.2159A>C" "r.(?)" "p.(Lys720Thr)" "" "0000726453" "00000642" "50" "13175" "0" "13175" "0" "c.*11162A>C" "r.(=)" "p.(=)" "" "0000726474" "00025638" "50" "1778" "0" "1778" "0" "c.1778C>T" "r.(?)" "p.(Thr593Met)" "" "0000726474" "00000642" "50" "1691" "0" "1691" "0" "c.1691C>T" "r.(?)" "p.(Thr564Met)" "" "0000808059" "00025638" "30" "1831" "0" "1831" "0" "c.1831G>A" "r.(?)" "p.(Ala611Thr)" "" "0000808059" "00000642" "30" "1744" "0" "1744" "0" "c.1744G>A" "r.(?)" "p.(Ala582Thr)" "" "0000808060" "00025638" "30" "1674" "0" "1674" "0" "c.1674G>A" "r.(?)" "p.(Thr558=)" "" "0000808060" "00000642" "30" "1587" "0" "1587" "0" "c.1587G>A" "r.(?)" "p.(Thr529=)" "" "0000813621" "00025638" "90" "1556" "5" "1556" "5" "c.1556+5G>A" "r.spl" "p.?" "" "0000813621" "00000642" "90" "1469" "5" "1469" "5" "c.1469+5G>A" "r.spl" "p.?" "" "0000813622" "00025638" "90" "2084" "0" "2084" "0" "c.2084A>G" "r.2084a>g" "p.Gln695Arg" "" "0000813622" "00000642" "90" "1997" "0" "1997" "0" "c.1997A>G" "r.(?)" "p.(Gln666Arg)" "" "0000813623" "00025638" "90" "1556" "5" "1556" "5" "c.1556+5G>A" "r.spl" "p.?" "" "0000813623" "00000642" "90" "1469" "5" "1469" "5" "c.1469+5G>A" "r.spl" "p.?" "" "0000813624" "00025638" "90" "2084" "0" "2084" "0" "c.2084A>G" "r.2084a>g" "p.Gln695Arg" "" "0000813624" "00000642" "90" "1997" "0" "1997" "0" "c.1997A>G" "r.(?)" "p.(Gln666Arg)" "" "0000813792" "00025638" "90" "1556" "5" "1556" "5" "c.1556+5G>A" "r.spl" "p.?" "" "0000813792" "00000642" "90" "1469" "5" "1469" "5" "c.1469+5G>A" "r.spl" "p.?" "" "0000813793" "00025638" "90" "2084" "0" "2084" "0" "c.2084A>G" "r.2084a>g" "p.Gln695Arg" "" "0000813793" "00000642" "90" "1997" "0" "1997" "0" "c.1997A>G" "r.(?)" "p.(Gln666Arg)" "" "0000813794" "00025638" "90" "1556" "5" "1556" "5" "c.1556+5G>A" "r.spl" "p.?" "" "0000813794" "00000642" "90" "1469" "5" "1469" "5" "c.1469+5G>A" "r.spl" "p.?" "" "0000813795" "00025638" "90" "2084" "0" "2084" "0" "c.2084A>G" "r.2084a>g" "p.Gln695Arg" "" "0000813795" "00000642" "90" "1997" "0" "1997" "0" "c.1997A>G" "r.(?)" "p.(Gln666Arg)" "" "0000813796" "00025638" "90" "2084" "0" "2084" "0" "c.2084A>G" "r.2084a>g" "p.Gln695Arg" "" "0000813796" "00000642" "90" "1997" "0" "1997" "0" "c.1997A>G" "r.(?)" "p.(Gln666Arg)" "" "0000813797" "00025638" "90" "1556" "5" "1556" "5" "c.1556+5G>A" "r.spl" "p.?" "" "0000813797" "00000642" "90" "1469" "5" "1469" "5" "c.1469+5G>A" "r.spl" "p.?" "" "0000813804" "00025638" "90" "1556" "5" "1556" "5" "c.1556+5G>A" "r.spl" "p.?" "" "0000813804" "00000642" "90" "1469" "5" "1469" "5" "c.1469+5G>A" "r.spl" "p.?" "" "0000813805" "00025638" "90" "2084" "0" "2084" "0" "c.2084A>G" "r.2084a>g" "p.Gln695Arg" "" "0000813805" "00000642" "90" "1997" "0" "1997" "0" "c.1997A>G" "r.(?)" "p.(Gln666Arg)" "" "0000813806" "00025638" "90" "2084" "0" "2084" "0" "c.2084A>G" "r.(?)" "p.(Gln695Arg)" "" "0000813806" "00000642" "90" "1997" "0" "1997" "0" "c.1997A>G" "r.(?)" "p.(Gln666Arg)" "" "0000854940" "00025638" "30" "2253" "0" "2253" "0" "c.2253G>A" "r.(?)" "p.(Val751=)" "" "0000854940" "00000642" "30" "14939" "0" "14939" "0" "c.*12926G>A" "r.(=)" "p.(=)" "" "0000854963" "00025638" "30" "2046" "0" "2046" "0" "c.2046C>T" "r.(?)" "p.(Leu682=)" "" "0000854963" "00000642" "30" "1959" "0" "1959" "0" "c.1959C>T" "r.(?)" "p.(Leu653=)" "" "0000865306" "00025638" "50" "2458" "0" "2458" "0" "c.2458C>T" "r.(?)" "p.(Arg820Cys)" "" "0000865306" "00000642" "50" "15671" "0" "15671" "0" "c.*13658C>T" "r.(=)" "p.(=)" "" "0000865336" "00025638" "30" "1734" "0" "1734" "0" "c.1734T>C" "r.(?)" "p.(Asp578=)" "" "0000865336" "00000642" "30" "1647" "0" "1647" "0" "c.1647T>C" "r.(?)" "p.(Asp549=)" "" "0000982559" "00025638" "30" "2046" "0" "2046" "0" "c.2046C>T" "r.(?)" "p.(Leu682=)" "" "0000982559" "00000642" "30" "1959" "0" "1959" "0" "c.1959C>T" "r.(?)" "p.(Leu653=)" "" "0001041938" "00025638" "50" "1454" "0" "1454" "0" "c.1454G>T" "r.(?)" "p.(Cys485Phe)" "" "0001041938" "00000642" "50" "1367" "0" "1367" "0" "c.1367G>T" "r.(?)" "p.(Cys456Phe)" "" "0001041986" "00025638" "50" "1247" "0" "1247" "0" "c.1247C>A" "r.(?)" "p.(Pro416Gln)" "" "0001041986" "00000642" "50" "1160" "0" "1160" "0" "c.1160C>A" "r.(?)" "p.(Pro387Gln)" "" "0001041991" "00025638" "30" "609" "-1122" "609" "-1122" "c.609-1122C>T" "r.(=)" "p.(=)" "" "0001041991" "00000642" "30" "522" "-1122" "522" "-1122" "c.522-1122C>T" "r.(=)" "p.(=)" "" "0001055759" "00025638" "50" "2239" "0" "2239" "0" "c.2239C>G" "r.(?)" "p.(His747Asp)" "" "0001055759" "00000642" "50" "14925" "0" "14925" "0" "c.*12912C>G" "r.(=)" "p.(=)" "" "0001055760" "00025638" "50" "1778" "0" "1778" "0" "c.1778C>T" "r.(?)" "p.(Thr593Met)" "" "0001055760" "00000642" "50" "1691" "0" "1691" "0" "c.1691C>T" "r.(?)" "p.(Thr564Met)" "" "0001066588" "00025638" "50" "1945" "0" "1945" "0" "c.1945G>T" "r.(?)" "p.(Val649Phe)" "" "0001066588" "00000642" "50" "1858" "0" "1858" "0" "c.1858G>T" "r.(?)" "p.(Val620Phe)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 25 "{{screeningid}}" "{{variantid}}" "0000000209" "0000002652" "0000000209" "0000005642" "0000000209" "0000005643" "0000000209" "0000005644" "0000000209" "0000005645" "0000000209" "0000005646" "0000000210" "0000010658" "0000000210" "0000010659" "0000000210" "0000013619" "0000000210" "0000013620" "0000000210" "0000013621" "0000104508" "0000169433" "0000386216" "0000813621" "0000386216" "0000813622" "0000386217" "0000813623" "0000386217" "0000813624" "0000386325" "0000813792" "0000386325" "0000813793" "0000386326" "0000813794" "0000386326" "0000813795" "0000386327" "0000813796" "0000386328" "0000813797" "0000386331" "0000813804" "0000386331" "0000813805" "0000386332" "0000813806"