### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = VIM) # 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}}" "VIM" "vimentin" "10" "p13" "unknown" "NG_012413.1" "UD_132118980016" "" "https://www.LOVD.nl/VIM" "" "1" "12692" "7431" "193060" "1" "1" "1" "1" "This database is one of the \"Eye disease\" gene variant databases.\r\nEstablishment of this gene variant database (LSDB) was performed by Johan den Dunnen, supported by Global Variome." "" "g" "https://databases.lovd.nl/shared/refseq/VIM_codingDNA.html" "1" "" "This database is one of the \"Eye disease\" gene variant databases." "-1" "" "-1" "00001" "2010-03-01 00:00:00" "00006" "2020-11-26 19:48:18" "00000" "2024-04-19 20:27:30" ## 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}}" "00022604" "VIM" "vimentin" "001" "NM_003380.3" "" "NP_003371.2" "" "" "" "-413" "1723" "1401" "17270258" "17279592" "" "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}}" "00198" "?" "unclassified / mixed" "" "" "" "" "" "00006" "2013-09-13 14:21:47" "00006" "2024-11-23 09:38:12" "00296" "CTRCT" "cataract (CTRCT)" "" "" "" "" "" "00006" "2014-01-16 08:42:13" "00006" "2015-03-07 14:30:33" "00312" "FAP1" "adenomatous polyposis, familial, type 1 (FAP-1, Gardner syndrome)" "AD" "175100" "" "" "" "00006" "2014-01-27 14:53:36" "00006" "2021-12-10 21:51:32" "01236" "CTRCT30" "cataract, type 30 (CTRCT-30, pulvurent)" "AD" "116300" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "04214" "-" "retinal disease" "" "" "" "" "" "00006" "2015-02-27 19:48:07" "00001" "2023-03-09 14:26:26" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "VIM" "01236" ## Individuals ## Do not remove or alter this header ## ## Count = 9 "{{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}}" "00013434" "" "" "" "1" "" "00100" "" "" "F" "" "Germany" "" "" "no (pedigree)" "" "" "" "00059928" "" "" "" "1" "" "00001" "" "45y female patient" "F" "" "" "" "0" "" "" "DE" "" "00290017" "" "" "" "21" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00385514" "" "" "" "1" "" "00000" "{PMID:Lenassi 2020:31848469}" "retrospective analysis" "M" "" "(United Kingdom (Great Britain))" "" "0" "" "" "" "17004217" "00434036" "" "" "" "3" "" "00006" "{PMID:Zhai 2017:28450710}" "4-generation family, 3 affected (3M)" "M" "" "China" "" "0" "" "" "" "Fam14" "00444908" "" "" "" "1" "" "00006" "{PMID:Ma 2016:26694549}" "2-generation family, 1 affected, unaffected parents" "M" "" "Australia" "" "0" "" "" "" "Fam25PatII1" "00445070" "" "" "" "1" "" "00006" "{PMID:Kessel 2021:34169787}" "patient" "" "" "Denmark" "" "0" "" "" "" "CC0000553" "00446498" "" "" "" "2" "" "00006" "{PMID:Liu 2023:37337769}" "2-generation family, affected mother/daughter" "F" "" "China" "" "0" "" "" "" "Fam105Pat286" "00446499" "" "" "00446498" "1" "" "00006" "{PMID:Liu 2023:37337769}" "mother" "F" "" "China" "" "0" "" "" "" "Fam105Pat287" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 9 "{{individualid}}" "{{diseaseid}}" "00013434" "00312" "00059928" "00296" "00290017" "00198" "00385514" "04214" "00434036" "00296" "00444908" "00296" "00445070" "00296" "00446498" "00296" "00446499" "00296" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00198, 00296, 00312, 01236, 04214 ## Count = 8 "{{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/Cysts}}" "{{Phenotype/Enzyme/CPK}}" "{{Phenotype/Heart/Myocardium}}" "{{Phenotype/Lung}}" "{{Phenotype/Eye/Retina}}" "{{Phenotype/Neoplasm}}" "{{Phenotype/Diagnosis/Definite}}" "{{Phenotype/Diagnosis/Initial}}" "{{Phenotype/Diagnosis/Criteria}}" "0000012121" "00312" "00013434" "00100" "Isolated (sporadic)" "" "no additional phenotype data available; colorectal phenotype classical, ? nr polyps" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "0000046420" "00296" "00059928" "00001" "Unknown" "" "pulverent cataract" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "0000279309" "04214" "00385514" "00000" "Familial, autosomal dominant" "" "" "<1y" "" "" "" "" "" "" "" "" "" "" "bilateral paediatric cataract" "congenital cataracts; trisomy 21" "" "0000324415" "00296" "00434036" "00006" "Familial, autosomal dominant" "6y" "posterior polar cataract" "" "" "" "" "" "" "" "" "" "" "" "CTRCT30" "cataract" "" "0000334158" "00296" "00444908" "00006" "Isolated (sporadic)" "" "see paper; ..., bilateral cataract, 1y-visual acuity 6/36 bilateral" "" "" "" "" "" "" "" "" "" "" "" "CTCRT30" "cataract" "" "0000334322" "00296" "00445070" "00006" "Familial, autosomal dominant" "" "cataract" "" "" "" "" "" "" "" "" "" "" "" "CTRCT30" "cataract" "" "0000335714" "00296" "00446498" "00006" "Familial, autosomal dominant" "" "bilateral congenital cataract" "" "" "" "" "" "" "" "" "" "" "" "" "congenital catarct" "" "0000335715" "00296" "00446499" "00006" "Familial, autosomal dominant" "" "bilateral congenital cataract" "" "" "" "" "" "" "" "" "" "" "" "" "congenital catarct" "" ## Screenings ## Do not remove or alter this header ## ## Count = 9 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000013350" "00013434" "1" "00100" "00100" "2011-11-30 15:31:35" "00006" "2019-08-02 20:11:40" "SEQ" "DNA" "leukocytes" "screen APC gene (index patient)" "0000059915" "00059928" "1" "00001" "00006" "2010-03-13 17:15:30" "" "" "SEQ" "DNA" "" "" "0000291185" "00290017" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000386743" "00385514" "1" "00000" "03840" "2021-10-12 17:40:23" "" "" "SEQ-NG" "DNA" "blood" "144 genes panel tested" "0000435499" "00434036" "1" "00006" "00006" "2023-03-17 19:03:16" "" "" "SEQ;SEQ-NG" "DNA" "" "gene panel" "0000446477" "00444908" "1" "00006" "00006" "2023-12-28 19:27:56" "" "" "SEQ;SEQ-NG" "DNA" "" "gene panel" "0000446640" "00445070" "1" "00006" "00006" "2024-01-02 15:26:57" "" "" "SEQ;SEQ-NG" "DNA" "" "" "0000448071" "00446498" "1" "00006" "00006" "2024-01-17 16:49:48" "" "" "SEQ;SEQ-NG" "DNA" "" "792 gene panel" "0000448072" "00446499" "1" "00006" "00006" "2024-01-17 16:49:48" "" "" "SEQ;SEQ-NG" "DNA" "" "792 gene panel" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 3 "{{screeningid}}" "{{geneid}}" "0000013350" "APC" "0000059915" "VIM" "0000386743" "VIM" ## 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 = 21 "{{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}}" "0000090667" "21" "90" "10" "17271872" "17271872" "subst" "0" "00001" "VIM_000001" "g.17271872G>A" "" "{PMID:Müller 2009:19126778}, {OMIM193060:0001}" "" "596G>A" "not in 384 control chromosomes; located in coil 1B" "Germline" "" "" "0" "" "" "g.17229873G>A" "" "pathogenic" "" "0000090668" "0" "90" "10" "17271872" "17271872" "subst" "0" "00001" "VIM_000001" "g.17271872G>A" "" "{PMID:Müller 2009:19126778}, {OMIM193060:0001}" "" "" "expression cloning, forms aberrant vimentin cytoskeleton, increased proteasome activity; severe kinetic defect vimentin assembly (in vitro/in vivo)" "Germline" "" "" "0" "" "" "g.17229873G>A" "" "pathogenic" "" "0000319599" "0" "30" "10" "17277158" "17277158" "subst" "0.00719921" "01943" "VIM_000002" "g.17277158C>T" "" "" "" "VIM(NM_003380.4):c.1009-10C>T" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.17235159C>T" "" "likely benign" "" "0000319600" "0" "50" "10" "17277184" "17277184" "subst" "4.06118E-6" "01943" "VIM_000003" "g.17277184G>A" "" "" "" "VIM(NM_003380.4):c.1025G>A (p.R342H)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.17235185G>A" "" "VUS" "" "0000539625" "0" "30" "10" "17277894" "17277894" "subst" "4.06243E-6" "01943" "VIM_000004" "g.17277894C>T" "" "" "" "VIM(NM_003380.4):c.1273+6C>T" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.17235895C>T" "" "likely benign" "" "0000539626" "0" "30" "10" "17278283" "17278283" "subst" "8.13372E-6" "01943" "VIM_000005" "g.17278283G>A" "" "" "" "VIM(NM_003380.4):c.1274-10G>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.17236284G>A" "" "likely benign" "" "0000539628" "0" "30" "10" "17279237" "17279237" "subst" "0.000124247" "01943" "VIM_000007" "g.17279237C>T" "" "" "" "VIM(NM_003380.4):c.1368C>T (p.N456=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.17237238C>T" "" "likely benign" "" "0000612390" "0" "50" "10" "17271974" "17271974" "subst" "0.000177563" "01943" "VIM_000008" "g.17271974C>G" "" "" "" "VIM(NM_003380.4):c.553C>G (p.L185V)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.17229975C>G" "" "VUS" "" "0000612391" "0" "30" "10" "17275822" "17275822" "subst" "8.12143E-5" "01943" "VIM_000009" "g.17275822G>A" "" "" "" "VIM(NM_003380.4):c.774G>A (p.V258=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.17233823G>A" "" "likely benign" "" "0000647874" "1" "10" "10" "17277158" "17277158" "subst" "0.00719921" "03575" "VIM_000002" "g.17277158C>T" "21/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "21 heterozygous, no homozygous; {DB:CLININrs79719081}" "Germline" "" "rs79719081" "0" "" "" "g.17235159C>T" "" "benign" "" "0000690697" "0" "50" "10" "17271919" "17271919" "subst" "4.13134E-6" "01943" "VIM_000010" "g.17271919C>G" "" "" "" "VIM(NM_003380.4):c.498C>G (p.N166K)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000690698" "0" "50" "10" "17277210" "17277210" "subst" "3.65456E-5" "01943" "VIM_000011" "g.17277210T>G" "" "" "" "VIM(NM_003380.4):c.1051T>G (p.F351V)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000722770" "0" "50" "10" "17278364" "17278364" "del" "0" "02329" "VIM_000006" "g.17278364del" "" "" "" "VIM(NM_003380.5):c.1345delA (p.T449Lfs*57)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000804381" "0" "30" "10" "17276796" "17276796" "subst" "0.000227409" "01943" "VIM_000012" "g.17276796A>G" "" "" "" "VIM(NM_003380.4):c.987A>G (p.E329=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000814423" "0" "50" "10" "17277239" "17277239" "subst" "2.84241E-5" "00000" "VIM_000013" "g.17277239C>G" "" "{PMID:Lenassi 2020:31848469}" "" "VIM c.1080C>G p.(Asp360Glu) het" "heterozygous" "Germline" "?" "" "0" "" "" "g.17235240C>G" "" "VUS" "ACMG" "0000921512" "11" "90" "10" "17272708" "17272708" "subst" "4.06081E-6" "00006" "VIM_000014" "g.17272708A>G" "" "{PMID:Zhai 2017:28450710}" "" "" "" "Germline" "" "" "0" "" "" "g.17230709A>G" "" "pathogenic (dominant)" "" "0000954819" "0" "70" "10" "17271436" "17271436" "del" "0" "00006" "VIM_000015" "g.17271436del" "" "{PMID:Ma 2016:26694549}" "" "" "parental samples unavailable" "Germline/De novo (untested)" "" "" "0" "" "" "g.17229437del" "" "likely pathogenic (dominant)" "" "0000954993" "1" "50" "10" "17277291" "17277291" "subst" "1.6246E-5" "00006" "VIM_000016" "g.17277291C>T" "" "{PMID:Kessel 2021:34169787}" "" "" "VUS PM2, PP3" "Germline" "" "" "0" "" "" "g.17235292C>T" "" "VUS" "" "0000957451" "21" "50" "10" "17275596" "17275596" "subst" "0.000194924" "00006" "VIM_000017" "g.17275596A>G" "" "{PMID:Liu 2023:37337769}" "" "" "" "Germline" "yes" "rs116800063" "0" "" "" "g.17233597A>G" "rs116800063" "VUS" "" "0000957452" "0" "50" "10" "17275596" "17275596" "subst" "0.000194924" "00006" "VIM_000017" "g.17275596A>G" "" "{PMID:Liu 2023:37337769}" "" "" "" "Germline" "yes" "rs116800063" "0" "" "" "g.17233597A>G" "rs116800063" "VUS" "" "0000978989" "0" "50" "10" "17271972" "17271972" "subst" "0" "02327" "VIM_000018" "g.17271972G>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 VIM ## Count = 21 "{{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}}" "0000090667" "00022604" "90" "451" "0" "451" "0" "c.451G>A" "r.(?)" "p.(Glu151Lys)" "2" "0000090668" "00022604" "90" "451" "0" "451" "0" "c.451G>A" "r.(?)" "p.(Glu151Lys)" "2" "0000319599" "00022604" "30" "1009" "-10" "1009" "-10" "c.1009-10C>T" "r.(=)" "p.(=)" "" "0000319600" "00022604" "50" "1025" "0" "1025" "0" "c.1025G>A" "r.(?)" "p.(Arg342His)" "" "0000539625" "00022604" "30" "1273" "6" "1273" "6" "c.1273+6C>T" "r.(=)" "p.(=)" "" "0000539626" "00022604" "30" "1274" "-10" "1274" "-10" "c.1274-10G>A" "r.(=)" "p.(=)" "" "0000539628" "00022604" "30" "1368" "0" "1368" "0" "c.1368C>T" "r.(?)" "p.(Asn456=)" "" "0000612390" "00022604" "50" "553" "0" "553" "0" "c.553C>G" "r.(?)" "p.(Leu185Val)" "" "0000612391" "00022604" "30" "774" "0" "774" "0" "c.774G>A" "r.(?)" "p.(Val258=)" "" "0000647874" "00022604" "10" "1009" "-10" "1009" "-10" "c.1009-10C>T" "r.(=)" "p.(=)" "" "0000690697" "00022604" "50" "498" "0" "498" "0" "c.498C>G" "r.(?)" "p.(Asn166Lys)" "" "0000690698" "00022604" "50" "1051" "0" "1051" "0" "c.1051T>G" "r.(?)" "p.(Phe351Val)" "" "0000722770" "00022604" "50" "1345" "0" "1345" "0" "c.1345del" "r.(?)" "p.(Thr449LeufsTer57)" "" "0000804381" "00022604" "30" "987" "0" "987" "0" "c.987A>G" "r.(?)" "p.(Glu329=)" "" "0000814423" "00022604" "50" "1080" "0" "1080" "0" "c.1080C>G" "r.(?)" "p.(Asp360Glu)" "" "0000921512" "00022604" "90" "623" "0" "623" "0" "c.623A>G" "r.(?)" "p.(Gln208Arg)" "" "0000954819" "00022604" "70" "15" "0" "15" "0" "c.15del" "r.(?)" "p.(Val6CysfsTer26)" "" "0000954993" "00022604" "50" "1132" "0" "1132" "0" "c.1132C>T" "r.(?)" "p.(Arg378Cys)" "" "0000957451" "00022604" "50" "635" "0" "635" "0" "c.635A>G" "r.(?)" "p.(Asn212Ser)" "4" "0000957452" "00022604" "50" "635" "0" "635" "0" "c.635A>G" "r.(?)" "p.(Asn212Ser)" "4" "0000978989" "00022604" "50" "551" "0" "551" "0" "c.551G>A" "r.(?)" "p.(Arg184His)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 9 "{{screeningid}}" "{{variantid}}" "0000013350" "0000090668" "0000059915" "0000090667" "0000291185" "0000647874" "0000386743" "0000814423" "0000435499" "0000921512" "0000446477" "0000954819" "0000446640" "0000954993" "0000448071" "0000957451" "0000448072" "0000957452"