### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = LIMS2) # 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}}" "LIMS2" "LIM and senescent cell antigen-like domains 2" "2" "q21.1" "unknown" "NG_042235.1" "UD_132610623218" "" "https://www.LOVD.nl/LIMS2" "" "1" "16084" "55679" "607908" "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/LIMS2_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2017-05-05 19:28:43" "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}}" "00024255" "LIMS2" "transcript variant 1" "003" "NM_001136037.2" "" "NP_001129509.2" "" "" "" "-166" "1952" "1092" "128432764" "128395996" "00006" "2017-05-05 19:32:22" "" "" ## 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" "00244" "MYOP" "myopathy (MYOP)" "" "" "" "" "" "00006" "2013-10-12 23:00:55" "00006" "2019-06-19 11:52:31" "05126" "LGMD" "dystrophy, muscular, limb-girdle (LGMD)" "" "" "" "" "" "00006" "2016-01-26 06:05:36" "" "" "05266" "LGMDR25;LGMD2X" "dystrophy, muscular, limb-girdle, autosomal recessive, type 25 (LGMD2X)" "AR" "616812" "" "" "" "00006" "2017-05-05 19:14:54" "00006" "2024-01-12 21:09:35" "05267" "LGMD2W;MDRCMTT" "dystrophy, muscular, autosomal recessive, with cardiomyopathy and triangular tongue (LGMD-2W)" "AR" "616827" "" "" "" "00006" "2017-05-05 19:27:35" "00006" "2024-01-12 21:08:38" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "LIMS2" "05267" ## Individuals ## Do not remove or alter this header ## ## Count = 6 "{{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}}" "00104045" "" "" "" "2" "" "00006" "{PMID:Chardon 2015:25589244}, {DOI:Chardon 2015:10.1111/cge.12561}" "2-generation family, affected brother/sister, unaffected heterozygous carrier parents" "F;M" "no" "Canada" "" "0" "" "" "" "25589244-Fam" "00287377" "" "" "" "1" "" "03564" "" "" "F" "?" "Belgium" "20y" "0" "" "" "" "" "00292244" "" "" "" "24" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00292245" "" "" "" "62" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00304687" "" "" "" "1" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00388599" "" "" "" "1" "" "00006" "{PMID:Chakravorty 2020:33250842}" "" "M" "" "India" "" "0" "" "" "India" "Pat23" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 6 "{{individualid}}" "{{diseaseid}}" "00104045" "05266" "00287377" "05126" "00292244" "00198" "00292245" "00198" "00304687" "00198" "00388599" "00244" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00198, 00244, 05126, 05266, 05267 ## Count = 3 "{{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}}" "0000081987" "05266" "00104045" "00006" "Familial, autosomal recessive" "" "see paper; ..., both sibs met early motor milestones; 5y both developed proximal weakness, with calf hypertrophy, macroglossia; weakness progressed to severe quadriparesis; 12y-both siblings\r\nrequired manual wheelchair and motorized wheelchair at 19y" "" "" "" "" "" "" "" "" "" "" "" "0000221979" "05126" "00287377" "03564" "Unknown" "19y" "psoas weakness, pelvic girdle weakness, tibialis anterior weakness, easy fatigability" "12y" "19y" "proximal lower-limb weakness" "" "" "" "" "" "" "muscular dystrophy" "" "0000282139" "00244" "00388599" "00006" "Familial, autosomal recessive" "16y" "proximal muscle weakness; CK level 855 IU/L; Soleus and Medial Gastrocnemius muscle MRI showing fatty replacement and atrophy; toe walking, difficulty climbing stairs and getting up from ground, winging of scapula and tendo-achilis contractures; most affected muscles: Serratus anterior, hip adductors, iliopsoas, hamstrings, and tibialis anterior" "6y" "" "" "" "" "" "" "" "" "" "" ## Screenings ## Do not remove or alter this header ## ## Count = 6 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000104516" "00104045" "1" "00006" "00006" "2017-05-05 19:39:46" "" "" "SEQ" "DNA" "" "" "0000288548" "00287377" "1" "03564" "03564" "2020-02-14 15:25:43" "" "" "-" "DNA" "blood" "" "0000293412" "00292244" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000293413" "00292245" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000305816" "00304687" "1" "03575" "00006" "2020-06-24 11:55:42" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000389841" "00388599" "1" "00006" "00006" "2021-11-04 20:51:09" "" "" "SEQ-NG" "DNA" "" "WES" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 1 "{{screeningid}}" "{{geneid}}" "0000104516" "LIMS2" ## 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 = 23 "{{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}}" "0000169457" "21" "70" "2" "128412081" "128412081" "subst" "2.03046E-5" "00006" "LIMS2_000001" "g.128412081G>C" "" "{PMID:Chardon 2015:25589244}, {DOI:Chardon 2015:10.1111/cge.12561}, {OMIM607908:0001}" "" "" "" "Germline" "yes" "" "0" "" "" "g.127654507G>C" "" "likely pathogenic" "" "0000169458" "21" "70" "2" "128412067" "128412067" "subst" "2.43665E-5" "00006" "LIMS2_000002" "g.128412067G>A" "" "{PMID:Chardon 2015:25589244}, {DOI:Chardon 2015:10.1111/cge.12561}, {OMIM607908:0001}" "" "" "" "Germline" "yes" "rs768056213" "0" "" "" "g.127654493G>A" "" "likely pathogenic" "" "0000169459" "0" "70" "2" "128396914" "128396914" "subst" "0" "00006" "LIMS2_000003" "g.128396914A>G" "" "{PMID:Chardon 2015:25589244}, {DOI:Chardon 2015:10.1111/cge.12561}, {OMIM607908:0002}" "" "" "" "Germline" "yes" "rs869025562" "0" "" "" "g.127639339A>G" "" "likely pathogenic" "" "0000279089" "0" "10" "2" "128412453" "128412453" "subst" "0.0138742" "02330" "LIMS2_000007" "g.128412453G>A" "" "" "" "LIMS2(NM_001161403.3):c.189C>T (p.(Tyr63=)), LIMS2(NM_001161404.2):c.174C>T (p.Y58=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.127654879G>A" "" "benign" "" "0000279090" "0" "10" "2" "128400608" "128400608" "subst" "0.556308" "02330" "LIMS2_000006" "g.128400608C>T" "" "" "" "LIMS2(NM_001161404.2):c.384G>A (p.K128=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.127643033C>T" "" "benign" "" "0000279091" "0" "50" "2" "128400583" "128400583" "subst" "0" "02330" "LIMS2_000005" "g.128400583G>A" "" "" "" "LIMS2(NM_001161404.2):c.409C>T (p.R137W)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.127643008G>A" "" "VUS" "" "0000279092" "0" "10" "2" "128397728" "128397728" "subst" "0.0138852" "02330" "LIMS2_000004" "g.128397728G>C" "" "" "" "LIMS2(NM_001161404.2):c.788-8C>G" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.127640153G>C" "" "benign" "" "0000509156" "0" "30" "2" "128396920" "128396922" "del" "0" "02326" "GPR17_000001" "g.128396920_128396922del" "" "" "" "LIMS2(NM_001161404.1):c.949_951delAAG (p.K317del)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.127639345_127639347del" "" "likely benign" "" "0000509157" "0" "30" "2" "128407597" "128407597" "subst" "0.000231723" "01804" "GPR17_000002" "g.128407597G>A" "" "" "" "GPR17(NM_001161415.1):c.11G>A (p.(Arg4Gln))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000509158" "0" "30" "2" "128408826" "128408826" "subst" "0.000158236" "01804" "GPR17_000003" "g.128408826G>A" "" "" "" "GPR17(NM_001161415.1):c.601G>A (p.(Val201Met))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.127651252G>A" "" "likely benign" "" "0000509160" "0" "50" "2" "128431256" "128431257" "dup" "0" "02326" "GPR17_000005" "g.128431256_128431257dup" "" "" "" "LIMS2(NM_001136037.3):c.73_74dupTG (p.W25Cfs*90)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.127673682_127673683dup" "" "VUS" "" "0000606090" "0" "50" "2" "128412086" "128412086" "subst" "0" "02326" "GPR17_000006" "g.128412086T>C" "" "" "" "LIMS2(NM_001161404.1):c.256A>G (p.M86V)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.127654512T>C" "" "VUS" "" "0000644803" "0" "50" "2" "128431289" "128431289" "del" "0" "03564" "LIMS2_000009" "g.128431289del" "" "" "" "41del" "" "Germline/De novo (untested)" "" "" "0" "" "" "g.127673715del" "" "VUS" "" "0000650101" "1" "30" "2" "128400622" "128400622" "subst" "0.00513319" "03575" "LIMS2_000010" "g.128400622G>A" "24/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "24 heterozygous; {DB:CLININrs145123078}" "Germline" "" "rs145123078" "0" "" "" "g.127643047G>A" "" "likely benign" "" "0000650102" "1" "10" "2" "128412453" "128412453" "subst" "0.0138742" "03575" "LIMS2_000007" "g.128412453G>A" "62/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "62 heterozygous, no homozygous; {DB:CLININrs35765118}" "Germline" "" "rs35765118" "0" "" "" "g.127654879G>A" "" "benign" "" "0000669504" "3" "30" "2" "128400622" "128400622" "subst" "0.00513319" "03575" "LIMS2_000010" "g.128400622G>A" "1/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "1 homozygous; {DB:CLININrs145123078}" "Germline" "" "rs145123078" "0" "" "" "g.127643047G>A" "" "likely benign" "" "0000799660" "0" "30" "2" "128400622" "128400622" "subst" "0.00513319" "01804" "LIMS2_000010" "g.128400622G>A" "" "" "" "LIMS2(NM_001136037.2):c.451C>T (p.(Arg151Cys))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000819288" "0" "90" "2" "128397696" "128397696" "subst" "0" "00006" "LIMS2_000011" "g.128397696C>T" "" "{PMID:Chakravorty 2020:33250842}" "" "" "" "Germline" "" "" "0" "" "" "" "" "pathogenic" "" "0000947350" "0" "30" "2" "128415109" "128415109" "subst" "0.00210384" "02326" "GPR17_000004" "g.128415109G>A" "" "" "" "LIMS2(NM_001136037.3):c.105C>T (p.A35=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000991609" "0" "50" "2" "128393882" "128393882" "subst" "0.000126112" "01804" "GPR17_000007" "g.128393882G>A" "" "" "" "MYO7B(NM_001080527.1):c.6028G>A (p.(Ala2010Thr))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000991610" "0" "50" "2" "128398555" "128398558" "del" "0" "01804" "GPR17_000008" "g.128398555_128398558del" "" "" "" "LIMS2(NM_001161403.1):c.669_672delCTGT (p.(Cys224fs))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001032354" "0" "30" "2" "128412453" "128412453" "subst" "0.0138742" "01804" "LIMS2_000007" "g.128412453G>A" "" "" "" "LIMS2(NM_001161403.3):c.189C>T (p.(Tyr63=)), LIMS2(NM_001161404.2):c.174C>T (p.Y58=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0001032355" "0" "50" "2" "128421884" "128421884" "subst" "0" "01804" "GPR17_000009" "g.128421884T>C" "" "" "" "LIMS2(NM_017980.5):c.79A>G (p.(Thr27Ala))" "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 LIMS2 ## Count = 23 "{{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}}" "0000169457" "00024255" "70" "342" "0" "342" "0" "c.342C>G" "r.(?)" "p.(Asn114Lys)" "5" "0000169458" "00024255" "70" "356" "0" "356" "0" "c.356C>T" "r.(?)" "p.(Pro119Leu)" "5" "0000169459" "00024255" "70" "1034" "0" "1034" "0" "c.1034T>C" "r.(?)" "p.(Leu345Pro)" "11" "0000279089" "00024255" "10" "255" "0" "255" "0" "c.255C>T" "r.(?)" "p.(Tyr85=)" "" "0000279090" "00024255" "10" "465" "0" "465" "0" "c.465G>A" "r.(?)" "p.(Lys155=)" "" "0000279091" "00024255" "50" "490" "0" "490" "0" "c.490C>T" "r.(?)" "p.(Arg164Trp)" "" "0000279092" "00024255" "10" "869" "-8" "869" "-8" "c.869-8C>G" "r.(=)" "p.(=)" "" "0000509156" "00024255" "30" "1030" "0" "1032" "0" "c.1030_1032del" "r.(?)" "p.(Lys344del)" "" "0000509157" "00024255" "30" "425" "4401" "425" "4401" "c.425+4401C>T" "r.(=)" "p.(=)" "" "0000509158" "00024255" "30" "425" "3172" "425" "3172" "c.425+3172C>T" "r.(=)" "p.(=)" "" "0000509160" "00024255" "50" "73" "0" "74" "0" "c.73_74dup" "r.(?)" "p.(Trp25CysfsTer90)" "" "0000606090" "00024255" "50" "337" "0" "337" "0" "c.337A>G" "r.(?)" "p.(Met113Val)" "" "0000644803" "00024255" "50" "42" "0" "42" "0" "c.42del" "r.(?)" "p.(Ser15Profs*9)" "1" "0000650101" "00024255" "30" "451" "0" "451" "0" "c.451C>T" "r.(?)" "p.(Arg151Cys)" "" "0000650102" "00024255" "10" "255" "0" "255" "0" "c.255C>T" "r.(=)" "p.(=)" "" "0000669504" "00024255" "30" "451" "0" "451" "0" "c.451C>T" "r.(?)" "p.(Arg151Cys)" "" "0000799660" "00024255" "30" "451" "0" "451" "0" "c.451C>T" "r.(?)" "p.(Arg151Cys)" "" "0000819288" "00024255" "90" "893" "0" "893" "0" "c.893G>A" "r.(?)" "p.(Trp298*)" "" "0000947350" "00024255" "30" "105" "0" "105" "0" "c.105C>T" "r.(?)" "p.(Ala35=)" "" "0000991609" "00024255" "50" "4066" "0" "4066" "0" "c.*2974C>T" "r.(=)" "p.(=)" "" "0000991610" "00024255" "50" "735" "0" "738" "0" "c.735_738del" "r.(?)" "p.(Cys246Profs*39)" "" "0001032354" "00024255" "30" "255" "0" "255" "0" "c.255C>T" "r.(?)" "p.(Tyr85=)" "" "0001032355" "00024255" "50" "78" "-6748" "78" "-6748" "c.78-6748A>G" "r.(=)" "p.(=)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 8 "{{screeningid}}" "{{variantid}}" "0000104516" "0000169457" "0000104516" "0000169458" "0000104516" "0000169459" "0000288548" "0000644803" "0000293412" "0000650101" "0000293413" "0000650102" "0000305816" "0000669504" "0000389841" "0000819288"