### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = CDH4) # 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}}" "CDH4" "cadherin 4, type 1, R-cadherin (retinal)" "20" "q13.3" "unknown" "NC_000020.10" "UD_134753658761" "" "https://www.LOVD.nl/CDH4" "" "1" "1763" "1002" "603006" "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/CDH4_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2017-02-10 11:11:20" "00008" "2022-04-06 13:34:11" ## 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}}" "00004813" "CDH4" "transcript variant 1" "001" "NM_001794.3" "" "NP_001785.2" "" "" "" "-88" "6423" "2751" "59827482" "60515673" "" "0000-00-00 00:00:00" "" "" ## Diseases ## Do not remove or alter this header ## ## Count = 3 "{{id}}" "{{symbol}}" "{{name}}" "{{inheritance}}" "{{id_omim}}" "{{tissues}}" "{{features}}" "{{remarks}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "00198" "?" "unclassified / mixed" "" "" "" "" "" "00006" "2013-09-13 14:21:47" "00006" "2024-11-23 09:38:12" "00201" "INFM" "infertility, male (INFM)" "" "" "" "" "" "00006" "2013-09-14 21:03:39" "00006" "2015-12-07 07:11:25" "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 = 0 ## Individuals ## Do not remove or alter this header ## ## Count = 3 "{{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}}" "00150193" "" "" "" "2" "" "00006" "{PMID:Karaca 2015:26539891}" "" "" "" "" "" "0" "family structure in paper" "" "" "26539891-FamBAB4860" "00274230" "" "" "" "1" "" "00006" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "M" "" "United States" "" "0" "" "" "" "DGAP230" "00407357" "" "" "" "1" "" "00000" "{PMID:Borràs 2013:23534816}" "" "" "" "Spain" "" "0" "" "" "Spanish" "RP-645" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 3 "{{individualid}}" "{{diseaseid}}" "00150193" "00198" "00274230" "00201" "00407357" "04214" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00198, 00201, 04214 ## 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}}" "0000122595" "00198" "00150193" "00006" "Unknown" "" "intellectual diability, frontoparietal cortical atrophy, CCH, microcephaly, seizures, strabismus, scoliosis, pectus excavatum, osteoporosis" "" "" "" "" "" "" "" "" "" "" "" "0000209175" "00201" "00274230" "00006" "Unknown" "28y" "see paper; ..., 2y of infertility, severe oligozoospermia" "" "" "" "" "" "" "" "" "" "oligozoospermia" "" "0000299711" "04214" "00407357" "00000" "Familial, autosomal dominant" "" "" "" "" "" "" "" "" "" "" "" "severe autosomal dominant retinitis pigmentosa (adRP)" "" ## Screenings ## Do not remove or alter this header ## ## Count = 3 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000151048" "00150193" "1" "00006" "00006" "2018-01-13 12:41:38" "" "" "SEQ-NG-I" "DNA" "" "WES" "0000275389" "00274230" "1" "00006" "00006" "2019-12-26 12:58:23" "" "" "microscope;SEQ" "DNA" "" "" "0000408605" "00407357" "1" "00000" "00008" "2022-04-06 13:32:24" "" "" "SEQ-NG;SEQ" "DNA" "blood" "" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 3 "{{screeningid}}" "{{geneid}}" "0000151048" "CDH4" "0000275389" "SYCP2" "0000408605" "SPTBN5" ## 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 = 6 "{{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}}" "0000244213" "3" "90" "20" "60503452" "60503452" "subst" "0" "00006" "CDH4_000001" "g.60503452G>C" "" "{PMID:Karaca 2015:26539891}" "" "NM_001794: c.G1976C; p.R659P" "" "Germline" "" "" "0" "" "" "g.61928394G>C" "" "pathogenic" "" "0000570136" "0" "30" "20" "60448927" "60448927" "subst" "1.62553E-5" "01943" "CDH4_000002" "g.60448927G>A" "" "" "" "CDH4(NM_001794.5):c.1021G>A (p.V341I)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.61873871G>A" "" "likely benign" "" "0000570137" "0" "30" "20" "60499443" "60499443" "subst" "9.34777E-5" "01943" "CDH4_000003" "g.60499443C>T" "" "" "" "CDH4(NM_001794.5):c.1680C>T (p.N560=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.61924385C>T" "" "likely benign" "" "0000629388" "0" "90" "20" "0" "0" "" "0" "00006" "SYCP2_000008" "g.59969994_qterdelins[TGATTCAGATTC;NC_000022.10:g.21433936_qter]" "" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "chr20:g.59969993::TGATTCAGATTC::chr22:g.21433936" "SYCP2 expression RNA increased >20-fold" "De novo" "" "" "0" "" "46,XY,t(20;22)(q13.3;q11.2)" "" "" "VUS" "" "0000629392" "0" "50" "20" "0" "0" "" "0" "00006" "CDH4_000004" "NC_000022.10:g.21433935_qterdelins[NC_000020.10:g.59970004_qter]" "" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "chr22:g.21433934::chr20:g.59970004" "" "DUPLICATE record" "" "" "0" "" "46,XY,t(20;22)(q13.3;q11.2)" "" "" "VUS" "" "0000845535" "0" "50" "20" "60318655" "60318655" "subst" "0.000168997" "00000" "CDH4_000005" "g.60318655A>G" "Novel" "{PMID:Borràs 2013:23534816}" "" "c.206A>G" "" "Germline" "no" "" "0" "" "" "" "" "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 CDH4 ## Count = 6 "{{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}}" "0000244213" "00004813" "90" "1976" "0" "1976" "0" "c.1976G>C" "r.(?)" "p.(Arg659Pro)" "12" "0000570136" "00004813" "30" "1021" "0" "1021" "0" "c.1021G>A" "r.(?)" "p.(Val341Ile)" "" "0000570137" "00004813" "30" "1680" "0" "1680" "0" "c.1680C>T" "r.(?)" "p.(Asn560=)" "" "0000629388" "00004813" "90" "0" "" "0" "" "c.169+140000::TGATTCAGATTC::NC_000022.10:g.21433936" "r.?" "p.?" "2i" "0000629392" "00004813" "90" "0" "" "0" "" "NC_000020.10:g.59970004::c.169+140011" "r.?" "p.?" "2i" "0000845535" "00004813" "50" "206" "0" "206" "0" "c.206A>G" "r.(?)" "p.(Gln69Arg)" "3" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 4 "{{screeningid}}" "{{variantid}}" "0000151048" "0000244213" "0000275389" "0000629388" "0000275389" "0000629392" "0000408605" "0000845535"