### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = SYCP2) # 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}}" "SYCP2" "synaptonemal complex protein 2" "20" "q13.33" "unknown" "NC_000020.10" "UD_136017914152" "" "https://www.LOVD.nl/SYCP2" "" "1" "11490" "10388" "604105" "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/SYCP2_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2019-12-26 12:42:56" "00000" "2026-01-20 18:57:21" ## 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}}" "00020616" "SYCP2" "synaptonemal complex protein 2" "001" "NM_014258.2" "" "NP_055073.2" "" "" "" "-139" "5341" "4593" "58507209" "58438618" "" "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}}" "00201" "INFM" "infertility, male (INFM)" "" "" "" "" "" "00006" "2013-09-14 21:03:39" "00006" "2015-12-07 07:11:25" "05472" "HYDM" "mole, hydatidiform, recurrent (HYDM)" "" "" "" "" "" "00006" "2018-09-29 23:17:06" "" "" "05800" "SPGF1" "spermatogenic failure, type 1 (SPGF1)" "AR" "258150" "" "" "" "00006" "2020-07-26 16:53:18" "" "" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "SYCP2" "05800" ## Individuals ## Do not remove or alter this header ## ## Count = 5 "{{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}}" "00274230" "" "" "" "1" "" "00006" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "M" "" "United States" "" "0" "" "" "" "DGAP230" "00274231" "" "" "" "1" "" "00006" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "M" "" "Germany" "" "0" "" "" "" "M1686" "00274232" "" "" "" "1" "" "00006" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "2-generation family, 1 affected, unaffected heterozygous carrier mother" "M" "" "Germany" "" "0" "" "" "" "M1581" "00274233" "" "" "" "1" "" "00006" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "M" "" "Germany" "" "0" "" "" "" "M1401" "00454560" "" "" "" "1" "" "00764" "" "" "F" "" "" "" "0" "" "" "" "" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 5 "{{individualid}}" "{{diseaseid}}" "00274230" "00201" "00274231" "00201" "00274232" "00201" "00274233" "00201" "00454560" "05472" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00201, 05472, 05800 ## Count = 4 "{{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}}" "0000209175" "00201" "00274230" "00006" "Unknown" "28y" "see paper; ..., 2y of infertility, severe oligozoospermia" "" "" "" "" "" "" "" "" "oligozoospermia" "0000209176" "00201" "00274231" "00006" "Unknown" "29y" "see paper; ..., 1y6m of infertility, cryptozoospermia" "" "" "" "" "" "" "" "" "cryptozoospermia" "0000209177" "00201" "00274232" "00006" "Unknown" "27y" "see paper; ..., 2y6m of infertility, cryptozoospermia" "" "" "" "" "" "" "" "" "cryptozoospermia" "0000209178" "00201" "00274233" "00006" "Unknown" "39y" "see paper; ..., infertility of 17y, azoospermia" "" "" "" "" "" "" "" "" "azoospermia" ## Screenings ## Do not remove or alter this header ## ## Count = 5 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000275389" "00274230" "1" "00006" "00006" "2019-12-26 12:58:23" "" "" "microscope;SEQ" "DNA" "" "" "0000275390" "00274231" "1" "00006" "00006" "2019-12-26 12:58:23" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000275391" "00274232" "1" "00006" "00006" "2019-12-26 12:58:23" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000275392" "00274233" "1" "00006" "00006" "2019-12-26 12:58:23" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000456173" "00454560" "1" "00764" "00764" "2024-09-14 15:51:40" "" "" "SEQ-NG-I" "DNA" "" "" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 5 "{{screeningid}}" "{{geneid}}" "0000275389" "SYCP2" "0000275390" "SYCP2" "0000275391" "SYCP2" "0000275392" "SYCP2" "0000456173" "SYCP2" ## 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 = 16 "{{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}}" "0000328551" "0" "50" "20" "58440630" "58440630" "subst" "0.000140774" "01804" "SYCP2_000001" "g.58440630C>T" "" "" "" "SYCP2(NM_014258.2):c.4456G>A (p.(Glu1486Lys))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.59865575C>T" "" "VUS" "" "0000328552" "0" "50" "20" "58450319" "58450319" "subst" "0.000116383" "01804" "SYCP2_000002" "g.58450319T>C" "" "" "" "SYCP2(NM_014258.2):c.3349+7A>G (p.(=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.59875264T>C" "" "VUS" "" "0000328553" "0" "50" "20" "58489038" "58489038" "subst" "0.000117697" "01804" "SYCP2_000003" "g.58489038G>C" "" "" "" "SYCP2(NM_014258.2):c.822C>G (p.(Asp274Glu))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.59913983G>C" "" "VUS" "" "0000328554" "0" "50" "20" "58490603" "58490603" "subst" "0.000122687" "01804" "SYCP2_000004" "g.58490603A>T" "" "" "" "SYCP2(NM_014258.2):c.516T>A (p.(=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.59915548A>T" "" "VUS" "" "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" "" "0000629389" "0" "90" "20" "58467389" "58467392" "del" "0" "00006" "SYCP2_000005" "g.58467389_58467392del" "" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "" "" "Germline/De novo (untested)" "" "" "0" "" "" "g.59892334_59892337del" "{CV-SCV:000920592}" "pathogenic" "" "0000629390" "21" "90" "20" "58455506" "58455510" "del" "0" "00006" "SYCP2_000006" "g.58455506_58455510del" "" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "" "" "Germline" "" "" "0" "" "" "g.59880451_59880455del" "" "pathogenic (recessive)" "" "0000629391" "0" "90" "20" "58452523" "58452527" "del" "0" "00006" "SYCP2_000007" "g.58452523_58452527del" "" "{PMID:Schilit 2020:31866047}, {DOI:Schilit 2020:10.1016/j.ajhg.2019.11.013}" "" "" "" "Germline/De novo (untested)" "" "" "0" "" "" "g.59877468_59877472del" "{CV-SCV:000920593}" "pathogenic (recessive)" "" "0000983870" "0" "30" "20" "58440873" "58440873" "subst" "0.00331711" "01804" "SYCP2_000009" "g.58440873G>A" "" "" "" "SYCP2(NM_014258.4):c.4368C>T (p.(Ser1456=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000983871" "0" "30" "20" "58441612" "58441612" "subst" "0.00367085" "01804" "SYCP2_000010" "g.58441612C>T" "" "" "" "SYCP2(NM_014258.4):c.4158G>A (p.(Thr1386=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000983872" "0" "30" "20" "58450519" "58450519" "subst" "2.04735E-5" "01804" "SYCP2_000011" "g.58450519C>T" "" "" "" "SYCP2(NM_014258.4):c.3156G>A (p.(Glu1052=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000983873" "0" "30" "20" "58476871" "58476871" "subst" "0" "01804" "SYCP2_000012" "g.58476871T>C" "" "" "" "SYCP2(NM_014258.4):c.1034-6A>G" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000983874" "0" "30" "20" "58496438" "58496438" "subst" "0.00433543" "01804" "SYCP2_000013" "g.58496438A>G" "" "" "" "SYCP2(NM_014258.4):c.95T>C (p.(Ile32Thr))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0001005508" "0" "50" "20" "58467445" "58467447" "del" "0" "01804" "SYCP2_000014" "g.58467445_58467447del" "" "" "" "SYCP2(NM_014258.2):c.1965_1967delATC (p.(Ser656del))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001008355" "3" "90" "20" "58457222" "58457222" "subst" "0" "00764" "SYCP2_000015" "g.58457222T>C" "" "" "" "" "" "Germline" "" "" "0" "" "" "g.59882167T>C" "" "pathogenic" "ACMG" "0001067360" "0" "30" "20" "58486827" "58486827" "subst" "1.25613E-5" "02327" "SYCP2_000016" "g.58486827A>T" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" ## 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 SYCP2 ## Count = 16 "{{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}}" "0000328551" "00020616" "50" "4456" "0" "4456" "0" "c.4456G>A" "r.(?)" "p.(Glu1486Lys)" "" "0000328552" "00020616" "50" "3349" "7" "3349" "7" "c.3349+7A>G" "r.(=)" "p.(=)" "" "0000328553" "00020616" "50" "822" "0" "822" "0" "c.822C>G" "r.(?)" "p.(Asp274Glu)" "" "0000328554" "00020616" "50" "516" "0" "516" "0" "c.516T>A" "r.(?)" "p.(Ile172=)" "" "0000629388" "00020616" "90" "0" "0" "0" "0" "c.=" "r.=|(20_?)" "p.=" "" "0000629389" "00020616" "90" "2022" "0" "2025" "0" "c.2022_2025del" "r.(?)" "p.(Lys674Asnfs*8)" "" "0000629390" "00020616" "90" "2793" "0" "2797" "0" "c.2793_2797del" "r.(?)" "p.(Lys932Serfs*3)" "" "0000629391" "00020616" "90" "3067" "0" "3071" "0" "c.3067_3071del" "r.(?)" "p.(Lys1023Leufs*2)" "" "0000983870" "00020616" "30" "4368" "0" "4368" "0" "c.4368C>T" "r.(?)" "p.(=)" "" "0000983871" "00020616" "30" "4158" "0" "4158" "0" "c.4158G>A" "r.(?)" "p.(=)" "" "0000983872" "00020616" "30" "3156" "0" "3156" "0" "c.3156G>A" "r.(?)" "p.(=)" "" "0000983873" "00020616" "30" "1034" "-6" "1034" "-6" "c.1034-6A>G" "r.(=)" "p.(=)" "" "0000983874" "00020616" "30" "95" "0" "95" "0" "c.95T>C" "r.(?)" "p.(Ile32Thr)" "" "0001005508" "00020616" "50" "1965" "0" "1967" "0" "c.1965_1967del" "r.(?)" "p.(Ser658del)" "" "0001008355" "00020616" "90" "2530" "-2" "2530" "-2" "c.2530-2A>G" "r.spl" "p.?" "" "0001067360" "00020616" "30" "950" "0" "950" "0" "c.950T>A" "r.(?)" "p.(Phe317Tyr)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 5 "{{screeningid}}" "{{variantid}}" "0000275389" "0000629388" "0000275390" "0000629389" "0000275391" "0000629390" "0000275392" "0000629391" "0000456173" "0001008355"