### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = SYNE4) # 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}}" "SYNE4" "spectrin repeat containing, nuclear envelope family member 4" "19" "q13.12" "unknown" "NC_000019.9" "UD_136094504853" "" "http://www.LOVD.nl/SYNE4" "" "1" "26703" "163183" "615535" "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/SYNE4_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2016-03-23 08:59:37" "00000" "2022-05-09 16:01:56" ## 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}}" "00020633" "SYNE4" "spectrin repeat containing, nuclear envelope family member 4" "001" "NM_001039876.1" "" "NP_001034965.1" "" "" "" "-89" "1452" "1215" "36499672" "36494002" "" "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" "03993" "DFNB76" "deafness, autosomal recessive, type 76 (DFNB-76)" "AR" "615540" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "05086" "HL" "hearing loss (HL)" "" "" "" "" "" "00006" "2015-10-23 11:41:05" "00006" "2015-10-23 11:43:00" "05103" "deafness" "deafness" "" "" "" "" "" "00006" "2015-12-02 12:30:46" "00006" "2017-08-25 19:47:08" "05688" "ODCD" "odontochondrodysplasia (ODCD, osteochondrodysplasia)" "AR" "184260" "" "" "" "00006" "2020-01-31 09:10:03" "00006" "2021-01-13 11:07:22" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "SYNE4" "03993" ## 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}}" "00060261" "" "" "" "6" "" "01542" "{PMID:Horn 2013:23348741}, {DOI:Horn 2013:10.1172/JCI66911}" "" "" "yes" "Israel" "" "0" "" "" "Iraq;Jewish" "" "00060265" "" "" "" "4" "" "00006" "{PMID:Horn 2013:23348741}, {DOI:Horn 2013:10.1172/JCI66911}" "524 hearing controls" "" "" "" "" "0" "" "" "" "" "00276341" "" "" "" "1" "" "00006" "{PMID:Gariballa 2017:28322503}" "2-generation family, 1 affected, unaffected heterozygous carrier parents/relatives" "F" "yes" "United Arab Emirates" "" "0" "" "" "" "" "00285363" "" "" "" "1" "" "00004" "" "" "" "" "" "" "0" "" "" "" "" "00285364" "" "" "" "1" "" "00004" "{PMID:Horn 2013:23348741}" "" "" "" "" "" "0" "" "" "" "" "00292097" "" "" "" "1" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 5 "{{individualid}}" "{{diseaseid}}" "00060261" "03993" "00276341" "05688" "00285363" "05103" "00285364" "05086" "00292097" "00198" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00198, 03993, 05086, 05103, 05688 ## Count = 4 "{{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}}" "0000046750" "03993" "00060261" "01542" "Familial, autosomal recessive" "" "Postlingual, progressive NSHL" "" "" "" "" "" "" "" "" "" "" "" "0000210930" "05688" "00276341" "00006" "Familial, autosomal recessive" "3y" "see paper; ..., bilateral hip dislocations, short upper limbs, normal developmental milestones, delayed speech, flat midface, short upturned nose, thin lips, mild rhizomelic shortening upper limbs with contractures right elbow, genu valgum with mild bowing femur; 2y6m severe bilateral sensorineural hearing loss" "" "" "" "" "" "" "" "" "STLS" "osteochondrodysplasia" "" "0000218305" "05086" "00285364" "00008" "Unknown" "" "" "" "" "" "" "" "" "" "" "" "Hearing loss, high-frequency, progressive" "" "0000218638" "05103" "00285363" "00008" "Familial, autosomal recessive" "" "" "" "" "" "" "" "" "" "" "type 76" "deafness, autosomal recessive" "" ## 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}}" "0000060247" "00060261" "1" "01542" "01542" "2016-03-23 07:23:24" "" "" "SEQ-NG-I" "DNA" "blood" "" "0000060252" "00060265" "1" "00006" "00006" "2016-03-23 10:32:44" "" "" "SEQ" "DNA" "" "" "0000277487" "00276341" "1" "00006" "00006" "2020-01-31 10:08:04" "" "" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "WES" "0000286513" "00285363" "1" "00004" "00008" "2020-02-05 13:36:16" "" "" "?" "DNA" "" "" "0000286514" "00285364" "1" "00004" "00008" "2020-02-05 13:36:16" "" "" "?" "DNA" "" "" "0000293265" "00292097" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 4 "{{screeningid}}" "{{geneid}}" "0000060252" "SYNE4" "0000277487" "COL27A1" "0000286513" "SYNE4" "0000286514" "SYNE4" ## 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 = 14 "{{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}}" "0000091244" "3" "90" "19" "36499169" "36499170" "del" "0" "01542" "SYNE4_000001" "g.36499169_36499170del" "2/185 cases (homozygous)" "{PMID:Horn 2013:23348741}, {DOI:Horn 2013:10.1172/JCI66911}" "" "228_229delAT (W77VfsX16)" "found in 4/524 heterozygous hearing controls" "Germline" "yes" "" "0" "" "" "g.36008267_36008268del" "" "pathogenic" "" "0000091249" "1" "90" "19" "36499169" "36499170" "del" "0" "00006" "SYNE4_000001" "g.36499169_36499170del" "4/524 controls" "{PMID:Horn 2013:23348741}, {DOI:Horn 2013:10.1172/JCI66911}" "" "228_229delAT (W77VfsX16)" "" "Germline" "" "" "0" "" "" "g.36008267_36008268del" "" "pathogenic" "" "0000316143" "0" "30" "19" "36499446" "36499446" "subst" "0.000537083" "01943" "SYNE4_000002" "g.36499446C>T" "" "" "" "SYNE4(NM_001039876.2):c.128+10G>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.36008544C>T" "" "likely benign" "" "0000567046" "0" "30" "19" "36496291" "36496291" "subst" "0.00125495" "01943" "ALKBH6_000001" "g.36496291C>G" "" "" "" "SYNE4(NM_001039876.2):c.916G>C (p.G306R)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.36005389C>G" "" "likely benign" "" "0000567047" "0" "30" "19" "36497439" "36497439" "subst" "0.00013158" "01943" "ALKBH6_000002" "g.36497439C>T" "" "" "" "SYNE4(NM_001039876.2):c.753G>A (p.P251=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.36006537C>T" "" "likely benign" "" "0000567048" "0" "30" "19" "36499185" "36499185" "subst" "0.000233655" "01943" "ALKBH6_000003" "g.36499185G>A" "" "" "" "SYNE4(NM_001039876.2):c.213C>T (p.A71=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.36008283G>A" "" "likely benign" "" "0000632317" "21" "30" "19" "36498137" "36498137" "subst" "4.70788E-6" "00006" "SYNE4_000003" "g.36498137C>G" "" "{PMID:Gariballa 2017:28322503}" "" "" "" "Germline" "" "" "0" "" "" "g.36007235C>G" "" "benign" "" "0000642255" "1" "99" "19" "36498114" "36498114" "subst" "1.51592E-5" "00004" "SYNE4_000004" "g.36498114G>T" "" "{DB:DVD}" "" "" "" "SUMMARY record" "" "" "0" "" "" "g.36007212G>T" "" "pathogenic" "" "0000642256" "1" "99" "19" "36499169" "36499170" "del" "0" "00004" "SYNE4_000001" "g.36499169_36499170del" "" "{DB:DVD}, {PMID:Horn 2013:23348741}" "" "" "" "SUMMARY record" "" "" "0" "" "" "g.36008267_36008268del" "" "pathogenic" "" "0000649954" "1" "50" "19" "36494352" "36494352" "subst" "0.000514742" "03575" "SYNE4_000005" "g.36494352C>T" "1/2794 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "conflicting interpretations of pathogenicity; 1 heterozygous, no homozygous; {DB:CLININrs141202530}" "Germline" "" "rs141202530" "0" "" "" "g.36003450C>T" "" "VUS" "" "0000698120" "0" "30" "19" "36498133" "36498133" "subst" "0.000613789" "03779" "SYNE4_000006" "g.36498133T>G" "" "" "" "" "" "CLASSIFICATION record" "" "rs200994810" "0" "" "" "" "" "likely benign" "" "0000727293" "0" "50" "19" "36497501" "36497501" "subst" "0" "01943" "ALKBH6_000004" "g.36497501C>T" "" "" "" "SYNE4(NM_001039876.2):c.691G>A (p.G231R)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000808832" "0" "50" "19" "36494352" "36494352" "subst" "0.000514742" "01943" "SYNE4_000005" "g.36494352C>T" "" "" "" "SYNE4(NM_001039876.2):c.1102G>A (p.V368M)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000866045" "0" "30" "19" "36499577" "36499577" "subst" "0.000857358" "01943" "ALKBH6_000005" "g.36499577G>A" "" "" "" "SYNE4(NM_001039876.2):c.7C>T (p.L3=)" "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 SYNE4 ## Count = 14 "{{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}}" "0000091244" "00020633" "90" "228" "0" "229" "0" "c.228_229del" "r.(?)" "p.(Trp77Valfs*16)" "2" "0000091249" "00020633" "90" "228" "0" "229" "0" "c.228_229del" "r.(?)" "p.(Trp77Valfs*16)" "2" "0000316143" "00020633" "30" "128" "10" "128" "10" "c.128+10G>A" "r.(=)" "p.(=)" "" "0000567046" "00020633" "30" "916" "0" "916" "0" "c.916G>C" "r.(?)" "p.(Gly306Arg)" "" "0000567047" "00020633" "30" "753" "0" "753" "0" "c.753G>A" "r.(?)" "p.(Pro251=)" "" "0000567048" "00020633" "30" "213" "0" "213" "0" "c.213C>T" "r.(?)" "p.(Ala71=)" "" "0000632317" "00020633" "30" "313" "0" "313" "0" "c.313G>C" "r.(?)" "p.(Glu105Gln)" "" "0000642255" "00020633" "99" "336" "0" "336" "0" "c.336C>A" "r.(?)" "p.(Ser112Arg)" "3" "0000642256" "00020633" "99" "228" "0" "229" "0" "c.228_229del" "r.(?)" "p.(Tyr76*)" "2" "0000649954" "00020633" "50" "1102" "0" "1102" "0" "c.1102G>A" "r.(?)" "p.(Val368Met)" "" "0000698120" "00020633" "30" "317" "0" "317" "0" "c.317A>C" "r.(?)" "p.(Gln106Pro)" "" "0000727293" "00020633" "50" "691" "0" "691" "0" "c.691G>A" "r.(?)" "p.(Gly231Arg)" "" "0000808832" "00020633" "50" "1102" "0" "1102" "0" "c.1102G>A" "r.(?)" "p.(Val368Met)" "" "0000866045" "00020633" "30" "7" "0" "7" "0" "c.7C>T" "r.(?)" "p.(Leu3=)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 6 "{{screeningid}}" "{{variantid}}" "0000060247" "0000091244" "0000060252" "0000091249" "0000277487" "0000632317" "0000286513" "0000642255" "0000286514" "0000642256" "0000293265" "0000649954"