### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = SPEF2) # 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}}" "SPEF2" "sperm flagellar 2" "5" "p13.2" "unknown" "NC_000005.9" "UD_132438693860" "" "https://www.LOVD.nl/SPEF2" "" "1" "26293" "79925" "610172" "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/SPEF2_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2019-12-23 14:13:15" "00000" "2025-11-01 13:22:20" ## 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}}" "00025484" "SPEF2" "transcript variant 1" "004" "NM_024867.3" "" "NP_079143.3" "" "" "" "-111" "5527" "5469" "35617989" "35814713" "00006" "2019-12-23 14:15:54" "" "" ## 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" "04249" "macular dystrophy" "dystrophy, macular" "" "" "" "" "" "00006" "2015-05-04 22:10:58" "00006" "2024-02-15 21:18:39" "06684" "SPGF43" "Spermatogenic failure 43" "AR" "618751" "" "" "" "00006" "2021-12-10 23:20:41" "" "" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "SPEF2" "06684" ## Individuals ## Do not remove or alter this header ## ## Count = 4 "{{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}}" "00273465" "" "" "" "1" "" "00006" "{PMID:Liu 2020:31048344}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "M" "yes" "China" "" "0" "" "" "" "FamA028" "00273466" "" "" "" "1" "" "00006" "{PMID:Liu 2020:31048344}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "M" "yes" "China" "" "0" "" "" "" "FamA042" "00273467" "" "" "" "2" "" "00006" "{PMID:Liu 2020:31048344}" "2-generation family, 2 affected brothers, unaffected heterozygous carrier parents" "M" "yes" "China" "" "0" "" "" "" "FamF003" "00451057" "" "" "" "1" "" "00006" "{PMID:Hitti-Malin 2024:38540785}, {DOI:Hitti-Malin 2024:10.3390/biom14030367}" "" "" "" "" "" "0" "" "" "" "066781" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 4 "{{individualid}}" "{{diseaseid}}" "00273465" "00201" "00273466" "00201" "00273467" "00201" "00451057" "04249" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00201, 04249, 06684 ## Count = 3 "{{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}}" "0000208439" "00201" "00273465" "00006" "Familial, autosomal recessive" "" "see paper; …" "" "" "" "" "" "" "" "" "male infetrility" "0000208440" "00201" "00273466" "00006" "Familial, autosomal recessive" "" "see paper; …" "" "" "" "" "" "" "" "" "male infetrility" "0000208441" "00201" "00273467" "00006" "Familial, autosomal recessive" "" "see paper; …" "" "" "" "" "" "" "" "" "male infetrility" ## Screenings ## Do not remove or alter this header ## ## Count = 4 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000274622" "00273465" "1" "00006" "00006" "2019-12-23 14:32:08" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000274623" "00273466" "1" "00006" "00006" "2019-12-23 14:32:08" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000274624" "00273467" "1" "00006" "00006" "2019-12-23 14:32:08" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000452656" "00451057" "1" "00006" "00006" "2024-05-31 11:39:36" "" "" "SEQ" "DNA" "" "smMIP-based 105 iMD/AMD genes" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 3 "{{screeningid}}" "{{geneid}}" "0000274622" "SPEF2" "0000274623" "SPEF2" "0000274624" "SPEF2" ## 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 = 10 "{{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}}" "0000308769" "0" "50" "5" "35700675" "35700675" "subst" "0" "01943" "SPEF2_000001" "g.35700675C>A" "" "" "" "SPEF2(NM_024867.4):c.2219C>A (p.A740D)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.35700573C>A" "" "VUS" "" "0000308770" "0" "50" "5" "35763641" "35763641" "subst" "8.50546E-5" "01943" "SPEF2_000002" "g.35763641G>C" "" "" "" "SPEF2(NM_024867.4):c.3638G>C (p.R1213P)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.35763539G>C" "" "VUS" "" "0000330307" "0" "50" "5" "35779244" "35779244" "subst" "0.000134459" "01804" "SPEF2_000003" "g.35779244C>T" "" "" "" "SPEF2(NM_024867.3):c.4243C>T (p.(Arg1415Cys))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.35779142C>T" "" "VUS" "" "0000628582" "3" "90" "5" "35654760" "35654760" "subst" "8.13531E-6" "00006" "SPEF2_000006" "g.35654760C>T" "" "{PMID:Liu 2020:31048344}" "" "" "" "Germline" "" "" "0" "" "" "g.35654658C>T" "" "pathogenic (recessive)" "" "0000628583" "3" "90" "5" "35753795" "35753795" "del" "0" "00006" "SPEF2_000005" "g.35753795del" "" "{PMID:Liu 2020:31048344}" "" "3400delA" "" "Germline" "" "" "0" "" "" "g.35753693del" "" "pathogenic (recessive)" "" "0000628584" "3" "90" "5" "35740279" "35740279" "del" "0" "00006" "SPEF2_000004" "g.35740279del" "" "{PMID:Liu 2020:31048344}" "" "3240delT" "" "Germline" "yes" "" "0" "" "" "g.35740177del" "" "pathogenic (recessive)" "" "0000720407" "0" "90" "5" "35800188" "35800188" "dup" "0" "01943" "SPEF2_000007" "g.35800188dup" "" "" "" "SPEF2(NM_024867.4):c.4949dupG (p.S1650Rfs*26)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "pathogenic" "" "0000912319" "0" "50" "5" "35763802" "35763802" "subst" "0.00109229" "02325" "SPEF2_000008" "g.35763802A>T" "" "" "" "SPEF2(NM_024867.4):c.3799A>T (p.M1267L)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000987001" "0" "70" "5" "35763687" "35763687" "del" "0" "00006" "SPEF2_000009" "g.35763687del" "" "{PMID:Hitti-Malin 2024:38540785}, {DOI:Hitti-Malin 2024:10.3390/biom14030367}" "" "" "case unsolved" "Germline" "" "" "0" "" "" "g.35763585del" "" "likely pathogenic" "ACMG" "0001051939" "0" "30" "5" "35727857" "35727857" "subst" "0.0480799" "01804" "SPEF2_000010" "g.35727857G>A" "" "" "" "SPEF2(NM_024867.4):c.2995G>A (p.(Ala999Thr))" "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 SPEF2 ## Count = 10 "{{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}}" "0000308769" "00025484" "50" "2219" "0" "2219" "0" "c.2219C>A" "r.(?)" "p.(Ala740Asp)" "" "0000308770" "00025484" "50" "3638" "0" "3638" "0" "c.3638G>C" "r.(?)" "p.(Arg1213Pro)" "" "0000330307" "00025484" "50" "4243" "0" "4243" "0" "c.4243C>T" "r.(?)" "p.(Arg1415Cys)" "" "0000628582" "00025484" "90" "910" "0" "910" "0" "c.910C>T" "r.(?)" "p.(Arg304*)" "" "0000628583" "00025484" "90" "3400" "0" "3400" "0" "c.3400del" "r.(?)" "p.(Ile1134Serfs*13)" "" "0000628584" "00025484" "90" "3240" "0" "3240" "0" "c.3240del" "r.(?)" "p.(Phe1080Leufs*2)" "" "0000720407" "00025484" "90" "4949" "0" "4949" "0" "c.4949dup" "r.(?)" "p.(Ser1650Argfs*26)" "" "0000912319" "00025484" "50" "3799" "0" "3799" "0" "c.3799A>T" "r.(?)" "p.(Met1267Leu)" "" "0000987001" "00025484" "70" "3684" "0" "3684" "0" "c.3684del" "r.(?)" "p.(Lys1228AsnfsTer4)" "" "0001051939" "00025484" "30" "2995" "0" "2995" "0" "c.2995G>A" "r.(?)" "p.(Ala999Thr)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 4 "{{screeningid}}" "{{variantid}}" "0000274622" "0000628582" "0000274623" "0000628583" "0000274624" "0000628584" "0000452656" "0000987001"