### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = AMY1A) # 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}}" "AMY1A" "amylase, alpha 1A (salivary)" "1" "p21" "unknown" "NC_000001.10" "UD_136085533556" "" "http://www.LOVD.nl/AMY1A" "" "1" "474" "276" "104700" "1" "1" "1" "1" "All amylase gene CNV haplotypes are linked to the AMY2B gene. Haplotypes are described based on the total number of AMY1, AMY2A and AMY2B genes resp., like AMY-3-1-1 (hg19 reference haplotype).\r\nEstablishment of this gene variant database (LSDB) was supported by the Leiden University Medical Center (LUMC), Leiden, Nederland." "" "g" "http://databases.lovd.nl/shared/refseq/AMY1A_codingDNA.html" "1" "" "All AMY gene CNV haplotypes have been linked to the AMY2B gene." "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2016-11-13 16:23:46" "00000" "2020-06-04 18:35:37" ## 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}}" "00002448" "AMY1A" "transcript variant 2" "001" "NM_001008221.1" "" "NP_001008222.1" "" "" "" "-214" "1567" "1536" "104198141" "104207173" "" "0000-00-00 00:00:00" "" "" ## Diseases ## Do not remove or alter this header ## ## Count = 1 "{{id}}" "{{symbol}}" "{{name}}" "{{inheritance}}" "{{id_omim}}" "{{tissues}}" "{{features}}" "{{remarks}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "00000" "Healthy/Control" "Healthy individual / control" "" "" "" "" "" "00000" "2012-07-26 17:29:43" "" "" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 0 ## Individuals ## Do not remove or alter this header ## ## Count = 9 "{{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}}" "00087114" "" "" "" "1" "" "00006" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "" "" "" "" "0" "" "" "European" "" "00087115" "" "" "" "1" "" "00006" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "" "" "Japan" "" "0" "" "" "" "" "00087116" "" "" "" "1" "" "00006" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "" "" "" "" "0" "" "" "" "" "00087117" "" "" "" "1" "" "00006" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "" "" "" "" "0" "" "" "" "" "00087118" "" "" "" "1" "" "01810" "Shwan, submitted" "" "" "" "" "" "0" "" "" "Africa, Yoruban" "" "00087119" "" "" "" "1" "" "01810" "Shwan, submitted" "" "" "" "" "" "0" "" "" "Africa, Yoruban" "" "00087120" "" "" "" "1" "" "01810" "Shwan, submitted" "" "" "" "" "" "0" "" "" "Africa, Yoruban" "" "00087121" "" "" "" "1" "" "01810" "Shwan, submitted" "father of NA19120" "" "" "" "" "0" "" "" "Africa, Yoruban" "" "00087122" "" "" "" "1" "" "01810" "Shwan, submitted" "" "" "" "" "" "0" "" "" "Africa, Yoruban" "" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{individualid}}" "{{diseaseid}}" "00087114" "00000" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00000 ## Count = 0 ## Screenings ## Do not remove or alter this header ## ## Count = 9 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000087252" "00087114" "1" "00006" "00006" "2016-11-12 19:39:59" "00006" "2016-11-12 20:39:23" "FISHf;PCR;SEQ-NG" "DNA" "" "" "0000087253" "00087115" "1" "00006" "00006" "2016-11-12 20:11:02" "00006" "2016-11-12 20:38:39" "FISHf;PCR;SEQ-NG" "DNA" "" "" "0000087254" "00087116" "1" "00006" "00006" "2016-11-12 20:28:11" "" "" "FISHf;PCR;SEQ-NG" "DNA" "" "" "0000087255" "00087117" "1" "00006" "00006" "2016-11-13 09:47:06" "" "" "FISHf;PCR;SEQ-NG" "DNA" "" "" "0000087257" "00087118" "1" "01810" "00006" "2016-11-13 11:12:57" "" "" "FISHf;PCR;SEQ-NG" "DNA" "" "" "0000087258" "00087119" "1" "01810" "00006" "2016-11-13 12:23:57" "" "" "FISHf;PCR;SEQ-NG" "DNA" "" "" "0000087259" "00087120" "1" "01810" "00006" "2016-11-13 13:04:46" "" "" "FISHf;PCR;SEQ-NG" "DNA" "" "" "0000087260" "00087121" "1" "01810" "00006" "2016-11-13 14:02:11" "" "" "FISHf;PCR;SEQ-NG" "DNA" "" "" "0000087261" "00087122" "1" "01810" "00006" "2016-11-13 14:55:28" "" "" "FISHf;PCR;SEQ-NG" "DNA" "" "" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 45 "{{screeningid}}" "{{geneid}}" "0000087252" "AMY1A" "0000087252" "AMY1B" "0000087252" "AMY1C" "0000087252" "AMY2A" "0000087252" "AMY2B" "0000087253" "AMY1A" "0000087253" "AMY1B" "0000087253" "AMY1C" "0000087253" "AMY2A" "0000087253" "AMY2B" "0000087254" "AMY1A" "0000087254" "AMY1B" "0000087254" "AMY1C" "0000087254" "AMY2A" "0000087254" "AMY2B" "0000087255" "AMY1A" "0000087255" "AMY1B" "0000087255" "AMY1C" "0000087255" "AMY2A" "0000087255" "AMY2B" "0000087257" "AMY1A" "0000087257" "AMY1B" "0000087257" "AMY1C" "0000087257" "AMY2A" "0000087257" "AMY2B" "0000087258" "AMY1A" "0000087258" "AMY1B" "0000087258" "AMY1C" "0000087258" "AMY2A" "0000087258" "AMY2B" "0000087259" "AMY1A" "0000087259" "AMY1B" "0000087259" "AMY1C" "0000087259" "AMY2A" "0000087259" "AMY2B" "0000087260" "AMY1A" "0000087260" "AMY1B" "0000087260" "AMY1C" "0000087260" "AMY2A" "0000087260" "AMY2B" "0000087261" "AMY1A" "0000087261" "AMY1B" "0000087261" "AMY1C" "0000087261" "AMY2A" "0000087261" "AMY2B" ## 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 = 12 "{{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}}" "0000140409" "3" "90" "1" "104153701" "104161396" "" "0" "00006" "AMY2B_010011" "g.[104153701_104161396del;104161926_104226715del]" "" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "104161926_104226715del" "75 kb deletion AMY2A-AMY1A region" "Germline" "" "" "0" "" "" "" "" "pathogenic" "" "0000140410" "1" "50" "1" "104162309" "104256477" "dup" "0" "00006" "AMY2B_011122" "g.104162309_104256477dup" "" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "" "haplotype with duplicated copy AMY1A-AMY1B region, named H2 by Groot 1990 and AH5 by Usher et al" "Germline" "" "" "0" "" "" "g.103619687_103713855dup" "" "VUS" "" "0000140411" "2" "70" "1" "104161939" "104256107" "" "0" "00006" "AMY2B_011166" "g.104161939_104256107[6]" "" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "" "haplotype with 6 copies of AMY1A-AMY1B region and 13 copies of AMY1" "Germline" "" "" "0" "" "" "" "" "likely pathogenic" "" "0000140413" "2" "50" "1" "104161939" "104256107" "" "0" "00006" "AMY2B_011133" "g.104161939_104256107[3]" "" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "" "haplotype with 3 copies of AMY1A-AMY1B region and 7 copies of AMY1" "Germline" "" "" "0" "" "" "" "" "VUS" "" "0000140414" "1" "50" "1" "104103724" "104219543" "dup" "0" "00006" "AMY2B_022211" "g.104103724_104219543dup" "" "{PMID:Carpenter 2015:25788522}, {DOI:Carpenter 2015:10.1093/hmg/ddv098}" "" "" "116 kb duplication AMY2B-AMY2A-AMY1A region" "Germline" "" "" "0" "" "" "" "" "VUS" "" "0000140418" "11" "70" "1" "104153400" "104211327" "" "0" "01810" "AMY2B_044301" "g.[(104153400_104211327)inv; (104219543_104219544)ins(104103733_104219543[2]); (104219544_104262492)delins(104103733_104168400)]" "" "Shwan, submitted" "" "" "quadruplication allele with inverted AMY2A-AMY1A copy followed by two AMY2B-AMY2A-AMY1A copies and one AMY2B-AMY2A-AMY1C copy" "Germline" "" "" "0" "" "" "" "" "likely pathogenic" "" "0000140420" "2" "70" "1" "104153400" "104211327" "" "0" "01810" "AMY2B_055401" "g.[(104153400_104211327)inv; (104219543_104219544)ins(104103733_104219543[3]); (104219544_104262492)delins(104103733_104168400)]" "" "Shwan, submitted" "" "" "quintuplication allele with inverted AMY2A-AMY1A copy followed by three AMY2B-AMY2A-AMY1A and one AMY2B-AMY2A-AMY1C copies" "Germline" "" "" "0" "" "" "" "" "likely pathogenic" "" "0000140421" "21" "30" "1" "104153400" "104211327" "" "0" "01810" "AMY2B_033201" "g.[(104153400_104211327)inv; (104219543_104219544)ins(104103733_104219543); (104219544_104262492)delins(104103733_104168400)]" "" "Shwan, submitted" "" "" "triplication allele with inverted AMY2A-AMY1A copy followed by two repeats of (AMY2B-AMY2A-AMY1) copies" "Germline" "" "" "0" "" "" "" "" "likely benign" "" "0000140425" "1" "10" "1" "104229645" "104229646" "ins" "0" "01810" "AMY2B_012211" "g.(104229645_104229646)ins(104135020_1042219543)inv" "" "Shwan, submitted" "" "" "allele with inverted duplication of AMY2A-AMY1A region between AMY1A and AMY1B" "Germline" "" "" "0" "" "" "" "" "benign" "" "0000140426" "2" "70" "1" "104262492" "104262493" "" "0" "01810" "AMY2B_012341" "g.[104262492_104262493ins104168400_104211327;10415020_104262492;104168400_104262492]" "" "Shwan, submitted" "" "" "complex allele with, between AMYP1 and AMY1C, insertion of AMY1-AMY2A-(AMY1A-AMY1B-AMYP1[2])" "Germline" "" "" "0" "" "" "" "" "likely pathogenic" "" "0000140427" "11" "70" "1" "104262492" "104262493" "" "0" "01810" "AMY2B_012341" "g.[104262492_104262493ins104168400_104211327;10415020_104262492;104168400_104262492]" "" "Shwan, submitted" "" "" "complex allele with, between AMYP1 and AMY1C, insertion of AMY1-AMY2A-(AMY1A-AMY1B-AMYP1[2])" "Germline" "" "" "0" "" "" "" "" "likely pathogenic" "" "0000140429" "21" "70" "1" "104219543" "104262492" "" "0" "01810" "AMY2B_023201" "g.[104219543_104262492delins104103733_104200568;104153629_104168400]" "" "Shwan, submitted" "" "" "" "Germline" "" "" "0" "" "" "" "" "likely pathogenic" "" ## 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 AMY1A ## Count = 12 "{{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}}" "{{VariantOnTranscript/Haplotype}}" "0000140409" "00002448" "90" "-1" "0" "1537" "0" "c.(?_-1)_(*1_?)del" "r.0" "p.0" "_1_11_" "" "0000140410" "00002448" "70" "-1" "0" "1537" "0" "c.(?_-1)_(*1_?)dup" "r.?" "p.?" "_1_11_" "" "0000140411" "00002448" "90" "0" "0" "0" "0" "c.(?_-1)_(*1_?)[6]" "r.?" "p.?" "_1_11_" "" "0000140413" "00002448" "90" "0" "0" "0" "0" "c.(?_-1)_(*1_?)[3]" "r.?" "p.?" "_1_11_" "" "0000140414" "00002448" "50" "-1" "0" "1537" "0" "c.(?_-1)_(*1_?)dup" "r.?" "p.?" "_1_11_" "" "0000140418" "00002448" "70" "0" "0" "0" "0" "c.(?_-1)_(*1_?)[3]" "r.?" "p.?" "_1_11_" "" "0000140420" "00002448" "70" "0" "0" "0" "0" "c.(?_-1)_(*1_?)[4]" "r.?" "p.?" "_1_11_" "" "0000140421" "00002448" "70" "-1" "0" "1537" "0" "c.(?_-1)_(*1_?)dup" "r.?" "p.?" "_1_11_" "" "0000140425" "00002448" "70" "-8388608" "0" "8388607" "0" "c.?ins(?_-1)_(*1_?)inv" "r.?" "p.?" "_1_11_" "" "0000140426" "00002448" "70" "0" "0" "0" "0" "c.(?_-1)_(*1_?)[3]" "r.?" "p.?" "_1_11_" "" "0000140427" "00002448" "70" "0" "0" "0" "0" "c.(?_-1)_(*1_?)[3]" "r.?" "p.?" "_1_11_" "" "0000140429" "00002448" "70" "0" "0" "0" "0" "c.(?_-1)_(*1_?)[1.5]" "r.?" "p.?" "_1_11_" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 12 "{{screeningid}}" "{{variantid}}" "0000087252" "0000140409" "0000087253" "0000140410" "0000087253" "0000140411" "0000087254" "0000140413" "0000087255" "0000140414" "0000087257" "0000140418" "0000087258" "0000140420" "0000087259" "0000140421" "0000087259" "0000140427" "0000087260" "0000140425" "0000087260" "0000140426" "0000087261" "0000140429"