### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = ITGAM) # 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}}" "ITGAM" "integrin, alpha M (complement component 3 receptor 3 subunit)" "16" "p11.2" "unknown" "NG_011719.1" "UD_132084450804" "" "http://www.LOVD.nl/ITGAM" "" "1" "6149" "3684" "120980" "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/ITGAM_codingDNA.html" "1" "" "" "-1" "" "-1" "00000" "2012-09-13 00:00:00" "00006" "2016-02-14 00:37:19" "00000" "2024-04-19 20:27:30" ## 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}}" "00024105" "ITGAM" "transcript variant 1" "001" "NM_001145808.1" "" "NP_001139280.1" "" "" "" "-98" "4647" "3462" "31271288" "31344213" "00006" "2016-02-14 00:35:00" "" "" ## Diseases ## Do not remove or alter this header ## ## Count = 4 "{{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" "01157" "CHTE" "Hypothyroidism, central, testicular enlargement (CHTE)" "XLR" "300888" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "02887" "SLEB6" "lupus erythematosus, systemic, type 6 (SLEB-6)" "" "609939" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "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 = 1 "{{geneid}}" "{{diseaseid}}" "ITGAM" "02887" ## 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}}" "00000208" "" "" "" "1" "" "00037" "{PMID:Sun 2011:23143598}, {DOI:Sun 2011:10.1038/ng.2453}" "" "M" "no" "Netherlands" "" "0" "" "" "" "" "00050683" "" "" "" "2" "" "00006" "{PMID:DDDS 2015:25533962}, {DOI:DDDS 2015:10.1038/nature14135}" "family, affected sibling(s)" "M" "" "United Kingdom (Great Britain)" "" "0" "Decipher" "" "" "" "00291445" "" "" "" "9" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00362000" "" "" "" "1" "" "00000" "{PMID:Duvvari 2016:27007659}" "patient" "" "" "Netherlands" "" "0" "" "" "white" "Pat3AB" "00390025" "" "" "" "1" "" "00000" "{PMID:Ruberto 2020:32507954}" "" "?" "" "Italy" "" "0" "" "" "" "3" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 5 "{{individualid}}" "{{diseaseid}}" "00000208" "01157" "00050683" "00198" "00291445" "00198" "00362000" "04214" "00390025" "04214" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00198, 01157, 02887, 04214 ## 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}}" "0000037295" "00198" "00050683" "00006" "Unknown" "" "microcephaly, abnormality of the outer ear, prominent metopic ridge, narrow mouth, inferior vermis hypoplasia, delayed speech and language development" "" "" "" "" "" "" "" "" "" "" "" "0000038983" "01157" "00000208" "00006" "Familial, X-linked recessive" "" "central hypothyroidism (FT4 0.50-0.99of lower limit normal), no prolactin deficiency, age sonographic determination testicular volume 17.64y, testicular volume right/left 21/20 (7.3–16ml)" "" "3w" "" "" "" "" "" "" "" "" "" "0000257393" "04214" "00362000" "00000" "Unknown" "" "" "" "" "" "" "" "" "" "" "" "age-related macular degeneration, cuticular drusen" "" "0000283565" "04214" "00390025" "00000" "Unknown" "11m" "Pale and tilted optic disk associated to hypoplasia, tortuous retinal vessels, non-homogeneous macula" "" "" "" "" "" "" "" "" "Retinal dystrophy" "" "" ## 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}}" "0000000209" "00000208" "1" "00037" "00001" "2012-09-13 12:02:03" "" "" "SEQ-NG-I" "DNA" "" "" "0000050628" "00050683" "1" "00006" "00006" "2015-09-27 16:16:40" "" "" "SEQ;SEQ-NG-I" "DNA" "" "" "0000292613" "00291445" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000363228" "00362000" "1" "00000" "00006" "2021-04-13 14:21:59" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000391266" "00390025" "1" "00000" "03840" "2021-11-08 12:01:50" "" "" "arrayCGH" "DNA" "" "targeted sequencing with 1 of 4 panels of OFTALMOgenics probes" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 1 "{{screeningid}}" "{{geneid}}" "0000391266" "CLN3" ## 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 = 24 "{{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}}" "0000005579" "0" "30" "16" "31309805" "31309805" "subst" "0" "00037" "ITGAM_000001" "g.31309805C>T" "" "" "" "" "" "Germline" "" "" "0" "" "" "g.31298484C>T" "" "likely benign" "" "0000079608" "0" "90" "16" "27183151" "31888684" "dup" "0" "00006" "CLN3_000010" "g.27183151_31888684dup" "" "{PMID:DDDS 2015:25533962}, {DOI:DDDS 2015:10.1038/nature14135}" "" "" "mosaicism, copy number 3 in 0.33 cells" "Somatic" "" "" "0" "" "" "g.27171830_31877363dup" "" "pathogenic" "" "0000251807" "0" "30" "16" "31309134" "31309134" "subst" "0.000667183" "02326" "ITGAM_000004" "g.31309134A>T" "" "" "" "ITGAM(NM_001145808.2):c.1569A>T (p.A523=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.31297813A>T" "" "likely benign" "" "0000255899" "0" "50" "16" "31341430" "31341430" "subst" "0.000573436" "01943" "ITGAM_000007" "g.31341430A>G" "" "" "" "ITGAM(NM_001145808.1):c.3008A>G (p.E1003G)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.31330109A>G" "" "VUS" "" "0000281583" "0" "10" "16" "31342608" "31342608" "subst" "0.931386" "02325" "ITGAM_000008" "g.31342608T>C" "" "" "" "ITGAM(NM_001145808.2):c.3390+12T>C" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.31331287T>C" "" "benign" "" "0000281584" "0" "10" "16" "31343005" "31343005" "subst" "0.154552" "02325" "ITGAM_000009" "g.31343005C>T" "" "" "" "ITGAM(NM_001145808.2):c.3439C>T (p.P1147S)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.31331684C>T" "" "benign" "" "0000289760" "0" "30" "16" "31288298" "31288298" "subst" "6.12565E-5" "01943" "ITGAM_000002" "g.31288298T>C" "" "" "" "ITGAM(NM_001145808.1):c.1141T>C (p.Y381H)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.31276977T>C" "" "likely benign" "" "0000289761" "0" "30" "16" "31289440" "31289440" "subst" "0" "01943" "ITGAM_000003" "g.31289440G>A" "" "" "" "ITGAM(NM_001145808.1):c.1356+10G>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.31278119G>A" "" "likely benign" "" "0000289762" "0" "50" "16" "31309175" "31309175" "subst" "0.000381974" "01943" "ITGAM_000005" "g.31309175C>T" "" "" "" "ITGAM(NM_001145808.1):c.1610C>T (p.T537M)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.31297854C>T" "" "VUS" "" "0000289763" "0" "50" "16" "31336912" "31336912" "subst" "0.000377763" "01943" "ITGAM_000006" "g.31336912T>C" "" "" "" "ITGAM(NM_001145808.1):c.2600T>C (p.I867T)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.31325591T>C" "" "VUS" "" "0000557978" "0" "10" "16" "31273129" "31273129" "subst" "0.661554" "02325" "ITGAM_000010" "g.31273129T>C" "" "" "" "ITGAM(NM_001145808.2):c.134+11T>C" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31261808T>C" "" "benign" "" "0000557979" "0" "30" "16" "31277145" "31277145" "subst" "4.07295E-6" "01943" "ITGAM_000011" "g.31277145C>T" "" "" "" "ITGAM(NM_001145808.1):c.252C>T (p.A84=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31265824C>T" "" "likely benign" "" "0000557980" "0" "30" "16" "31308825" "31308825" "subst" "4.0704E-6" "01943" "ITGAM_000012" "g.31308825T>A" "" "" "" "ITGAM(NM_001145808.1):c.1357-10T>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31297504T>A" "" "likely benign" "" "0000557981" "0" "30" "16" "31336701" "31336701" "subst" "0.000631529" "02326" "ITGAM_000013" "g.31336701C>A" "" "" "" "ITGAM(NM_001145808.2):c.2484C>A (p.S828=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31325380C>A" "" "likely benign" "" "0000557982" "0" "30" "16" "31336875" "31336875" "subst" "1.21834E-5" "01943" "ITGAM_000014" "g.31336875G>A" "" "" "" "ITGAM(NM_001145808.1):c.2563G>A (p.E855K)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31325554G>A" "" "likely benign" "" "0000557983" "0" "10" "16" "31336888" "31336888" "subst" "0.157551" "02325" "ITGAM_000015" "g.31336888C>T" "" "" "" "ITGAM(NM_001145808.2):c.2576C>T (p.A859V)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31325567C>T" "" "benign" "" "0000557984" "0" "30" "16" "31340609" "31340609" "subst" "0.000785914" "01943" "ITGAM_000016" "g.31340609G>T" "" "" "" "ITGAM(NM_001145808.1):c.2856G>T (p.M952I)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31329288G>T" "" "likely benign" "" "0000615959" "0" "30" "16" "31284720" "31284720" "subst" "0.000190902" "01943" "ITGAM_000017" "g.31284720A>G" "" "" "" "ITGAM(NM_001145808.1):c.739A>G (p.K247E)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31273399A>G" "" "likely benign" "" "0000615960" "0" "50" "16" "31286900" "31286900" "subst" "5.68777E-5" "02325" "ITGAM_000018" "g.31286900C>T" "" "" "" "ITGAM(NM_001145808.2):c.889C>T (p.R297C)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.31275579C>T" "" "VUS" "" "0000649302" "1" "10" "16" "31341424" "31341424" "subst" "0.00783558" "03575" "ITGAM_000019" "g.31341424C>A" "9/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "9 heterozygous, no homozygous; {DB:CLININrs41321249}" "Germline" "" "rs41321249" "0" "" "" "g.31330103C>A" "" "benign" "" "0000763720" "0" "50" "16" "31336059" "31336059" "subst" "4.89241E-5" "00000" "ITGAM_000020" "g.31336059C>T" "" "{PMID:Duvvari 2016:27007659}" "" "2248C>T" "" "Germline" "" "" "0" "" "" "g.31324738C>T" "" "VUS" "" "0000820998" "0" "70" "16" "28100001" "34600000" "del" "0" "00000" "CRYM_000000" "g.28100001_34600000del" "" "{PMID:Ruberto 2020:32507954}" "" "CGH array, microdeletion in 16p11.2" "zygosity not written; probable breakpoints; pathogenic in literature; genes ANKS4B,CRYM,NPIPB3,SMG1P3,RRN3P3,MIR3680-1,MIR3680-2,SLC7A5P2,LOC101927814,METTL9,IGSF6,OTOA,OTOAP1,RRN3P1,NPIPB4,NPIPB5,UQCRC2,PDZD9,MOSMO,VWA3A,EEF2K,POLR3E,CDR2,MFSD13B,HS3ST2,USP31,SCNN1G,SCNN1B,COG7,GGA2,EARS2,UBFD1,NDUFAB1,PALB2,DCTN5,PLK1,ERN2,CHP2" "Unknown" "?" "" "0" "" "" "g.28500001_35300000del" "" "likely pathogenic" "" "0000981864" "0" "30" "16" "31284718" "31284718" "subst" "0.0021772" "01804" "ITGAM_000021" "g.31284718G>A" "" "" "" "ITGAM(NM_000632.4):c.737G>A (p.(Arg246Gln))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000981865" "0" "50" "16" "31336273" "31336273" "subst" "0.000182193" "01804" "ITGAM_000022" "g.31336273T>A" "" "" "" "ITGAM(NM_000632.4):c.2290-6T>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "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 ITGAM ## Count = 24 "{{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}}" "0000005579" "00024105" "30" "1710" "530" "1710" "530" "c.1710+530C>T" "r.(?)" "p.(=)" "14i" "0000079608" "00024105" "00" "-4088235" "0" "549118" "0" "c.-4088235_*545656dup" "" "" "" "0000251807" "00024105" "30" "1569" "0" "1569" "0" "c.1569A>T" "r.(?)" "p.(Ala523=)" "" "0000255899" "00024105" "50" "3008" "0" "3008" "0" "c.3008A>G" "r.(?)" "p.(Glu1003Gly)" "" "0000281583" "00024105" "10" "3390" "12" "3390" "12" "c.3390+12T>C" "r.(=)" "p.(=)" "" "0000281584" "00024105" "10" "3439" "0" "3439" "0" "c.3439C>T" "r.(?)" "p.(Pro1147Ser)" "" "0000289760" "00024105" "30" "1141" "0" "1141" "0" "c.1141T>C" "r.(?)" "p.(Tyr381His)" "" "0000289761" "00024105" "30" "1356" "10" "1356" "10" "c.1356+10G>A" "r.(=)" "p.(=)" "" "0000289762" "00024105" "50" "1610" "0" "1610" "0" "c.1610C>T" "r.(?)" "p.(Thr537Met)" "" "0000289763" "00024105" "50" "2600" "0" "2600" "0" "c.2600T>C" "r.(?)" "p.(Ile867Thr)" "" "0000557978" "00024105" "10" "134" "11" "134" "11" "c.134+11T>C" "r.(=)" "p.(=)" "" "0000557979" "00024105" "30" "252" "0" "252" "0" "c.252C>T" "r.(?)" "p.(Ala84=)" "" "0000557980" "00024105" "30" "1357" "-10" "1357" "-10" "c.1357-10T>A" "r.(=)" "p.(=)" "" "0000557981" "00024105" "30" "2484" "0" "2484" "0" "c.2484C>A" "r.(?)" "p.(Ser828=)" "" "0000557982" "00024105" "30" "2563" "0" "2563" "0" "c.2563G>A" "r.(?)" "p.(Glu855Lys)" "" "0000557983" "00024105" "10" "2576" "0" "2576" "0" "c.2576C>T" "r.(?)" "p.(Ala859Val)" "" "0000557984" "00024105" "30" "2856" "0" "2856" "0" "c.2856G>T" "r.(?)" "p.(Met952Ile)" "" "0000615959" "00024105" "30" "739" "0" "739" "0" "c.739A>G" "r.(?)" "p.(Lys247Glu)" "" "0000615960" "00024105" "50" "889" "0" "889" "0" "c.889C>T" "r.(?)" "p.(Arg297Cys)" "" "0000649302" "00024105" "10" "3002" "0" "3002" "0" "c.3002C>A" "r.(?)" "p.(Thr1001Asn)" "" "0000763720" "00024105" "50" "2248" "0" "2248" "0" "c.2248C>T" "r.(?)" "p.(Arg750Trp)" "" "0000820998" "00024105" "70" "-3171385" "0" "3260434" "0" "c.-3171385_*3256972del" "r.0?" "p.0?" "" "0000981864" "00024105" "30" "737" "0" "737" "0" "c.737G>A" "r.(?)" "p.(Arg246Gln)" "" "0000981865" "00024105" "50" "2293" "-6" "2293" "-6" "c.2293-6T>A" "r.(=)" "p.(=)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 5 "{{screeningid}}" "{{variantid}}" "0000000209" "0000005579" "0000050628" "0000079608" "0000292613" "0000649302" "0000363228" "0000763720" "0000391266" "0000820998"