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{"sheet":"table_s1","index":0,"n_rows":152,"n_cols":7,"rows_kept":152,"flags":["formulas_cached_only"]}
["gene","variant","allele count","status","LOFTEE flags","manual curation result","comments"]
["HTT","4-003076620-AGC-A",14,"loftee","lcr"]
["HTT","4-003076623-AGCAG-A",14,"loftee","lcr"]
["HTT","4-003076631-CAG-C",1,"loftee","lcr"]
["HTT","4-003076632-AGC-A",11,"loftee","lcr"]
["HTT","4-003076632-AGCAGCAGCAGCAGCAGCAGCAG-A",1,"loftee","lcr"]
["HTT","4-003076635-AGCAGCAGCAGCAGCAGCAG-A",10,"loftee","lcr"]
["HTT","4-003076635-AGCAGCAGCAGCAGCAGCAGCAGCAGCAACAG-A",1,"loftee","lcr"]
["HTT","4-003076638-AGCAGCAGCAGCAGCAGCAG-A",1,"loftee","lcr"]
["HTT","4-003076638-AGC-A",54,"loftee","lcr"]
["HTT","4-003076640-CAG-C",116,"loftee","lcr"]
["HTT","4-003076641-AGC-A",32,"loftee","lcr"]
["HTT","4-003076641-AGCAGCAGCAGCAG-A",55,"loftee","lcr"]
["HTT","4-003076644-AGC-A",31,"loftee","lcr"]
["HTT","4-003076644-AGCAGCAGCAGCAG-A",1,"loftee","lcr"]
["HTT","4-003076644-AGCAGCAGCAG-A",31,"loftee","lcr"]
["HTT","4-003076644-AGCAGCAGCAGCAGCAGCAACAG-A",110,"loftee","lcr"]
["HTT","4-003076646-CAG-C",2,"loftee","lcr"]
["HTT","4-003076647-AGC-A",161,"loftee","lcr"]
["HTT","4-003076647-AGCAGCAGCAGCAGCAACAG-A",3,"loftee","lcr"]
["HTT","4-003076647-AGCAGCAGCAG-A",6,"loftee","lcr"]
["HTT","4-003076649-CAG-C",8,"loftee","lcr"]
["HTT","4-003076650-AGC-A",2673,"loftee","lcr"]
["HTT","4-003076650-AGCAG-A",128,"loftee","lcr"]
["HTT","4-003076650-AGCAGCAG-A",26,"loftee","lcr"]
["HTT","4-003076650-AGCAGCAGCAGCAACAG-A",2,"loftee","lcr"]
["HTT","4-003076653-AGC-A",80,"loftee","lcr"]
["HTT","4-003076653-AG-A",1594,"loftee","lcr"]
["HTT","4-003076653-AGCAG-A",1078,"loftee","lcr"]
["HTT","4-003076654-G-GCCGC",2,"loftee","lcr"]
["HTT","4-003076655-CAGCAGCAACA-C",2,"loftee","lcr"]
["HTT","4-003076655-CAG-C",20,"loftee","lcr"]
["HTT","4-003076656-AG-A",84,"loftee","lcr"]
["HTT","4-003076656-A-ACC",2,"loftee","lcr"]
["HTT","4-003076656-AGCAGCAACAG-A",4,"loftee","lcr"]
["HTT","4-003076658-CAG-C",287,"loftee","lcr"]
["HTT","4-003076658-CAGCAACA-C",2,"loftee","lcr"]
["HTT","4-003076658-CA-C",1,"loftee","lcr"]
["HTT","4-003076659-AG-A",1,"loftee","lcr"]
["HTT","4-003076659-AGCAACAG-A",14,"loftee","lcr"]
["HTT","4-003076659-A-ACC",2,"loftee","lcr"]
["HTT","4-003076661-CAACA-C",8,"loftee","lcr"]
["HTT","4-003076662-AACAG-A",251,"curated",null,"not_LoF","CAG repeat artifact"]
["HTT","4-003076663-A-AGCAGCAGCAGCAGCAGCAG",2,"loftee","lcr"]
["HTT","4-003076663-A-AGCAGCAGCAGCAGCAGCAGCAGCAG",1,"loftee","lcr"]
["HTT","4-003076663-A-AGCAGCAGCAG",1,"loftee","lcr"]
["HTT","4-003076663-A-AGCAGCAGCAGCAGCAG",2,"loftee","lcr"]
["HTT","4-003076665-A-ACCGCC",49,"loftee","lcr"]
["HTT","4-003076669-GC-G",2,"loftee","lcr"]
["HTT","4-003076670-C-CAGCAGCAG",1,"loftee","lcr"]
["HTT","4-003076670-C-CAGCAGCAGCAG",1,"loftee","lcr"]
["HTT","4-003076672-ACC-A",79,"loftee","lcr"]
["HTT","4-003076680-CG-C",3,"loftee","lcr"]
["HTT","4-003076682-CCG-C",3,"loftee","lcr"]
["HTT","4-003076703-CTTCCT-C",1,"curated",null,"not_LoF","repeat region"]
["HTT","4-003076704-T-TCC",3,"curated",null,"likely_not_LoF","repeat region, nearby SNP"]
["HTT","4-003076710-AG-A",1,"curated",null,null,"repeat region"]
["HTT","4-003088708-TTGTC-T",1,true,null,"LoF","true 4bp deletion"]
["HTT","4-003088729-CAT-C",1,true,null,"LoF","true 2bp deletion"]
["HTT","4-003107083-G-A",1,true,null,"LoF","essential splice acceptor lost. possible downstream rescue site is out-of-frame"]
["HTT","4-003117118-C-T",3,true,null,"LoF","true stop codon"]
["HTT","4-003131650-G-A",1,true,null,"LoF","true essential splice acceptor lost. 2 downstream splice rescue sites but both out of frame"]
["HTT","4-003133110-CA-C",1,true,null,"LoF","true 1bp deletion"]
["HTT","4-003133110-CAG-C",7,true,null,"LoF","true 2bp deletion"]
["HTT","4-003136141-GTC-G",1,true,null,"LoF","true 2bp deletion"]
["HTT","4-003136269-T-G",1,"curated",null,"uncertain_LoF","raw reads not available. would be a true splice donor loss"]
["HTT","4-003138025-C-T",3,true,null,"likely_LoF","likely stop codon, though there is an outside chance it creates a splice donor that preserves frame"]
["HTT","4-003156065-C-T",2,true,null,"LoF","true stop codon"]
["HTT","4-003158859-G-GT",1,true,null,"LoF","true 1bp insertion"]
["HTT","4-003174671-C-T",1,true,null,"LoF","true stop codon"]
["HTT","4-003174707-C-T",1,true,null,"LoF","true stop codon"]
["HTT","4-003176464-C-T",1,true,null,"LoF","true stop codon"]
["HTT","4-003176787-C-T",1,true,null,"LoF","true stop codon"]
["HTT","4-003176796-C-T",1,true,null,"LoF","true stop codon"]
["HTT","4-003184144-C-T",1,true,null,"LoF","true stop codon"]
["HTT","4-003189579-CAAAT-C",1,true,null,"LoF","true 4bp deletion"]
["HTT","4-003205754-CAA-C",1,"curated",null,"uncertain_LoF","raw reads not available"]
["HTT","4-003205876-G-A",1,"curated",null,"likely_not_LoF","potential in-frame rescue site 3bp upstream"]
["HTT","4-003209047-A-AT",1,true,null,"LoF","true 1bp insertion"]
["HTT","4-003211578-TC-T",1,"curated",null,"likely_not_LoF","1bp deletion could be avoided by using potential splice acceptor at subsequent codon"]
["HTT","4-003211677-G-T",1,true,null,"likely_LoF","MNP - D-1 and +1 site are both mutated to T. appears would still be true splice disruptor though"]
["HTT","4-003215736-C-T",1,true,null,"LoF","true stop codon"]
["HTT","4-003216836-G-A",1,"curated",null,"likely_not_LoF","potential in-frame donor rescue 6bp downstream"]
["HTT","4-003221937-CG-C",1,true,null,"LoF","true 1bp deletion"]
["HTT","4-003222036-G-A",1,true,null,"LoF","true essential splice donor loss"]
["HTT","4-003224113-G-T",1,true,null,"LoF","true essential splice acceptor lost"]
["HTT","4-003225261-CA-C",1,true,null,"LoF","true 1bp deletion"]
["HTT","4-003237874-A-T",1,true,null,"LoF","true essential splice acceptor lost"]
["HTT","4-003240172-A-G",1,"curated",null,"uncertain_LoF","raw reads not available"]
["HTT","4-003240338-T-C",1,"curated",null,"likely_not_LoF","GC splice donor might still function, also alternate in-frame GT donor 9 bp upstream"]
["HTT","4-003241749-C-CT",1,"loftee","lc_lof"]
["HTT","4-003241757-C-T",1,"loftee","lc_lof"]
["MAPT","17-044039722-G-T",1,"curated",null,"not_LoF","rescued by alternate start codon M11, with good Kozak context"]
["MAPT","17-044049312-G-T",1,"curated",null,"not_LoF","non-constitutive exon"]
["MAPT","17-044049312-G-A",2,"curated",null,"not_LoF","non-constitutive exon"]
["MAPT","17-044049445-G-A",1,"curated",null,"not_LoF","not a real exon"]
["MAPT","17-044051838-G-A",5,"loftee","lc_lof"]
["MAPT","17-044051839-T-C",1,"loftee","lc_lof"]
["MAPT","17-044055646-TA-T",1,"loftee","lof_flag"]
["MAPT","17-044055647-A-T",39690,"loftee","lc_lof,lof_flag"]
["MAPT","17-044055710-A-AC",2,"loftee","lof_flag"]
["MAPT","17-044055746-G-A",1,"loftee","lof_flag"]
["MAPT","17-044060543-G-C",5,"curated",null,"not_LoF","non-constitutive exon"]
["MAPT","17-044060582-C-T",25,"loftee","lof_flag"]
["MAPT","17-044060652-A-AG",1,"loftee","lof_flag"]
["MAPT","17-044060675-C-T",5,"loftee","lof_flag"]
["MAPT","17-044060703-CAG-C",2,"loftee","lof_flag"]
["MAPT","17-044060717-C-CA",1,"loftee","lof_flag"]
["MAPT","17-044060724-CT-C",6,"loftee","lof_flag"]
["MAPT","17-044060788-AG-A",3,"loftee","lof_flag"]
["MAPT","17-044060842-CG-C",2,"loftee","lof_flag"]
["MAPT","17-044060877-A-AGGCCTCCCCAGCCCAAGATGGGC",1,"loftee","lof_flag"]
["MAPT","17-044060877-AGGCCTCCCCAGCCCAAGATGGGC-A",1,"loftee","lof_flag"]
["MAPT","17-044060917-C-CGCCAGAG",1,"loftee","lof_flag"]
["MAPT","17-044061006-T-TCCCA",1,"loftee","lof_flag"]
["MAPT","17-044061053-C-T",1,"loftee","lof_flag"]
["MAPT","17-044061059-GC-G",4,"loftee","lof_flag"]
["MAPT","17-044061065-CT-C",1,"loftee","lof_flag"]
["MAPT","17-044061078-TTCACGTGGAAA-T",1,"loftee","lof_flag"]
["MAPT","17-044061153-CAGGGGCCCCTGGAGAGGGGCCAG-C",2,"loftee","lof_flag"]
["MAPT","17-044061154-AGGGGCCCCTGGAGAGGGGCCAGAGGCCC-A",3,"loftee","lof_flag"]
["MAPT","17-044061182-CGG-C",1,"loftee","lof_flag"]
["MAPT","17-044061223-TC-T",3,"loftee","lof_flag"]
["MAPT","17-044061247-TG-T",1,"loftee","lof_flag"]
["MAPT","17-044067273-G-GA",1,"loftee","lof_flag"]
["MAPT","17-044067384-C-G",3,"loftee","lof_flag"]
["MAPT","17-044067395-TC-T",1,"loftee","lof_flag"]
["MAPT","17-044067403-C-T",26,"loftee","lof_flag"]
["MAPT","17-044067438-C-CA",1,"loftee","lof_flag"]
["MAPT","17-044071327-GCC-G",1,"curated",null,"not_LoF","non-constitutive exon"]
["MAPT","17-044071329-C-CGGGTA",1,"curated",null,"not_LoF","non-constitutive exon"]
["MAPT","17-044073963-A-ACC",1,"curated",null,"uncertain_LoF","raw reads not available"]
["MAPT","17-044096026-AGGACAGAGTCCAGTCGAAG-A",2,"curated",null,"not_LoF","actually in-frame. starting at K682 it becomes AAATGGT preserving frame "]
["MAPT","17-044096047-TTGGGTCCCTGGACAATATCACCCACGTCCCTGGCGGAGGAAATAAAAAGGTAAAGGG-T",2,"curated",null,"not_LoF","actually in-frame. this is the same exact variant as the previous one"]
["PRNP","20-004679975-C-T",2,true,null,null,"R37X"]
["PRNP","20-004679987-C-T",1,true,null,null,"Q41X"]
["PRNP","20-004680069-CT-C",1,"curated",null,"not_LoF","false variant call, apparent alignment artifact at octapeptide repeat region"]
["PRNP","20-004680071-CATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCT-C",1,"curated",null,"not_LoF","false variant call, apparent alignment artifact at octapeptide repeat region"]
["PRNP","20-004680089-C-T",1,true,null,null,"Q75X"]
["PRNP","20-004680108-G-A",1,true,null,null,"W81X"]
["PRNP","20-004680162-G-A",1,true,null,null,"W99X"]
["PRNP","20-004680257-G-T",1,true,null,null,"G131X"]
["PRNP","20-004680566-CT-C",1,"curated",null,"not_LoF","L234Pfs7X; possible pathogenic gain-of-function in dementia case. see Table S1 for details"]
["SNCA","4-090743391-C-TRUE",3,"loftee","lc_lof"]
["SOD1","21-033032095-GC-G",1,true,null,"LoF","true early frameshift, no rescue"]
["SOD1","21-033036098-TAAAGG-T",1,true,null,"likely_LoF","true 5bp frameshift deletion, splice site may be rescued by downstream AG but resulting frame is shifted."]
["SOD1","21-033036178-GA-G",4,true,null,"LoF"]
["SOD1","21-033038788-AATCCTCT-A",2,true,null,"LoF"]
["SOD1","21-033038833-T-C",1,true,null,"LoF"]
["SOD1","21-033039619-CG-C",2,true,null,"LoF"]
["SOD1","21-033039689-G-T",2,"curated",null,"not_LoF","alternative GT donor 3 bases upstream, in-frame"]
["SOD1","21-033039689-G-GT",2,"curated",null,"not_LoF","splice donor D +1 site G->GT insertion creates its own new splice donor"]