Disease associated variation - ClinVar Allele ID Type Name RS#dbSNP Phenotype IDs Chromosome Start Stop Reference Alternate 45747 deletion NM_001197104.1(KMT2A):c.8806_8809delGTCT (p.Val2936Terfs) 398122878 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118375413 118375416 GTCT - 45747 deletion NM_001197104.1(KMT2A):c.8806_8809delGTCT (p.Val2936Terfs) 398122878 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118504698 118504701 GTCT - 45748 deletion NM_001197104.1(KMT2A):c.8267delT (p.Leu2756Terfs) 398122879 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118374874 118374874 T - 45748 deletion NM_001197104.1(KMT2A):c.8267delT (p.Leu2756Terfs) 398122879 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118504159 118504159 T - 45749 deletion NM_001197104.1(KMT2A):c.6913delT (p.Ser2305Leufs) 398122880 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118373520 118373520 T - 45749 deletion NM_001197104.1(KMT2A):c.6913delT (p.Ser2305Leufs) 398122880 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118502805 118502805 T - 45750 single nucleotide variant NM_001197104.1(KMT2A):c.7144C>T (p.Arg2382Ter) 387907275 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118373751 118373751 C T 45750 single nucleotide variant NM_001197104.1(KMT2A):c.7144C>T (p.Arg2382Ter) 387907275 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118503036 118503036 C T 45751 duplication NM_001197104.1(KMT2A):c.4599dupT (p.Lys1534Terfs) 398122881 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118360867 118360867 T TT 45751 duplication NM_001197104.1(KMT2A):c.4599dupT (p.Lys1534Terfs) 398122881 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118490152 118490152 T TT 168850 single nucleotide variant NM_001197104.1(KMT2A):c.89C>G (p.Ala30Gly) 9332745 MedGen:CN169374 11 118307316 118307316 C G 168850 single nucleotide variant NM_001197104.1(KMT2A):c.89C>G (p.Ala30Gly) 9332745 MedGen:CN169374 11 118436601 118436601 C G 168851 single nucleotide variant NM_001197104.1(KMT2A):c.458C>G (p.Ser153Ter) 587783678 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118339515 118339515 C G 168851 single nucleotide variant NM_001197104.1(KMT2A):c.458C>G (p.Ser153Ter) 587783678 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118468800 118468800 C G 168852 deletion NM_001197104.1(KMT2A):c.2673_2674delGA (p.Arg893Glufs) 587783676 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118344547 118344548 GA - 168852 deletion NM_001197104.1(KMT2A):c.2673_2674delGA (p.Arg893Glufs) 587783676 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118473832 118473833 GA - 168853 single nucleotide variant NM_001197104.1(KMT2A):c.4284A>C (p.Ile1428=) 9332801 MedGen:CN169374 11 118355642 118355642 A C 168853 single nucleotide variant NM_001197104.1(KMT2A):c.4284A>C (p.Ile1428=) 9332801 MedGen:CN169374 11 118484927 118484927 A C 168854 single nucleotide variant NM_001197104.1(KMT2A):c.4426T>A (p.Cys1476Ser) 587783677 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118359422 118359422 T A 168854 single nucleotide variant NM_001197104.1(KMT2A):c.4426T>A (p.Cys1476Ser) 587783677 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118488707 118488707 T A 168855 single nucleotide variant NM_001197104.1(KMT2A):c.5679A>G (p.Leu1893=) 7107305 MedGen:CN169374 11 118368665 118368665 A G 168855 single nucleotide variant NM_001197104.1(KMT2A):c.5679A>G (p.Leu1893=) 7107305 MedGen:CN169374 11 118497950 118497950 A G 168856 single nucleotide variant NM_001197104.1(KMT2A):c.6572G>A (p.Arg2191Gln) 141727765 MedGen:CN169374 11 118373179 118373179 G A 168856 single nucleotide variant NM_001197104.1(KMT2A):c.6572G>A (p.Arg2191Gln) 141727765 MedGen:CN169374 11 118502464 118502464 G A 168857 single nucleotide variant NM_001197104.1(KMT2A):c.7254C>T (p.Asn2418=) 2071702 MedGen:CN169374 11 118373861 118373861 C T 168857 single nucleotide variant NM_001197104.1(KMT2A):c.7254C>T (p.Asn2418=) 2071702 MedGen:CN169374 11 118503146 118503146 C T 168858 single nucleotide variant NM_001197104.1(KMT2A):c.7831G>T (p.Glu2611Ter) 587783679 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118374438 118374438 G T 168858 single nucleotide variant NM_001197104.1(KMT2A):c.7831G>T (p.Glu2611Ter) 587783679 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118503723 118503723 G T 168859 single nucleotide variant NM_001197104.1(KMT2A):c.8095C>T (p.Arg2699Ter) 587783680 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118374702 118374702 C T 168859 single nucleotide variant NM_001197104.1(KMT2A):c.8095C>T (p.Arg2699Ter) 587783680 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118503987 118503987 C T 168860 single nucleotide variant NM_001197104.1(KMT2A):c.8961T>A (p.Thr2987=) 9332842 MedGen:CN169374 11 118375568 118375568 T A 168860 single nucleotide variant NM_001197104.1(KMT2A):c.8961T>A (p.Thr2987=) 9332842 MedGen:CN169374 11 118504853 118504853 T A 178383 single nucleotide variant NM_005933.3(KMT2A):c.2233C>T (p.Arg745Ter) 727503777 MedGen:CN029798,OMIM:122470 11 118473392 118473392 C T 178383 single nucleotide variant NM_005933.3(KMT2A):c.2233C>T (p.Arg745Ter) 727503777 MedGen:CN029798,OMIM:122470 11 118344107 118344107 C T 189077 deletion NM_001197104.1(KMT2A):c.7565_7568delCAGT (p.Val2523Lysfs) 797044565 MedGen:CN221809 11 118374172 118374175 CAGT - 189077 deletion NM_001197104.1(KMT2A):c.7565_7568delCAGT (p.Val2523Lysfs) 797044565 MedGen:CN221809 11 118503457 118503460 CAGT - 205267 deletion NM_001197104.1(KMT2A):c.1868delA (p.Lys623Serfs) 797044937 MeSH:D030342,MedGen:C0950123 11 118343742 118343742 A - 205267 deletion NM_001197104.1(KMT2A):c.1868delA (p.Lys623Serfs) 797044937 MeSH:D030342,MedGen:C0950123 11 118473027 118473027 A - 205767 single nucleotide variant NM_001197104.1(KMT2A):c.5494C>A (p.Pro1832Thr) 797045051 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118366545 118366545 C A 205767 single nucleotide variant NM_001197104.1(KMT2A):c.5494C>A (p.Pro1832Thr) 797045051 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118495830 118495830 C A 207814 single nucleotide variant NM_001197104.1(KMT2A):c.1504G>A (p.Glu502Lys) 9332772 MedGen:CN169374 11 118472663 118472663 G A 207814 single nucleotide variant NM_001197104.1(KMT2A):c.1504G>A (p.Glu502Lys) 9332772 MedGen:CN169374 11 118343378 118343378 G A 207815 single nucleotide variant NM_001197104.1(KMT2A):c.1810A>G (p.Met604Val) 150328852 MedGen:CN169374 11 118472969 118472969 A G 207815 single nucleotide variant NM_001197104.1(KMT2A):c.1810A>G (p.Met604Val) 150328852 MedGen:CN169374 11 118343684 118343684 A G 207816 deletion NM_001197104.1(KMT2A):c.6811delA (p.Arg2271Glyfs) 797045656 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118502703 118502703 A - 207816 deletion NM_001197104.1(KMT2A):c.6811delA (p.Arg2271Glyfs) 797045656 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118373418 118373418 A - 207817 single nucleotide variant NM_001197104.1(KMT2A):c.11084C>G (p.Ser3695Ter) 782477344 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118511963 118511963 C G 207817 single nucleotide variant NM_001197104.1(KMT2A):c.11084C>G (p.Ser3695Ter) 782477344 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118382678 118382678 C G 213605 duplication NM_001197104.1(KMT2A):c.3651dupG (p.Lys1218Glufs) 863224887 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118481731 118481731 G GG 213605 duplication NM_001197104.1(KMT2A):c.3651dupG (p.Lys1218Glufs) 863224887 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118352446 118352446 G GG 213606 single nucleotide variant NM_001197104.1(KMT2A):c.4086+1G>A 863224889 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118482496 118482496 G A 213606 single nucleotide variant NM_001197104.1(KMT2A):c.4086+1G>A 863224889 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118353211 118353211 G A 213607 single nucleotide variant NM_001197104.1(KMT2A):c.4342T>C (p.Cys1448Arg) 863224895 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118488623 118488623 T C 213607 single nucleotide variant NM_001197104.1(KMT2A):c.4342T>C (p.Cys1448Arg) 863224895 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118359338 118359338 T C 213608 duplication NM_001197104.1(KMT2A):c.10334dupC (p.Ser3446Phefs) 863224888 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118506226 118506226 C CC 213608 duplication NM_001197104.1(KMT2A):c.10334dupC (p.Ser3446Phefs) 863224888 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118376941 118376941 C CC 215424 single nucleotide variant NM_001197104.1(KMT2A):c.2905C>G (p.Leu969Val) 864309568 MedGen:CN169374 11 118474064 118474064 C G 215424 single nucleotide variant NM_001197104.1(KMT2A):c.2905C>G (p.Leu969Val) 864309568 MedGen:CN169374 11 118344779 118344779 C G 215425 single nucleotide variant NM_001197104.1(KMT2A):c.6329C>G (p.Ser2110Ter) 864309569 MedGen:CN221809 11 118501681 118501681 C G 215425 single nucleotide variant NM_001197104.1(KMT2A):c.6329C>G (p.Ser2110Ter) 864309569 MedGen:CN221809 11 118372396 118372396 C G 244018 single nucleotide variant NM_001197104.1(KMT2A):c.2633G>A (p.Arg878Gln) 879253756 Human Phenotype Ontology:HP:0000708,MedGen:CN000665;Human Phenotype Ontology:HP:0001488,MedGen:C1865916;Human Phenotype Ontology:HP:0012758,MedGen:CN185881 11 118473792 118473792 G A 244018 single nucleotide variant NM_001197104.1(KMT2A):c.2633G>A (p.Arg878Gln) 879253756 Human Phenotype Ontology:HP:0000708,MedGen:CN000665;Human Phenotype Ontology:HP:0001488,MedGen:C1865916;Human Phenotype Ontology:HP:0012758,MedGen:CN185881 11 118344507 118344507 G A 247053 single nucleotide variant NM_001197104.1(KMT2A):c.158C>T (p.Ala53Val) 9332747 MedGen:CN169374 11 118436670 118436670 C T 247053 single nucleotide variant NM_001197104.1(KMT2A):c.158C>T (p.Ala53Val) 9332747 MedGen:CN169374 11 118307385 118307385 C T 259977 single nucleotide variant NM_001197104.1(KMT2A):c.10217C>A (p.Ser3406Ter) 886039658 MedGen:CN221809 11 118376824 118376824 C A 259977 single nucleotide variant NM_001197104.1(KMT2A):c.10217C>A (p.Ser3406Ter) 886039658 MedGen:CN221809 11 118506109 118506109 C A 264412 deletion NM_001197104.1(KMT2A):c.8864_8868delTCTCA (p.Ile2955Argfs) 886041947 MedGen:CN221809 11 118375471 118375475 TCTCA - 264412 deletion NM_001197104.1(KMT2A):c.8864_8868delTCTCA (p.Ile2955Argfs) 886041947 MedGen:CN221809 11 118504756 118504760 TCTCA - 264447 single nucleotide variant NM_001197104.1(KMT2A):c.3565T>C (p.Cys1189Arg) 886041875 MedGen:CN221809 11 118348912 118348912 T C 264447 single nucleotide variant NM_001197104.1(KMT2A):c.3565T>C (p.Cys1189Arg) 886041875 MedGen:CN221809 11 118478197 118478197 T C 264455 single nucleotide variant NM_001197104.1(KMT2A):c.5251A>T (p.Lys1751Ter) 886041896 MedGen:CN221809 11 118365075 118365075 A T 264455 single nucleotide variant NM_001197104.1(KMT2A):c.5251A>T (p.Lys1751Ter) 886041896 MedGen:CN221809 11 118494360 118494360 A T 264585 single nucleotide variant NM_001197104.1(KMT2A):c.3301C>T (p.Arg1101Ter) 886041856 MedGen:CN228659;MedGen:CN221809 11 118347664 118347664 C T 264585 single nucleotide variant NM_001197104.1(KMT2A):c.3301C>T (p.Arg1101Ter) 886041856 MedGen:CN228659;MedGen:CN221809 11 118476949 118476949 C T 264591 single nucleotide variant NM_001197104.1(KMT2A):c.3560A>T (p.Gln1187Leu) 886041881 MedGen:CN221809 11 118348907 118348907 A T 264591 single nucleotide variant NM_001197104.1(KMT2A):c.3560A>T (p.Gln1187Leu) 886041881 MedGen:CN221809 11 118478192 118478192 A T 264597 single nucleotide variant NM_001197104.1(KMT2A):c.3991C>T (p.Gln1331Ter) 886041571 MedGen:CN221809 11 118352786 118352786 C T 264597 single nucleotide variant NM_001197104.1(KMT2A):c.3991C>T (p.Gln1331Ter) 886041571 MedGen:CN221809 11 118482071 118482071 C T 264599 deletion NM_001197104.1(KMT2A):c.9910_9911delCT (p.Leu3304Valfs) 886041834 MedGen:CN221809 11 118505802 118505803 CT - 264599 deletion NM_001197104.1(KMT2A):c.9910_9911delCT (p.Leu3304Valfs) 886041834 MedGen:CN221809 11 118376517 118376518 CT - 269584 single nucleotide variant NM_001197104.1(KMT2A):c.10580G>A (p.Arg3527Gln) 147844226 MedGen:CN169374 11 118377187 118377187 G A 269584 single nucleotide variant NM_001197104.1(KMT2A):c.10580G>A (p.Arg3527Gln) 147844226 MedGen:CN169374 11 118506472 118506472 G A 359911 single nucleotide variant NM_001197104.1(KMT2A):c.3464G>A (p.Cys1155Tyr) 1057518074 MedGen:CN221809 11 118478096 118478096 G A 359911 single nucleotide variant NM_001197104.1(KMT2A):c.3464G>A (p.Cys1155Tyr) 1057518074 MedGen:CN221809 11 118348811 118348811 G A 359985 single nucleotide variant NM_001197104.1(KMT2A):c.5287C>T (p.Arg1763Trp) 1057518296 MedGen:CN169374 11 118494396 118494396 C T 359985 single nucleotide variant NM_001197104.1(KMT2A):c.5287C>T (p.Arg1763Trp) 1057518296 MedGen:CN169374 11 118365111 118365111 C T 361201 duplication NM_005933.3(KMT2A):c.2318dupC (p.Ser774Valfs) 1057518649 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118344192 118344192 C CC 361201 duplication NM_005933.3(KMT2A):c.2318dupC (p.Ser774Valfs) 1057518649 MedGen:C1854630,OMIM:605130,Orphanet:ORPHA319182 11 118473477 118473477 C CC 361431 single nucleotide variant NM_001197104.1(KMT2A):c.2004T>G (p.Ser668=) 147102502 MedGen:CN221809 11 118473163 118473163 T G 361431 single nucleotide variant NM_001197104.1(KMT2A):c.2004T>G (p.Ser668=) 147102502 MedGen:CN221809 11 118343878 118343878 T G 361432 duplication NM_001197104.1(KMT2A):c.2515dupT (p.Thr840Tyrfs) -1 MedGen:CN221809 11 118473674 118473674 T TT 361432 duplication NM_001197104.1(KMT2A):c.2515dupT (p.Thr840Tyrfs) -1 MedGen:CN221809 11 118344389 118344389 T TT 361665 single nucleotide variant NM_001197104.1(KMT2A):c.10901-5A>G 369909433 MedGen:CN221809 11 118509943 118509943 A G 361665 single nucleotide variant NM_001197104.1(KMT2A):c.10901-5A>G 369909433 MedGen:CN221809 11 118380658 118380658 A G

Disease associated variation - GWASdb Chr Pos SNP ID(dbSNP 142) Ref Alt Ori SNP ID P-value Drug Name Drug Anno GWAS Trait HPO ID DO ID AA Type Trait or Drug 11 118341649 rs7948661 T C rs7948661 5.00E-06 Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined) HPOID:0000729|HPOID:0007018|HPOID:0007302|HPOID:0100753 DOID:0060041|DOID:1094|DOID:3312|DOID:1470|DOID:5419 C intron GWASdb_trait 11 118359161 rs572126 G A rs572126 0.000651617 Primary sclerosing cholangitis HPOID:0001080 DOID:14268 C intron GWASdb_trait

Disease associated variation - OMIM Ensembl_gene_ID Approved Gene Symbol MIM Number ENSG00000118058.20 KMT2A 159555