Gene Gene information from NCBI Gene database.
Entrez ID 4297
Gene name Lysine methyltransferase 2A
Gene symbol KMT2A
Synonyms (NCBI Gene)
ALL-1ALL1CXXC7GAS7HRXHTRXHTRX1MLLMLL1MLL1ATRX1WDSTS
Chromosome 11
Chromosome location 11q23.3
Summary This gene encodes a transcriptional coactivator that plays an essential role in regulating gene expression during early development and hematopoiesis. The encoded protein contains multiple conserved functional domains. One of these domains, the SET domain
SNPs SNP information provided by dbSNP.
151
SNP ID Visualize variation Clinical significance Consequence
rs563239 G>A,C Pathogenic Splice acceptor variant
rs150328852 A>G Conflicting-interpretations-of-pathogenicity Intron variant, missense variant, coding sequence variant
rs150800017 C>G,T Pathogenic Stop gained, missense variant, coding sequence variant
rs200497972 C>A,T Pathogenic, likely-benign Stop gained, coding sequence variant, synonymous variant
rs387907275 C>T Pathogenic Stop gained, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
164
miRTarBase ID miRNA Experiments Reference
MIRT006587 hsa-miR-221-3p qRT-PCRLuciferase reporter assayWestern blot 19749093
MIRT017178 hsa-miR-335-5p Microarray 18185580
MIRT031581 hsa-miR-16-5p Sequencing 20371350
MIRT032120 hsa-let-7d-5p Sequencing 20371350
MIRT051043 hsa-miR-17-5p CLASH 23622248
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
SOX4 Unknown 20019190
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
78
GO ID Ontology Definition Evidence Reference
GO:0002376 Process Immune system process IEA
GO:0003677 Function DNA binding IEA
GO:0003680 Function Minor groove of adenine-thymine-rich DNA binding NAS 1423624
GO:0003682 Function Chromatin binding IEA
GO:0005515 Function Protein binding IPI 11313484, 14992727, 15199122, 15960975, 18840606, 19187761, 19556245, 20541251, 20541477, 20581860, 20818375, 20969867, 21113167, 21220120, 22327296, 22665483, 22722839, 22936661, 23870121, 24735925, 24981860, 25082813, 25305204, 25751424, 26886794, 27705803, 29997176, 30021884, 336
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
159555 7132 ENSG00000118058
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q03164
Protein name Histone-lysine N-methyltransferase 2A (Lysine N-methyltransferase 2A) (EC 2.1.1.364) (ALL-1) (CXXC-type zinc finger protein 7) (Cysteine methyltransferase KMT2A) (EC 2.1.1.-) (Myeloid/lymphoid or mixed-lineage leukemia) (Myeloid/lymphoid or mixed-lineage
Protein function Histone methyltransferase that plays an essential role in early development and hematopoiesis (PubMed:12453419, PubMed:15960975, PubMed:19187761, PubMed:19556245, PubMed:20677832, PubMed:21220120, PubMed:26886794). Catalytic subunit of the MLL1/
PDB 2AGH , 2J2S , 2JYI , 2KKF , 2KU7 , 2KYU , 2LXS , 2LXT , 2MSR , 2MTN , 2W5Y , 2W5Z , 3EG6 , 3EMH , 3LQH , 3LQI , 3LQJ , 3P4F , 3U85 , 3U88 , 4ESG , 4GQ6 , 4NW3 , 5F5E , 5F6L , 5SVH , 6EMQ , 6KIU , 6KIV , 6KIX , 6KIZ , 6PWV , 6PWW , 6U9K , 6U9M , 6U9N , 6U9R , 6W5I , 6W5M , 6W5N , 7MBM , 7MBN , 7RZD , 7RZJ , 7S79 , 7S7D , 7S8A , 7S8E , 7S8F , 7U5V , 7W67
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02008 zf-CXXC 1147 1194 CXXC zinc finger domain Domain
PF00628 PHD 1481 1533 PHD-finger Domain
PF00628 PHD 1568 1627 PHD-finger Domain
PF13771 zf-HC5HC2H 1900 1978 Domain
PF05964 FYRN 2024 2071 F/Y-rich N-terminus Family
PF05965 FYRC 3666 3748 F/Y rich C-terminus Family
PF00856 SET 3840 3945 SET domain Family
Tissue specificity TISSUE SPECIFICITY: Heart, lung, brain and T- and B-lymphocytes.
Sequence
MAHSCRWRFPARPGTTGGGGGGGRRGLGGAPRQRVPALLLPPGPPVGGGGPGAPPSPPAV
AAAAAAAGSSGAGVPGGAAAASAASSSSASSSSSSSSSASSGPALLRVGPGFDAALQVSA
AIGTNLRRFRAVFGESGGGGGSGEDEQFLGFGSDEEVRVRSPTRSPSVKTSPRKPRGRPR
SGSDRNSAILSDPSVFSPLNKSETKSGDKIKKKDSKSIEKKRGRPPTFPGVKIKITHGKD
ISELPKGNKEDSLKKIKRTPSATFQQATKIKKLRAGKLSPLKSKFKTGKLQIGRKGVQIV
RRRGRPPSTERIKTPSGLLINSELEKPQKVRKDKEGTPPLTKEDKTVVRQSPRRIKPVRI
IPSSKRTDATIAKQLLQRAKKGAQKKIEKEAAQLQGRKVKTQVKNIRQFIMPVVSAISSR
IIKTPRRFIEDEDYDPPIKIARLESTPNSRFSAPSCGSSEKSSAASQHSSQMSSDSSRSS
SPSVDTSTDSQASEEIQVLPEERSDTPEVHPPLPISQSPENESNDRRSRRYSVSERSFGS
RTTKKLSTLQSAPQQQTSSSPPPPLLTPPPPLQPASSISDHTPWLMPPTIPLASPFLPAS
TAPMQGKRKSILREPTFRWTSLKHSRSEPQYFSSAKYAKEGLIRKPIFDNFRPPPLTPED
VGFASGFSASGTAASARLFSPLHSGTRFDMHKRSPLLRAPRFTPSEAHSRIFESVTLPSN
RTSAGTSSSGVSNRKRKRKVFSPIRSEPRSPSHSMRTRSGRLSSSELSPLTPPSSVSSSL
SISVSPLATSALNPTFTFPSHSLTQSGESAEKNQRPRKQTSAPAEPFSSSSPTPLFPWFT
PGSQTERGRNKDKAPEELSKDRDADKSVEKDKSRERDREREKENKRESRKEKRKKGSEIQ
SSSALYPVGRVSKEKVVGEDVATSSSAKKATGRKKSSSHDSGTDITSVTLGDTTAVKTKI
LIKKGRGNLEKTNLDLGPTAPSLEKEKTLCLSTPSSSTVKHSTSSIGSMLAQADKLPMTD
KRVASLLKKAKAQLCKIEKSKSLKQTDQPKAQGQESDSSETSVRGPRIKHVCRRAAVALG
RKRAVFPDDMPTLSALPWEEREKILSSMGNDDKSSIAGSEDAEPLAPPIKPIKPVTRNKA
PQEPPVKKGRRSRRCGQCPGCQVPEDCGVCTNCLDKPKFGGRNIKKQCCKMRKCQNLQWM
PSKAYLQKQAKAVKKKEKKSKTSEKKDSKESSVVKNVVDSSQKPTPSAREDPAPKKSSSE
PPPRKPVEEKSEEGNVSAPGPESKQATTPASRKSSKQVSQPALVIPPQPPTTGPPRKEVP
KTTPSEPKKKQPPPPESGPEQSKQKKVAPRPSIPVKQKPKEKEKPPPVNKQENAGTLNIL
STLSNGNSSKQKIPADGVHRIRVDFKEDCEAENVWEMGGLGILTSVPITPRVVCFLCASS
GHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRCKFCHVCGRQHQATKQLLECNK
CRNSYHPECLGPNYPTKPTKKKKVWICTKCVRC
KSCGSTTPGKGWDAQWSHDFSLCHDCA
KLFAKGNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYT
CVNCTER
HPAEWRLALEKELQISLKQVLTALLNSRTTSHLLRYRQAAKPPDLNPETEESI
PSRSSPEGPDPPVLTEVSKQDDQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINS
DGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFWEPNKVSSNSGMLPNAVLPPSLDH
NYAQWQEREENSHTEQPPLMKKIIPAPKPKGPGEPDSPTPLHPPTPPILSTDRSREDSPE
LNPPPGIEDNRQCALCLTYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKN
VHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCVFLDDKKVYCQRHR
DL
IKGEVVPENGFEVFRRVFVDFEGISLRRKFLNGLEPENIHMMIGSMTIDCLGILNDLSDC
EDKLFPIGYQCSRVYWSTTDARKRCVYTCKI
VECRPPVVEPDINSTVEHDENRTIAHSPT
SFTESSSKESQNTAEIISPPSPDRPPHSQTSGSCYYHVISKVPRIRTPSYSPTQRSPGCR
PLPSAGSPTPTTHEIVTVGDPLLSSGLRSIGSRRHSTSSLSPQRSKLRIMSPMRTGNTYS
RNNVSSVSTTGTATDLESSAKVVDHVLGPLNSSTSLGQNTSTSSNLQRTVVTVGNKNSHL
DGSSSSEMKQSSASDLVSKSSSLKGEKTKVLSSKSSEGSAHNVAYPGIPKLAPQVHNTTS
RELNVSKIGSFAEPSSVSFSSKEALSFPHLHLRGQRNDRDQHTDSTQSANSSPDEDTEVK
TLKLSGMSNRSSIINEHMGSSSRDRRQKGKKSCKETFKEKHSSKSFLEPGQVTTGEEGNL
KPEFMDEVLTPEYMGQRPCNNVSSDKIGDKGLSMPGVPKAPPMQVEGSAKELQAPRKRTV
KVTLTPLKMENESQSKNALKESSPASPLQIESTSPTEPISASENPGDGPVAQPSPNNTSC
QDSQSNNYQNLPVQDRNLMLPDGPKPQEDGSFKRRYPRRSARARSNMFFGLTPLYGVRSY
GEEDIPFYSSSTGKKRGKRSAEGQVDGADDLSTSDEDDLYYYNFTRTVISSGGEERLASH
NLFREEEQCDLPKISQLDGVDDGTESDTSVTATTRKSSQIPKRNGKENGTENLKIDRPED
AGEKEHVTKSSVGHKNEPKMDNCHSVSRVKTQGQDSLEAQLSSLESSRRVHTSTPSDKNL
LDTYNTELLKSDSDNNNSDDCGNILPSDIMDFVLKNTPSMQALGESPESSSSELLNLGEG
LGLDSNREKDMGLFEVFSQQLPTTEPVDSSVSSSISAEEQFELPLELPSDLSVLTTRSPT
VPSQNPSRLAVISDSGEKRVTITEKSVASSESDPALLSPGVDPTPEGHMTPDHFIQGHMD
ADHISSPPCGSVEQGHGNNQDLTRNSSTPGLQVPVSPTVPIQNQKYVPNSTDSPGPSQIS
NAAVQTTPPHLKPATEKLIVVNQNMQPLYVLQTLPNGVTQKIQLTSSVSSTPSVMETNTS
VLGPMGGGLTLTTGLNPSLPTSQSLFPSASKGLLPMSHHQHLHSFPAATQSSFPPNISNP
PSGLLIGVQPPPDPQLLVSESSQRTDLSTTVATPSSGLKKRPISRLQTRKNKKLAPSSTP
SNIAPSDVVSNMTLINFTPSQLPNHPSLLDLGSLNTSSHRTVPNIIKRSKSSIMYFEPAP
LLPQSVGGTAATAAGTSTISQDTSHLTSGSVSGLASSSSVLNVVSMQTTTTPTSSASVPG
HVTLTNPRLLGTPDIGSISNLLIKASQQSLGIQDQPVALPPSSGMFPQLGTSQTPSTAAI
TAASSICVLPSTQTTGITAASPSGEADEHYQLQHVNQLLASKTGIHSSQRDLDSASGPQV
SNFTQTVDAPNSMGLEQNKALSSAVQASPTSPGGSPSSPSSGQRSASPSVPGPTKPKPKT
KRFQLPLDKGNGKKHKVSHLRTSSSEAHIPDQETTSLTSGTGTPGAEAEQQDTASVEQSS
QKECGQPAGQVAVLPEVQVTQNPANEQESAEPKTVEEEESNFSSPLMLWLQQEQKRKESI
TEKKPKKGLVFEISSDDGFQICAESIEDAWKSLTDKVQEARSNARLKQLSFAGVNGLRML
GILHDAVVFLIEQLSGAKHCRNYKFRFH
KPEEANEPPLNPHGSARAEVHLRKSAFDMFNF
LASKHRQPPEYNPNDEEEEEVQLKSARRATSMDLPMPMRFRHLKKTSKEAVGVYRSPIHG
RGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATMHGN
AARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYK
FPIEDASNKLPCNCG
AKKCRKFLN
Sequence length 3969
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Lysine degradation
Metabolic pathways
Cushing syndrome
Transcriptional misregulation in cancer
  PKMTs methylate histone lysines
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
RUNX1 regulates transcription of genes involved in differentiation of HSCs
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
55
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Adrenal cortex carcinoma Pathogenic rs782297546 RCV004813092
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autism spectrum disorder Likely pathogenic rs141515578 RCV003128060
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cornelia de Lange syndrome 1 Pathogenic rs727503777 RCV000157053
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hirsutism Pathogenic rs1555039343 RCV001261359
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atypical behavior Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Abetalipoproteinemia Abetalipoproteinemia BEFREE 12620410
★☆☆☆☆
Found in Text Mining only
Acute Erythroblastic Leukemia Erythroblastic Leukemia BEFREE 9242213
★☆☆☆☆
Found in Text Mining only
Acute erythroleukemia Erythroleukemia CTD_human_DG 30926971
★☆☆☆☆
Found in Text Mining only
Acute erythroleukemia - M6a subtype Erythroleukemia CTD_human_DG 30926971
★☆☆☆☆
Found in Text Mining only
Acute erythroleukemia - M6b subtype Erythroleukemia CTD_human_DG 30926971
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia BEFREE 10025907, 10197596, 10374852, 10381524, 10457404, 10557043, 10583275, 10602503, 10700861, 10706136, 10738298, 10764144, 11069023, 11167824, 11187895
View all (172 more)
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 10374870, 10394590, 10457404, 10458233, 10557043, 10602437, 10607691, 10679915, 10738298, 10773450, 10825008, 10861294, 10865968, 11071360, 11167741
View all (199 more)
★☆☆☆☆
Found in Text Mining only
Acute Megakaryocytic Leukemias Megakaryocytic Leukemia BEFREE 15226186, 16111539, 26215111, 27114462
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 10648423, 10700861, 10719372, 10803509, 10905055, 11066077, 11289145, 11746988, 11809673, 11896537, 12127405, 12539741, 12547160, 12619163, 12791658
View all (56 more)
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia LHGDN 12547160
★☆☆☆☆
Found in Text Mining only