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Gene Symbol KMT2A
Synonyms ALL-1 | ALL1 | CXXC7 | GAS7 | HRX | HTRX | HTRX1 | MLL | MLL1 | MLL1A | TRX1 | WDSTS
Gene Description KMT2A, lysine methyltransferase 2A, also referred to as MLL, is a transcriptional coactivator that epigenetically regulates gene transcription via methylation and is primarily associated with hematopoietic and embyronic development (PMID: 26161385). KMT2A translocations are frequently observed in specific leukemias including acute myeloid, acute lymphoblastic, and mixed lineage (PMID: 17957188, PMID: 32243611).

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Variant Impact Protein Effect Variant Description Associated with drug Resistance
A2571V missense unknown KMT2A A2571V does not lie within any known functional domains of the Kmt2a protein (UniProt.org). A2571V has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
A3737V missense unknown KMT2A A3737V lies within the FYR C-terminal domain of the Kmt2a protein (UniProt.org). A3737V has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
act mut unknown gain of function KMT2A act mut indicates that this variant results in a gain of function in the Kmt2a protein. However, the specific amino acid change has not been identified.
amp none no effect KMT2A amplification indicates an increased number of copies of the KMT2A gene. However, the mechanism causing the increase is unspecified.
C1173R missense unknown KMT2A C1173R lies within the CXXC-type zinc finger domain of the Kmt2a protein (UniProt.org). C1173R has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
D2295N missense unknown KMT2A D2295N does not lie within any known functional domains of the Kmt2a protein (UniProt.org). D2295N has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
D2384E missense unknown KMT2A D2384E does not lie within any known functional domains of the Kmt2a protein (UniProt.org). D2384E has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
D3876N missense unknown KMT2A D3876N lies within the SET domain of the Kmt2a protein (UniProt.org). D3876N has been identified in sequencing studies (PMID: 22895193), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
D3921Y missense unknown KMT2A D3921Y lies within the SET domain of the Kmt2a protein (UniProt.org). D3921Y has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
D505N missense unknown KMT2A D505N does not lie within any known functional domains of the Kmt2a protein (UniProt.org). D505N has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
E1060D missense unknown KMT2A E1060D does not lie within any known functional domains of the Kmt2a protein (UniProt.org). E1060D has been identified in sequencing studies (PMID: 22810696), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
E1361* nonsense loss of function - predicted KMT2A E1361* results in a premature truncation of the Kmt2a protein at amino acid 1361 of 3969 (UniProt.org). Due to the loss of all known functional domains (UniProt.org), E1361* is predicted to lead to a loss of Kmt2a protein function.
E1472* nonsense loss of function - predicted KMT2A E1472* results in a premature truncation of the Kmt2a protein at amino acid 1472 of 3969 (UniProt.org). Due to the loss of all known functional domains (UniProt.org), E1472* is predicted to lead to a loss of Kmt2a protein function.
E1984K missense unknown KMT2A E1984K does not lie within any known functional domains of the Kmt2a protein (UniProt.org). E1984K has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
E2416K missense unknown KMT2A E2416K does not lie within any known functional domains of the Kmt2a protein (UniProt.org). E2416K has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
E2986K missense unknown KMT2A E2986K does not lie within any known functional domains of the Kmt2a protein (UniProt.org). E2986K has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
E3448K missense unknown KMT2A E3448K does not lie within any known functional domains of the Kmt2a protein (UniProt.org). E3448K has been identified in sequencing studies (PMID: 22810696), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
E3938K missense unknown KMT2A E3938K lies within the SET domain of the Kmt2a protein (UniProt.org). E3938K has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
F1458S missense unknown KMT2A F1458S lies within PHD-type zinc finger domain 1 of the Kmt2a protein (UniProt.org). F1458S has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
F1481L missense unknown KMT2A F1481L lies within PHD-type zinc finger domains 1 and 2 of the Kmt2a protein (UniProt.org). F1481L has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
F663V missense unknown KMT2A F663V does not lie within any known functional domains of the Kmt2a protein (UniProt.org). F663V has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
fusion fusion unknown KMT2A fusion indicates a fusion of the KMT2A gene, but the fusion partner is unknown.
G2349S missense unknown KMT2A G2349S does not lie within any known functional domains of the Kmt2a protein (UniProt.org). G2349S has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
G2610D missense unknown KMT2A G2610D does not lie within any known functional domains of the Kmt2a protein (UniProt.org). G2610D has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
G3376D missense unknown KMT2A G3376D does not lie within any known functional domains of the Kmt2a protein (UniProt.org). G3376D has been identified in sequencing studies (PMID: 22810696), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
G3842S missense unknown KMT2A G3842S lies within the SET domain of the Kmt2a protein (UniProt.org). G3842S has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
G3899V missense unknown KMT2A G3899V lies within the SET domain of the Kmt2a protein (UniProt.org). G3899V has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
G606E missense unknown KMT2A G606E does not lie within any known functional domains of the Kmt2a protein (UniProt.org). G606E has been identified in sequencing studies (PMID: 27245685), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
H3907D missense unknown KMT2A H3907D lies within the SET domain of the Kmt2a protein (UniProt.org). H3907D has been identified in sequencing studies (PMID: 23525077), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
inact mut unknown loss of function KMT2A inact mut indicates that this variant results in a loss of function of the Kmt2a protein. However, the specific amino acid change has not been identified.
K1103N missense unknown KMT2A K1103N does not lie within any known functional domains of the Kmt2a protein (UniProt.org). K1103N has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
K1256Q missense unknown KMT2A K1256Q does not lie within any known functional domains of the Kmt2a protein (UniProt.org). K1256Q has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
K1321T missense unknown KMT2A K1321T does not lie within any known functional domains of the Kmt2a protein (UniProt.org). K1321T has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
K1457N missense unknown KMT2A K1457N lies within PHD-type zinc finger domain 1 of the Kmt2a protein (UniProt.org). K1457N has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
K2276T missense unknown KMT2A K2276T does not lie within any known functional domains of the Kmt2a protein (UniProt.org). K2276T has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
K246N missense unknown KMT2A K246N does not lie within any known functional domains of the Kmt2a protein (UniProt.org). K246N has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
K254Q missense unknown KMT2A K254Q does not lie within any known functional domains of the Kmt2a protein (UniProt.org). K254Q has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
L3153V missense unknown KMT2A L3153V does not lie within any known functional domains of the Kmt2a protein (UniProt.org). L3153V has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
L597V missense unknown KMT2A L597V does not lie within any known functional domains of the Kmt2a protein (UniProt.org). L597V has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
M2213V missense unknown KMT2A M2213V does not lie within any known functional domains of the Kmt2a protein (UniProt.org). M2213V has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
mutant unknown unknown KMT2A mutant indicates an unspecified mutation in the KMT2A gene.
N3084S missense unknown KMT2A N3084S does not lie within any known functional domains of the Kmt2a protein (UniProt.org). N3084S has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
over exp none no effect KMT2A over exp indicates an over expression of the Kmt2a protein and/or mRNA. However, the mechanism causing the over expression is unspecified.
P2148S missense unknown KMT2A P2148S does not lie within any known functional domains of the Kmt2a protein (UniProt.org). P2148S has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
P2846H missense unknown KMT2A P2846H does not lie within any known functional domains of the Kmt2a protein (UniProt.org). P2846H has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
P2928L missense unknown KMT2A P2928L does not lie within any known functional domains of the Kmt2a protein (UniProt.org). P2928L has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
P2946S missense unknown KMT2A P2946S does not lie within any known functional domains of the Kmt2a protein (UniProt.org). P2946S has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
P3095Q missense unknown KMT2A P3095Q does not lie within any known functional domains of the Kmt2a protein (UniProt.org). P3095Q has been identified in sequencing studies (PMID: 22810696), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
P3407L missense unknown KMT2A P3407L does not lie within any known functional domains of the Kmt2a protein (UniProt.org). P3407L has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
positive unknown unknown KMT2A positive indicates the presence of the KMT2A gene, mRNA, and/or protein.
R1064* nonsense loss of function - predicted KMT2A R1064* results in a premature truncation of the Kmt2a protein at amino acid 1064 of 3969 (UniProt.org). Due to the loss of all known functional domains (UniProt.org), R1064* is predicted to lead to a loss of Kmt2a protein function.
R1151* nonsense loss of function - predicted KMT2A R1151* results in a premature truncation of the Kmt2a protein at amino acid 1151 of 3969 (UniProt.org). Due to the loss of all known functional domains (UniProt.org), R1151* is predicted to lead to a loss of Kmt2a protein function.
R1532C missense unknown KMT2A R1532C lies within PHD-type zinc finger domain 2 of the Kmt2a protein (UniProt.org). R1532C has been identified in sequencing studies (PMID: 30181556), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
R1976Q missense unknown KMT2A R1976Q lies within PHD-type zinc finger domain 4 of the Kmt2a protein (UniProt.org). R1976Q has been identified in sequencing studies (PMID: 35307972), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R2093M missense unknown KMT2A R2093M does not lie within any known functional domains of the Kmt2a protein (UniProt.org). R2093M has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R2160Q missense unknown KMT2A R2160Q does not lie within any known functional domains of the Kmt2a protein (UniProt.org). R2160Q has been identified in sequencing studies (PMID: 26343386), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R2379* nonsense loss of function - predicted KMT2A R2379* results in a premature truncation of the Kmt2a protein at amino acid 2379 of 3969 (UniProt.org). Due to the loss of most known functional domains (UniProt.org), R2379* is predicted to lead to a loss of Kmt2a protein function.
R2619C missense unknown KMT2A R2619C does not lie within any known functional domains of the Kmt2a protein (UniProt.org). R2619C has been identified in sequencing studies (PMID: 22895193), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
R2656* nonsense loss of function - predicted KMT2A R2656* results in a premature truncation of the Kmt2a protein at amino acid 2656 of 3969 (UniProt.org). Due to the loss of most known functional domains (UniProt.org), R2656* is predicted to lead to a loss of Kmt2a protein function.
R3656W missense unknown KMT2A R3656W does not lie within any known functional domains of the Kmt2a protein (UniProt.org). R3656W has been identified in sequencing studies (PMID: 28069802), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R3741Q missense unknown KMT2A R3741Q lies within the FYR C-terminal domain of the Kmt2a protein (UniProt.org). R3741Q has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R3841W missense gain of function - predicted KMT2A R3841W lies within the SET domain of the Kmt2a protein (UniProt.org). R3841W results in increased histone methyltransferase activity in isolation, and further stimulation is not achieved by WRA complex formation in vitro (PMID: 28182322), and therefore, is predicted to lead to a gain of Kmt2a protein function.
R3864C missense unknown KMT2A R3864C lies within the SET domain of the Kmt2a protein (UniProt.org). The functional effect of R3864C is conflicting, as it demonstrates increased histone methyltransferase activity in isolation, but decreased activity in the presence of WRA complex stimulation compared to wild-type Kmt2a in in vitro assays (PMID: 28182322), and therefore, its effect on Kmt2a protein function is unknown.
R3886* nonsense unknown KMT2A R3886* results in a premature truncation of the Kmt2a protein at amino acid 3886 of 3969 (UniProt.org). R3886* has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
R3903C missense unknown KMT2A R3903C lies within the SET domain of the Kmt2a protein (UniProt.org). R3903C has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R3903H missense loss of function - predicted KMT2A R3903H lies within the SET domain of the Kmt2a protein (UniProt.org). R3903H results in a loss of histone methyltransferase activity in in vitro assays (PMID: 28182322), and therefore, is predicted to lead to a loss of Kmt2a protein function.
R3932H missense unknown KMT2A R3932H lies within the SET domain of the Kmt2a protein (UniProt.org). R3932H has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R3965W missense unknown KMT2A R3965W lies within the Post-SET domain of the Kmt2a protein (UniProt.org). R3965W has not been characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R407* nonsense loss of function - predicted KMT2A R407* results in a premature truncation of the Kmt2a protein at amino acid 407 of 3969 (UniProt.org). Due to the loss of all known functional domains (UniProt.org), R407* is predicted to lead to a loss of Kmt2a protein function.
R427W missense unknown KMT2A R427W does not lie within any known functional domains of the Kmt2a protein (UniProt.org). R427W has been identified in sequencing studies (PMID: 37901334), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R652* nonsense loss of function - predicted KMT2A R652* results in a premature truncation of the Kmt2a protein at amino acid 652 of 3969 (UniProt.org). Due to the loss of all known functional domains (UniProt.org), R652* is predicted to lead to a loss of Kmt2a protein function.
R736M missense unknown KMT2A R736M does not lie within any known functional domains of the Kmt2a protein (UniProt.org). R736M has been identified in sequencing studies (PMID: 22810696, PMID: 32732356), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
R933Q missense unknown KMT2A R933Q does not lie within any known functional domains of the Kmt2a protein (UniProt.org). R933Q has been identified in sequencing studies (PMID: 22895193), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
rearrange unknown unknown KMT2A rearrangement indicates an unspecified rearrangement of the KMT2A gene.
S1062Y missense unknown KMT2A S1062Y does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S1062Y has been identified in sequencing studies (PMID: 24755471), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
S1152L missense unknown KMT2A S1152L lies within the CXXC-type zinc finger domain of the Kmt2a protein (UniProt.org). S1152L has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
S1643Y missense unknown KMT2A S1643Y does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S1643Y has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
S1685F missense unknown KMT2A S1685F does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S1685F has not been characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
S2690Y missense unknown KMT2A S2690Y does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S2690Y has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
S2771Y missense unknown KMT2A S2771Y does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S2771Y has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
S2785Y missense unknown KMT2A S2785Y does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S2785Y has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
S3120L missense unknown KMT2A S3120L does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S3120L has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
S3377L missense unknown KMT2A S3377L does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S3377L has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
S3576F missense unknown KMT2A S3576F does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S3576F has been identified in sequencing studies (PMID: 22810696), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Jan 2024).
S3865F missense loss of function - predicted KMT2A S3865F lies within the SET domain of the Kmt2a protein (UniProt.org). S3865F results in decreased Kmt2a histone methyltransferase activity alone or in complex with WRA complex in an in-vitro assay (PMID: 28182322), and therefore, is predicted to lead to a loss of Ktm2a protein function.
S466A missense unknown KMT2A S466A does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S466A has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
S534L missense unknown KMT2A S534L does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S534L has been identified in sequencing studies (PMID: 22810696), but has not been biochemically characterized and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
S774Vfs*12 frameshift loss of function - predicted KMT2A S774Vfs*12 indicates a shift in the reading frame starting at amino acid 774 and terminating 12 residues downstream causing a premature truncation of the 3969 amino acid Kmt2a protein (UniProt.org). Due to the loss of all known functional domains (UniProt.org), S774Vfs*12 is predicted to lead to a loss of Kmt2a protein function.
S902R missense unknown KMT2A S902R does not lie within any known functional domains of the Kmt2a protein (UniProt.org). S902R has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Oct 2023).
T1061fs frameshift loss of function - predicted KMT2A T1061fs results in a change in the amino acid sequence of the Kmt2a protein beginning at aa 1061 of 3969, likely resulting in premature truncation of the functional protein (UniProt.org). Due to the loss of all known functional domains (UniProt.org), T1061fs is predicted to lead to a loss of Kmt2a protein function.
T3868N missense unknown KMT2A T3868N lies within the SET domain of the Kmt2a protein (UniProt.org). T3868N has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
V2178A missense unknown KMT2A V2178A does not lie within any known functional domains of the Kmt2a protein (UniProt.org). V2178A has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
V2246G missense unknown KMT2A V2246G does not lie within any known functional domains of the Kmt2a protein (UniProt.org). V2246G has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).
W838Lfs*9 frameshift loss of function - predicted KMT2A W838Lfs*9 indicates a shift in the reading frame starting at amino acid 838 and terminating 9 residues downstream causing a premature truncation of the 3969 amino acid Kmt2a protein (UniProt.org). Due to the loss of all known functional domains (UniProt.org), W838Lfs*9 is predicted to lead to a loss of Kmt2a protein function.
Y3883S missense unknown KMT2A Y3883S lies within the SET domain of the Kmt2a protein (UniProt.org). Y3883S has not been characterized in the scientific literature and therefore, its effect on Kmt2a protein function is unknown (PubMed, Feb 2024).