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Other entities represented in this entry:
HGNC Approved Gene Symbol: KAT6A
SNOMEDCT: 1255319004;
Cytogenetic location: 8p11.21 Genomic coordinates (GRCh38): 8:41,929,479-42,051,987 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 8p11.21 | Arboleda-Tham syndrome | 616268 | Autosomal dominant | 3 |
The KAT6A gene encodes a lysine (K) acetyltransferase that is a member of the MYST family of proteins. It forms part of a histone acetyltransferase complex that acetylates lysine-9 residues in histone 3 (see HIST1H3A, 602810), thus regulating transcriptional activity and gene expression. KAT6A also has a role in acetylation of p53 (TP53; 191170) and thus regulates the p53 signaling pathway, which is involved in apoptosis and cellular metabolism (summary by Arboleda et al., 2015 and Tham et al., 2015).
Borrow et al. (1996) used positional cloning to identify a novel gene, MOZ, at the chromosome 8 breakpoint in the translocation t(8;16)(p11;p13), a cytogenetic hallmark for the M4/M5 subtype of acute myeloid leukemia (AML). The MOZ gene encodes a predicted 2,004-amino acid, 225-kD polypeptide with 2 bipartite nuclear localization domains. MOZ is a founding member of a group of highly conserved proteins characterized by a single C2HC3 zinc finger in conjunction with a putative acetyltransferase consensus domain. MOZ also contains two C4HC3 zinc finger domains, protein-interaction motifs associated with chromatin-bound proteins. These motifs suggested to the authors that MOZ may represent a chromatin-bound acetyltransferase. Protein acetylation is known to play a key role in gene activation, chromatin structure, and silencing.
Relevant to the work on MOZ is the description of the yeast gene designated SAS2 (for 'something about silencing-2') that encodes a protein important for transcriptional silencing and exit from the cell cycle (Reifsnyder et al., 1996). Both SAS2 and MOZ contain a region of homology to acetyltransferases, suggesting that mistargeting of these enzymes may be directly linked to formation of a transformed state. Reifsnyder et al. (1996) found that the GenBank human sequences most closely related to SAS2 and SAS3 are MOZ and the HIV-1 Tat-interacting protein, TIP60 (601409), located on 11q13.
The KAT6A gene comprises 18 exons, 16 of which are coding, and has at least 3 major splice forms that differ in their 5-prime UTRs (Tham et al., 2015).
Zhu et al. (2015) demonstrated that p53 (191170) gain-of-function mutants bind to and upregulate chromatin regulatory genes, including the methyltransferases MLL1 (KMT2A; 159555), MLL2 (KMT2D; 602113), and acetyltransferase MOZ, resulting in genomewide increases of histone methylation and acetylation. Analysis of The Cancer Genome Atlas showed specific upregulation of MLL1, MLL2, and MOZ in p53 gain-of-function patient-derived tumors, but not in wildtype p53 or p53-null tumors. Cancer cell proliferation was markedly lowered by genetic knockdown of MLL1 or by pharmacologic inhibition of the MLL1 methyltransferase complex. Zhu et al. (2015) concluded that their study revealed a novel chromatin mechanism underlying the progression of tumors with gain-of-function p53, and suggested possibilities for designing combinatorial chromatin-based therapies for treating individual cancers driven by prevalent gain-of-function p53 mutations.
Borrow et al. (1996) mapped the MOZ gene to chromosome 8p11.
MOZ/CBP Fusion Gene
The translocation t(8;16)(p11;p13) is a cytogenetic hallmark for the M4/M5 subtype of AML. Borrow et al. (1996) noted that patients with t(8;16) are classified as FAB M4 (myelomonocytic) or FAB M5 (monocytic), while cytochemical studies indicate a mixture of monocytic and granulocytic enzymes, suggesting a block in differentiation at the granulomonocytic stage. Another hallmark of the disease is a pronounced erythrophagocytosis by the blast cells in most cases. A high proportion of spontaneous patients present under the age of 17, and the outlook for both de novo and therapy-related t(8;16) patients is poor. By positional cloning on chromosome 16, Borrow et al. (1996) implicated the CREB-binding protein (CBP; 600140), a transcriptional adaptor/coactivator protein, in this disorder. Mutation in this protein is responsible for Rubinstein-Taybi syndrome (180849), a constitutional disorder characterized by mental retardation, dysmorphic facial features, and broad thumbs. Furthermore, patients have an increased risk for malignant tumors, particularly of the head (Miller and Rubinstein, 1995). Borrow et al. (1996) used positional cloning to identify the MOZ gene at the chromosome 8 breakpoint in the translocation.
The t(8;16)(p11;p13) translocation, which is strongly associated with AML displaying monocytic differentiation, erythrophagocytosis by the leukemic cells, and a poor response to chemotherapy, fuses the MOZ gene on chromosome 8p11 with the CBP gene on 16p13. Panagopoulos et al. (2003) sequenced the breakpoints in 4 t(8;16)-positive AML cases. The breaks clustered in both CBP intron 2 and MOZ intron 16, and were close to repetitive elements; in 1 case, an Alu-Alu junction for the MOZ/CBP hybrid was identified. All 4 cases showed additional genomic events (i.e., deletions, duplications, and insertions) in the breakpoint regions in both the MOZ and CBP genes. Thus, the translocation did not originate through a simple end-to-end fusion. The findings of multiple breaks and rearrangements suggested the involvement of a damage repair mechanism in the origin of this translocation.
MOZ/TIF2 Fusion Gene
Carapeti et al. (1998) identified an inv(8)(p11q13) associated with AML with M4/M5 morphology and prominent erythrophagocytosis by the blast cells. A novel fusion between MOZ and the nuclear receptor transcriptional coactivator TIF2 (NCOA2; 601993) was identified. Nucleotide 3745 of MOZ was joined to nucleotide 2768 of TIF2. TIF2 was then mapped to chromosome 8q13.2-q13.3. The fusion product MOZ/TIF2 retained the histone acetyltransferase (HAT) domains of both proteins and also the CBP-binding domain of TIF2. Carapeti et al. (1998) suggested that the phenotype observed arises by recruitment of CBP by MOZ/TIF2, resulting in modulation of the transcriptional activity of target genes by a mechanism involving abnormal histone acetylation.
Liang et al. (1998) also identified an inv(8)(p11q13) in cells derived from a patient with acute mixed lineage leukemia. She had AML with M0/M1 morphology and M7 by histochemical staining. The inversion created a fusion between the 5-prime end of MOZ mRNA (nucleotide 2974) and the 3-prime end of TIF2 mRNA (nucleotide 3744), which maintained the translational frame of the protein. The predicted fusion protein contained the zinc finger domains, the nuclear localization domains, the HAT domain, and a portion of the acidic domain of MOZ, coupled to the CBP interaction domain and the activation domains of TIF2. The breakpoint was distinct from the breakpoint in the t(8;16)(p11;p13) translocation in acute monocytic leukemia with erythrophagocytosis that fused MOZ with CBP (Carapeti et al., 1998). The reciprocal TIF2/MOZ fusion gene was not expressed, perhaps as a result of a deletion near the chromosome 8 centromere.
Deguchi et al. (2003) showed that MOZ/TIF2 has transforming properties in vitro and caused AML in a murine bone marrow transplant assay. The C2HC nucleosome recognition motif of MOZ was essential for transformation, whereas MOZ HAT activity was dispensable. However, MOZ/TIF2 interaction with CBP through the TIF2 CBP interaction domain was also essential for transformation. These results indicated that nucleosomal targeting by MOZ and recruitment of CBP by TIF2 are critical requirements for MOZ/TIF2 transformation, and indicated that MOZ gain of function can contribute to leukemogenesis.
Aikawa et al. (2010) found that mouse MOZ/TIF2-induced AML stem cells with high expression of Csf1r (164770) had increased leukemia initiating activity than AML stem cells with same amount of MOZ/TIF2 protein and low expression of Csf1r, when transplanted in irradiated mice. The high Csf1r expressing cells had the phenotype of granulocyte-macrophage progenitors and differentiated monocytes. In mice with leukemia due to these cells, treatment with a drug-inducible suicide gene targeting Csf1r-expressing cells resulted in curing of the leukemia for up to 6 months compared to controls. Induction of AML was suppressed in Csf1r-deficient mice, and Csf1r inhibitors slowed the progression of MOZ/TIF2-induced AML. Increased Csf1r expression was due mainly to the hematopoietic transcription factor PU.1 (SPI1; 165170), which was required for the initiation and maintenance of MOZ/TIF2-induced AML by increasing transcription of Csf1r. Aikawa et al. (2010) suggested that CSF1R is crucial for leukemia induced by MOZ fusion and indicated that targeting of PU.1 may be a therapeutic option.
In 4 unrelated children with Arboleda-Tham syndrome (ARTHS; 616268), Arboleda et al. (2015) identified 2 different de novo heterozygous truncating mutations in the KAT6A gene (601408.0001-601408.0002). The mutations were found by exome sequencing and confirmed by Sanger sequencing. Three of the patients were ascertained from a cohort of 298 individuals with developmental delay who underwent exome sequencing, thus representing about 1% (3 of 298) of patients. Studies of patient cells showed alterations in acetylation of histone H3 lysine-9 (H3K9) and H3K18, as well as changes in signaling downstream of p53, suggesting disruption of multiple pathways involved in apoptosis, metabolism, and transcriptional regulation.
In 6 patients, including a set of monozygotic twins, from 5 unrelated families with ARTHS, Tham et al. (2015) identified 5 different de novo heterozygous mutations in the KAT6A gene (see, e.g., 601408.0003-601408.0005). All the mutations were predicted to result in premature termination of the protein within the C-terminal acidic domain, leaving the HAT domain intact. No patient cells were available for studies, and functional studies of the variant were not performed.
Using trio whole-exome sequencing (WES) in 6 patients with a neurodevelopmental disorder with severe speech delay, hypotonia, and facial dysmorphism, Millan et al. (2016) identified 6 de novo mutations in the KAT6A gene. All but 1 were frameshift or nonsense mutations. One patient (patient 4) had an independent occurrence of the R1024X mutation (601408.0002) previously described by Arboleda et al. (2015).
Kennedy et al. (2019) identified 44 novel genetic variants in the KAT6A gene in 52 novel cases. Thirty-nine (88%) were truncating frameshift or nonsense mutations. Five, including 1 variant of uncertain significance (VUS), were missense mutations, and 4 patients had splice site changes. Kennedy et al. (2019) also identified hotspot nonsense pathogenic variants within the C-terminal exons (16 and 17) at amino acid positions 1019, 1024, and 1129 that accounted for 19% (13 of 68) of pathogenic variants in unrelated individuals. Kennedy et al. (2019) observed a bias of increased severity of developmental delay and an increased frequency of microcephaly, hypotonia, cardiac anomalies, and gastrointestinal complications associated with truncating pathogenic variants in the last 2 exons, suggesting a role for nonsense-mediated decay in mitigating the phenotype.
In a Taiwanese boy with ARTHS, Lin et al. (2020) identified a de novo heterozygous 1-bp deletion in exon 17 of the KAT6A gene (c.3411delA; 601408.0007). The mutation was identified by trio whole-genome sequencing and confirmed by Sanger sequencing. Functional studies were not performed.
Singh et al. (2023) performed a multiomics analysis of fibroblasts from 8 patients with ARTHS and 14 controls. RNAseq identified increased expression of 5 genes from the posterior HOXC gene cluster, HOXC11 (605559), HOXC10 (605560), HOXC-AS3, HOTAIR (611400) and HOXC-AS2. ATACseq experiments showed that several of these HOXC genes had differential chromatin accessibility. Histone acetylation studies showed that 2 loci bound to H3K23 acetylation were in the HOXC gene cluster. DNA methylation studies showed that CpG sites were hypomethylated in patients compared to controls.
Thomas et al. (2006) generated mice with a mutation in the Moz gene that resulted in a truncated protein lacking the C-terminal domains encoded by exon 16. They noted that these C-terminal domains are absent from fusion proteins produced by translocations involving MOZ. No Moz protein was expressed in homozygous mutant mice, even though mRNA was produced at normal levels. Homozygous mutant mice died at birth. Although not anemic, they failed to oxygenate their blood, probably as a result of aortic arch defects. Mutant mice also exhibited facial abnormalities, including cleft palate. At embryonic day 18.5, mutant embryos showed severe dysgenesis of both the thymus and spleen. Thymic lobes were small, poorly organized, and lacked a clear medulla. The spleen in mutant animals appeared only as a slightly thickened region of mesentery. Mutant fetal liver hematopoietic cells were incapable of contributing to the hematopoietic system of recipients after transplantation. Moz mutants showed profound defects in the stem cell compartment. Progenitors of all lineages were reduced in number; however, blood cell lineage commitment was unaffected.
Katsumoto et al. (2006) found that Moz-null mouse embryos died around embryonic day 15. Moz-null embryos had small livers, and some exhibited hemorrhaging, subcutaneous edema, and bent tail, but no other abnormalities were observed. In day-14.5 Moz-null embryos, hematopoietic stem cells, lineage-committed progenitors, and B-lineage cells were severely reduced. Arrest of erythroid maturation and elevated myeloid lineage populations were also observed. Moz-deficient fetal liver cells could not reconstitute hematopoiesis in recipients after transplantation. Microarray and flow cytometry revealed that expression of thrombopoietin receptor (MPL; 159530), Hoxa9 (142956), and Kit (164920) was downregulated. Katsumoto et al. (2006) concluded that MOZ is required for maintenance of hematopoietic stem cells and that it plays a role in differentiation of erythroid and myeloid cells.
Voss et al. (2012) found that mice with a homozygous C-terminal deletion allele of Kat6a had micrognathia, cleft palate, and absence or hypoplasia of the thymus. Homozygous mutant mice also had cardiovascular defects, including septal defects, and aortic arch abnormalities that were attributed to abnormal development of the fourth pharyngeal arch. These findings were similar to those observed in patients with DiGeorge syndrome (DGS; 188400), which results from mutation in the TBX1 gene (602054) or deletion of chromosome 22q11.2. Homozygous mutant Kat6a mice had significantly reduced levels of Tbx1 mRNA associated with decreased H3K9 acetylation at the Tbx1 locus. Similar clinical features were found in heterozygous Kat6a mutant mice either in combination with Tbx1 haploinsufficiency or upon exposure to retinoic acid, the latter indicating susceptibility to environmental effects. The findings indicated that Kat6a regulates the Tbx1 locus, is essential for proper development of the heart and thymus, and can be modified by environmental factors.
In 3 unrelated children (1-II-1, 2-II-2, 4-II-1) with Arboleda-Tham syndrome (ARTHS; 616268), Arboleda et al. (2015) identified a de novo heterozygous c.3385C-T transition in the last exon of the KAT6A gene, resulting in an arg1129-to-ter (R1129X) substitution, predicted to cause truncation within the acidic domain of the protein, thus leaving the HAT domain intact. The mutation, which occurred at a CpG base, was found by exome sequencing and confirmed by Sanger sequencing. It was not present in the Exome Variant Server or Exome Aggregation Consortium databases or in 1,815 in-house clinical exomes. Studies of patient cells showed that the mutation did not cause nonsense-mediated mRNA decay. Western blot analysis of cells derived from 1 patient showed changes in histone acetylation compared to controls, with a decrease in H3K9 acetylation and an increase in H3K18 acetylation. Although there were no changes in p53 (TP53; 191170) acetylation, there were significant changes in gene expression of genes involved in downstream p53 signaling.
In a girl (3-II-1) with Arboleda-Tham syndrome (ARTHS; 616268), Arboleda et al. (2015) identified a de novo heterozygous c.3070C-T transition in exon 16 of the KAT6A gene, resulting in an arg1024-to-ter (R1024X) substitution, predicted to cause truncation within the acidic domain of the protein, leaving the HAT domain intact. The mutation, which occurred at a CpG base, was found by exome sequencing and confirmed by Sanger sequencing. It was not present in the Exome Variant Server or Exome Aggregation Consortium databases or in 1,815 in-house clinical exomes.
Millan et al. (2016) reported a 5-year-old girl (patient 4) with the same variant, which was shown to have occurred de novo. This variant was not present in gnomAD on May 2, 2019 (Hamosh, 2019).
In a girl (family 1) with Arboleda-Tham syndrome (ARTHS; 616268), Tham et al. (2015) identified a de novo heterozygous 1-bp duplication (c.3879dupA) in the KAT6A gene, resulting in a frameshift and premature termination (Glu1294ArgfsTer19) within the acidic domain. The mutation was found by exome sequencing and confirmed by Sanger sequencing. No patient cells were available for studies, and functional studies of the variant were not performed.
In a pair of monozygotic twins (family 2) with Arboleda-Tham syndrome (ARTHS; 616268), Tham et al. (2015) identified a de novo heterozygous 2-bp deletion (c.3116_3117delCT) in the KAT6A gene, resulting in a frameshift and premature termination (Ser1039Ter) within the acidic domain. The mutation was found by exome sequencing and confirmed by Sanger sequencing. No patient cells were available for studies, and functional studies of the variant were not performed.
In a girl (family 4) with Arboleda-Tham syndrome (ARTHS; 616268), Tham et al. (2015) identified a de novo heterozygous c.4108G-T transversion in the KAT6A gene, resulting in a glu1370-to-ter (E1370X) substitution within the acidic domain. The mutation was found by exome sequencing and confirmed by Sanger sequencing. No patient cells were available for studies, and functional studies of the variant were not performed.
In a 6-year-old girl (patient 5) with Arboleda-Tham syndrome (ARTHS; 616268), Millan et al. (2016) identified heterozygosity for an A-to-G transition at nucleotide 1928 in the KAT6A gene that resulted in an asn-to-ser substitution at codon 643 (N643S). The mutation was shown to have occurred de novo. The mutation occurred in a highly conserved region of the gene encoding the catalytic MYST-type histone acetyltransferase domain. Functional studies were not performed.
The N643S mutation was not present in gnomAD on May 2, 2019 (Hamosh, 2019).
In a Taiwanese boy with Arboleda-Tham syndrome (ARTHS; 616268), Lin et al. (2020) identified a de novo heterozygous 1-bp deletion (c.3411delA, NM_006766.5) in exon 17 of the KAT6A gene, predicted to result in a frameshift and premature termination (Gly1139SerfsTer41). The mutation was identified by trio whole-genome sequencing and confirmed by Sanger sequencing. The mutation was not present in the ExAC database or the Taiwan BioBank. Functional studies were not performed.
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