KAT2A
lysine acetyltransferase 2A, the group of Bromodomain containing|ATAC complex|GCN5 related N-acetyltransferases|SAGA complex|Lysine acetyltransferases
Basic information
Region (hg38): 17:42113111-42121367
Previous symbols: [ "GCN5L2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KAT2A gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 32 | 33 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 1 | 32 | 2 | 5 |
Variants in KAT2A
This is a list of pathogenic ClinVar variants found in the KAT2A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-42113777-C-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 17-42113794-C-T | not specified | Uncertain significance (Jan 10, 2022) | ||
| 17-42113810-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 17-42113823-C-T | Likely benign (Nov 01, 2022) | |||
| 17-42114040-C-T | Benign (Apr 04, 2018) | |||
| 17-42114269-C-A | not specified | Uncertain significance (May 18, 2022) | ||
| 17-42114374-A-G | Benign (Apr 04, 2018) | |||
| 17-42114568-TCTGGGCCTGTTTGCGCTCAATCAG-T | See cases | Likely pathogenic (-) | ||
| 17-42114921-G-A | Benign (Jan 14, 2019) | |||
| 17-42114939-G-A | not specified | Uncertain significance (Jan 18, 2022) | ||
| 17-42115001-C-T | not specified | Uncertain significance (Aug 30, 2021) | ||
| 17-42115004-C-T | not specified | Uncertain significance (May 26, 2023) | ||
| 17-42115817-A-G | not specified | Uncertain significance (Aug 28, 2023) | ||
| 17-42117090-G-C | not specified | Uncertain significance (Jan 10, 2023) | ||
| 17-42117126-C-T | not specified | Uncertain significance (Feb 02, 2024) | ||
| 17-42117484-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 17-42117499-G-A | not specified | Uncertain significance (Oct 05, 2022) | ||
| 17-42117515-T-C | not specified | Uncertain significance (Dec 13, 2022) | ||
| 17-42117690-C-T | not specified | Uncertain significance (Dec 14, 2023) | ||
| 17-42117969-C-A | not specified | Uncertain significance (Jul 25, 2023) | ||
| 17-42118011-ACTGAAGCTGAGGAGAGAGAGAGACGTCAGGGATGGGGGG-A | Benign (Aug 28, 2018) | |||
| 17-42118351-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
| 17-42119389-C-T | not specified | Uncertain significance (Nov 15, 2021) | ||
| 17-42119597-G-A | not specified | Uncertain significance (Dec 14, 2021) | ||
| 17-42119624-A-G | not specified | Uncertain significance (Aug 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KAT2A | protein_coding | protein_coding | ENST00000225916 | 18 | 8251 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.573 | 0.427 | 125726 | 0 | 20 | 125746 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.82 | 256 | 495 | 0.517 | 0.0000310 | 5385 |
| Missense in Polyphen | 69 | 189.96 | 0.36323 | 2088 | ||
| Synonymous | 0.323 | 194 | 200 | 0.971 | 0.0000123 | 1665 |
| Loss of Function | 4.72 | 9 | 42.0 | 0.214 | 0.00000236 | 463 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000174 | 0.000174 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000468 | 0.0000462 |
| European (Non-Finnish) | 0.0000980 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protein lysine acyltransferase that can act both as a acetyltransferase and succinyltransferase, depending on the context (PubMed:29211711). Acts as a histone lysine succinyltransferase: catalyzes succinylation of histone H3 on 'Lys-79' (H3K79succ), with a maximum frequency around the transcription start sites of genes (PubMed:29211711). Succinylation of histones gives a specific tag for epigenetic transcription activation (PubMed:29211711). Association with the 2-oxoglutarate dehydrogenase complex, which provides succinyl-CoA, is required for histone succinylation (PubMed:29211711). In different complexes, functions either as an acetyltransferase (HAT) or as a succinyltransferase: in the SAGA and ATAC complexes, acts as a histone acetyltransferase (PubMed:17301242, PubMed:19103755, PubMed:29211711). Has significant histone acetyltransferase activity with core histones, but not with nucleosome core particles (PubMed:17301242, PubMed:19103755). Acetylation of histones gives a specific tag for epigenetic transcription activation (PubMed:17301242, PubMed:19103755, PubMed:29211711). Involved in long-term memory consolidation and synaptic plasticity: acts by promoting expression of a hippocampal gene expression network linked to neuroactive receptor signaling (By similarity). Acts as a positive regulator of T-cell activation: upon TCR stimulation, recruited to the IL2 promoter following interaction with NFATC2 and catalyzes acetylation of histone H3 at Lys-9 (H3K9ac), leading to promote IL2 expression (By similarity). Also acetylates non-histone proteins, such as CEBPB, PLK4 and TBX5 (PubMed:17301242, PubMed:29174768, PubMed:27796307). Involved in heart and limb development by mediating acetylation of TBX5, acetylation regulating nucleocytoplasmic shuttling of TBX5 (PubMed:29174768). Acts as a negative regulator of centrosome amplification by mediating acetylation of PLK4 (PubMed:27796307). {ECO:0000250|UniProtKB:Q9JHD2, ECO:0000269|PubMed:17301242, ECO:0000269|PubMed:19103755, ECO:0000269|PubMed:27796307, ECO:0000269|PubMed:29174768, ECO:0000269|PubMed:29211711}.;
- Pathway
- HTLV-I infection - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);TGF-Ncore;Notch Signaling Pathway;Notch Signaling Pathway;B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;Disease;RUNX3 regulates NOTCH signaling;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);Transcriptional regulation by RUNX3;Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;RNA Polymerase I Promoter Clearance;RNA Polymerase II Transcription;Chromatin modifying enzymes;Notch-HLH transcription pathway;RNA Polymerase I Transcription;NICD traffics to nucleus;RNA Polymerase I Transcription Initiation;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;Signaling by NOTCH1;NOTCH3 Intracellular Domain Regulates Transcription;Signaling by NOTCH3;Signaling by NOTCH;HATs acetylate histones;Ub-specific processing proteases;Deubiquitination;Chromatin organization;C-MYC pathway;Direct p53 effectors;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Diseases of signal transduction;Validated targets of C-MYC transcriptional activation;NOTCH1 Intracellular Domain Regulates Transcription;Regulation of nuclear SMAD2/3 signaling;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.185
Intolerance Scores
- loftool
- 0.543
- rvis_EVS
- -1.16
- rvis_percentile_EVS
- 6.17
Haploinsufficiency Scores
- pHI
- 0.975
- hipred
- Y
- hipred_score
- 0.704
- ghis
- 0.618
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kat2a
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- kat2a
- Affected structure
- paired fin
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- in utero embryonic development;somitogenesis;cytokine production;neural tube closure;chromatin remodeling;regulation of transcription by RNA polymerase II;heart development;long-term memory;cell population proliferation;response to organic cyclic compound;viral process;histone deubiquitination;protein deubiquitination;internal peptidyl-lysine acetylation;telencephalon development;metencephalon development;midbrain development;positive regulation of cell projection organization;regulation of protein stability;response to nutrient levels;positive regulation of histone acetylation;multicellular organism growth;positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter;histone H3 acetylation;histone H4-K12 acetylation;histone H3-K14 acetylation;regulation of regulatory T cell differentiation;positive regulation of gene expression, epigenetic;positive regulation of transcription by RNA polymerase II;negative regulation of centriole replication;regulation of synaptic plasticity;intracellular distribution of mitochondria;regulation of T cell activation;limb development;cellular response to tumor necrosis factor;alpha-tubulin acetylation;histone succinylation;cellular response to nerve growth factor stimulus;positive regulation of cardiac muscle cell differentiation
- Cellular component
- nuclear chromatin;extracellular space;nucleus;nucleoplasm;Ada2/Gcn5/Ada3 transcription activator complex;centrosome;STAGA complex;transcription factor TFTC complex;oxoglutarate dehydrogenase complex;mitotic spindle
- Molecular function
- chromatin binding;transcription coactivator activity;histone acetyltransferase activity;protein binding;transcription factor binding;H3 histone acetyltransferase activity;protein phosphatase binding;thiol-dependent ubiquitinyl hydrolase activity;histone deacetylase binding;histone acetyltransferase activity (H4-K12 specific);peptide-lysine-N-acetyltransferase activity;histone succinyltransferase activity