HAT1
protein-codinghistone acetyltransferase 1, the group of Lysine acetyltransferases
Gene summary
The protein encoded by this gene is a type B histone acetyltransferase (HAT) that is involved in the rapid acetylation of newly synthesized cytoplasmic histones, which are in turn imported into the nucleus for de novo deposition onto nascent DNA chains. Histone acetylation, particularly of histone H4, plays an important role in replication-dependent chromatin assembly. Specifically, this HAT can acetylate soluble but not nucleosomal histone H4 at lysines 5 and 12, and to a lesser degree, histone H2A at lysine 5. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jun 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~61.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HAT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003642.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 33 | 33 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 37 | 0 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003633.2 | 11 | MANE Select | |
| Ensembl | ENSP00000264108.4 | 11 | MANE Select | |
| Ensembl | ENSP00000407921.1 | 3 | Standard | |
| Ensembl | ENSP00000403466.2 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Alcoholism - Homo sapiens (human)
- Ethanol effects on histone modifications
- Chromatin modifying enzymes
- HATs acetylate histones
- EGFR1
Biological Process
- DNA packaging
- DNA replication-dependent nucleosome assembly
- DNA replication-independent nucleosome assembly
- chromatin silencing at telomere
- internal protein amino acid acetylation
Molecular Function
- histone acetyltransferase activity
- protein binding
- H4 histone acetyltransferase activity
- histone binding
Cellular Component
- nuclear chromosome, telomeric region
- nuclear chromatin
- nucleus
- nucleoplasm
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264108
- Coding exons
- 11
- Length
- 69642
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 125746
- p
- 0.0000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.54 | 156 | 220 | 0.708 | 0.0000114 | 2782 |
| Missense (PolyPhen) | 38 | 54.602 | 0.69594 | 702 | ||
| Synonymous | 1.77 | 56 | 75.6 | 0.741 | 0.00000397 | 728 |
| Loss of Function | 3.73 | 4 | 23.5 | 0.170 | 0.00000121 | 305 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000071 | 0.000070 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acetylates soluble but not nucleosomal histone H4 at 'Lys-5' (H4K5ac) and 'Lys-12' (H4K12ac) and, to a lesser extent, acetylates histone H2A at 'Lys-5' (H2AK5ac). Has intrinsic substrate specificity that modifies lysine in recognition sequence GXGKXG. May be involved in nucleosome assembly during DNA replication and repair as part of the histone H3.1 and H3.3 complexes. May play a role in DNA repair in response to free radical damage. {ECO:0000269|PubMed:11585814, ECO:0000269|PubMed:20953179, ECO:0000269|PubMed:22615379, ECO:0000269|PubMed:9427644}.;
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- LoFtool
- 0.333
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63.2
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.974
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |