HAT1

histone acetyltransferase 1, the group of Lysine acetyltransferases

Basic information

Region (hg38): 2:171922448-171983686

Links

ENSG00000128708

∙ NCBI:8520 ∙ OMIM:603053 ∙ HGNC:4821 ∙ Uniprot:O14929 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAT1 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						0
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in HAT1

This is a list of pathogenic ClinVar variants found in the HAT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
2-171925623-G-A	not specified	Uncertain significance (Sep 10, 2024)	3523990
2-171965411-C-T	not specified	Uncertain significance (Jun 09, 2022)	2227991
2-171965476-A-G	not specified	Uncertain significance (Dec 02, 2024)	3523993
2-171965478-T-G	not specified	Uncertain significance (Jul 12, 2022)	2300899
2-171965511-A-G	not specified	Uncertain significance (Feb 01, 2023)	2473797
2-171965821-A-G	not specified	Uncertain significance (Dec 16, 2021)	2267651
2-171966488-C-T	not specified	Uncertain significance (Sep 26, 2024)	3523991
2-171976174-A-T	not specified	Uncertain significance (Sep 01, 2021)	2362853
2-171979323-A-G	not specified	Uncertain significance (Mar 07, 2024)	3104312
2-171979334-A-G	not specified	Uncertain significance (Aug 12, 2022)	2391910
2-171983294-G-C	not specified	Uncertain significance (Oct 12, 2022)	2318207
2-171983323-C-T	not specified	Uncertain significance (Oct 10, 2023)	3104313
2-171983329-A-G	not specified	Uncertain significance (Sep 27, 2024)	3523992

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAT1	protein_coding	protein_coding	ENST00000264108	11	69642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.835	0.165	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	156	220	0.708	0.0000114	2782
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000715	0.0000703
Middle Eastern	0.000165	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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}.;
Pathway: Alcoholism - Homo sapiens (human);Ethanol effects on histone modifications;Chromatin modifying enzymes;HATs acetylate histones;EGFR1;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.134

Intolerance Scores

loftool: 0.333
rvis_EVS: 0.13
rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

pHI: 0.959
hipred: Y
hipred_score: 0.783
ghis: 0.615

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.974

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Hat1
Phenotype: skeleton phenotype; respiratory system phenotype; growth/size/body region phenotype; normal phenotype; 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); craniofacial phenotype; cellular phenotype;

Gene ontology

Biological process: DNA packaging;DNA replication-dependent nucleosome assembly;DNA replication-independent nucleosome assembly;chromatin silencing at telomere;internal protein amino acid acetylation;response to nutrient;histone H4 acetylation
Cellular component: nuclear chromosome, telomeric region;nuclear chromatin;nucleus;nucleoplasm;cytoplasm;nuclear matrix;protein-containing complex;intracellular membrane-bounded organelle
Molecular function: histone acetyltransferase activity;protein binding;H4 histone acetyltransferase activity;histone binding