KAT8

lysine acetyltransferase 8, the group of Zinc fingers C2HC-type|NSL histone acetyltransferase complex|MSL histone acetyltransferase complex|MYST type domain containing lysine acetyltransferases

Basic information

Region (hg38): 16:31114488-31131393

Previous symbols: [ "MYST1" ]

Links

ENSG00000103510 ∙ NCBI:84148 ∙ OMIM:609912 ∙ HGNC:17933 ∙ Uniprot:Q9H7Z6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Li-Ghorbani-Weisz-Hubshman syndrome (Moderate), mode of inheritance: AD
• Li-Ghorbani-Weisz-Hubshman syndrome (Strong), mode of inheritance: AD
• Li-Ghorbani-Weisz-Hubshman syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Li-Ghorbani-Weisz-Hubshman	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	31794431

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KAT8 gene.

• Li-Ghorbani-Weisz-Hubshman syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KAT8 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					2	2
missense	1	2	40	6	1	50
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			2	2		4
non coding						0
Total	1	2	45	6	3

Variants in KAT8

This is a list of pathogenic ClinVar variants found in the KAT8 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-31117693-G-C		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
16-31117711-T-TGCGGCGGGGACTTCAGGGGTC		Inborn genetic diseases	Uncertain significance (Oct 06, 2021)
16-31117713-C-T			Uncertain significance (Feb 21, 2022)
16-31117736-G-C		Li-Ghorbani-Weisz-Hubshman syndrome	Uncertain significance (May 20, 2021)
16-31117744-CGAGCCCGGGCCCGGGGA-C			Uncertain significance (Apr 27, 2023)
16-31117757-G-C		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
16-31117778-G-A			Uncertain significance (Dec 30, 2022)
16-31117791-C-G		not specified	Uncertain significance (Jan 17, 2024)
16-31117796-G-A		Inborn genetic diseases	Likely benign (Oct 03, 2022)
16-31117814-A-G		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
16-31117869-G-C		Inborn genetic diseases	Uncertain significance (Sep 14, 2021)
16-31117878-C-T			Uncertain significance (Jan 06, 2023)
16-31120243-A-G		Li-Ghorbani-Weisz-Hubshman syndrome • Inborn genetic diseases	Likely pathogenic (Sep 16, 2021)
16-31120245-G-A			Uncertain significance (Mar 08, 2021)
16-31120249-A-G		Li-Ghorbani-Weisz-Hubshman syndrome	Pathogenic (May 23, 2022)
16-31120336-C-A			Uncertain significance (Oct 06, 2022)
16-31120345-G-A		Li-Ghorbani-Weisz-Hubshman syndrome	Pathogenic (Aug 12, 2020)
16-31120347-C-T			Pathogenic (Jul 11, 2024)
16-31120348-G-A			Pathogenic (-)
16-31120424-G-C			Uncertain significance (Feb 01, 2022)
16-31120470-C-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2021)
16-31127031-C-G		Inborn genetic diseases	Likely benign (May 24, 2021)
16-31127034-G-A			Uncertain significance (Jan 21, 2023)
16-31127068-T-A			Uncertain significance (Feb 06, 2023)
16-31127088-G-A		Inborn genetic diseases	Likely benign (Feb 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KAT8	protein_coding	protein_coding	ENST00000448516	10	15640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.225	0.775	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.15	118	261	0.452	0.0000161	3007
Missense in Polyphen		28	88.622	0.31595		950
Synonymous	0.200	104	107	0.975	0.00000671	901
Loss of Function	3.49	6	24.7	0.243	0.00000121	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone acetyltransferase which may be involved in transcriptional activation. May influence the function of ATM. As part of the MSL complex it is involved in acetylation of nucleosomal histone H4 producing specifically H4K16ac. As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. That activity is less specific than the one of the MSL complex. Can also acetylate TP53/p53 at 'Lys-120'. {ECO:0000269|PubMed:12397079, ECO:0000269|PubMed:15923642, ECO:0000269|PubMed:20018852, ECO:0000269|PubMed:21217699, ECO:0000269|PubMed:22020126, ECO:0000269|PubMed:22547026}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization;p53 pathway (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.301
• hipred: Y
• hipred_score: 0.771
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kat8
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; embryo 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)

Zebrafish Information Network

• Gene name: kat8
• Affected structure: primitive hemopoiesis
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: regulation of autophagy;histone acetylation;myeloid cell differentiation;histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K16 acetylation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: histone acetyltransferase complex;kinetochore;nuclear chromatin;nucleus;nucleoplasm;nuclear matrix;MLL1 complex;MSL complex
• Molecular function: histone acetyltransferase activity;protein binding;transcription factor binding;acetyltransferase activity;enzyme binding;methylated histone binding;histone binding;histone acetyltransferase activity (H4-K5 specific);histone acetyltransferase activity (H4-K8 specific);metal ion binding;histone acetyltransferase activity (H4-K16 specific)