YEATS4

YEATS domain containing 4, the group of SRCAP complex|YEATS domain containing|Tip60/Nua4 histone acetyltransferase complex subunits

Basic information

Region (hg38): 12:69359709-69390870

Links

ENSG00000127337 ∙ NCBI:8089 ∙ OMIM:602116 ∙ HGNC:24859 ∙ Uniprot:O95619 ∙ 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 YEATS4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YEATS4 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YEATS4	protein_coding	protein_coding	ENST00000247843	7	31094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000746	0.765	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	44	117	0.377	0.00000569	1497
Missense in Polyphen		11	35.241	0.31214		450
Synonymous	-1.10	48	39.3	1.22	0.00000193	395
Loss of Function	1.10	8	12.1	0.659	5.06e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000544	0.000531
Ashkenazi Jewish	0.00	0.00
East Asian	0.000334	0.000326
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000152	0.000149
Middle Eastern	0.000334	0.000326
South Asian	0.0000681	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the NuA4 histone acetyltransferase (HAT) complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. This complex may be required for the activation of transcriptional programs associated with oncogene and proto-oncogene mediated growth induction, tumor suppressor mediated growth arrest and replicative senescence, apoptosis, and DNA repair. NuA4 may also play a direct role in DNA repair when recruited to sites of DNA damage. {ECO:0000269|PubMed:14966270}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization;C-MYB transcription factor network;Activation of the TFAP2 (AP-2) family of transcription factors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors (Consensus)

Intolerance Scores

• loftool: 0.465
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.677
• hipred: Y
• hipred_score: 0.723
• ghis: 0.681

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Yeats4

Gene ontology

• Biological process: mitotic cell cycle;cytoskeleton organization;regulation of growth;histone H4 acetylation;histone H2A acetylation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: Swr1 complex;nucleoplasm;nuclear matrix;nuclear membrane;NuA4 histone acetyltransferase complex
• Molecular function: DNA binding;DNA-binding transcription factor activity;structural constituent of cytoskeleton;protein binding;protein C-terminus binding