YEATS2

YEATS domain containing 2, the group of YEATS domain containing|ATAC complex

Basic information

Region (hg38): 3:183697797-183812624

Links

ENSG00000163872

∙ NCBI:55689 ∙ OMIM:613373 ∙ HGNC:25489 ∙ Uniprot:Q9ULM3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

benign adult familial myoclonic epilepsy (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, myoclonic, familial adult, 4	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	Neurologic	22713812; 31539032
Reported variants have involved intronic repeat expansions

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the YEATS2 gene.

not_specified (161 variants)
not_provided (13 variants)
Epilepsy,_familial_adult_myoclonic,_4 (13 variants)
YEATS2-related_disorder (5 variants)
Benign_adult_familial_myoclonic_epilepsy (1 variants)
Breast_ductal_adenocarcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YEATS2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018023.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			166 clinvar	10 clinvar	1 clinvar	177
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)				1 clinvar		1
Total	0	0	167	12	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YEATS2	protein_coding	protein_coding	ENST00000305135	30	114808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00361	124737	0	60	124797	0.000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.972	695	771	0.902	0.0000405	9124
Missense in Polyphen		155	200.45	0.77325		2447
Synonymous	1.04	276	299	0.924	0.0000176	2935
Loss of Function	6.56	13	73.9	0.176	0.00000397	860

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000935	0.000930
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000167
Finnish	0.000464	0.000464
European (Non-Finnish)	0.000202	0.000194
Middle Eastern	0.000168	0.000167
South Asian	0.00	0.00
Other	0.000496	0.000495

dbNSFP

Source: dbNSFP

Function: FUNCTION: Chromatin reader component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4. YEATS2 specifically recognizes and binds histone H3 crotonylated at 'Lys-27' (H3K27cr) (PubMed:27103431). Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors (PubMed:27103431). {ECO:0000269|PubMed:18838386, ECO:0000269|PubMed:19103755, ECO:0000269|PubMed:27103431}.;
Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.100

Intolerance Scores

loftool: 0.402
rvis_EVS: -1.08
rvis_percentile_EVS: 7.32

Haploinsufficiency Scores

pHI: 0.118
hipred: Y
hipred_score: 0.708
ghis: 0.588

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.244

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Yeats2
Phenotype

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;histone H3 acetylation;negative regulation of transcription, DNA-templated
Cellular component: Ada2/Gcn5/Ada3 transcription activator complex;mitotic spindle
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;TBP-class protein binding;histone binding;modification-dependent protein binding