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.

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.

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				1	1	2
missense			97	9	2	108
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	3	4
Total	0	0	97	11	7

Variants in YEATS2

This is a list of pathogenic ClinVar variants found in the YEATS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-183715196-G-A		not specified • Epilepsy, familial adult myoclonic, 4	Uncertain significance (Sep 26, 2023)
3-183715253-G-A		not specified	Uncertain significance (Jun 26, 2023)
3-183717669-A-G		not specified	Uncertain significance (May 31, 2023)
3-183717726-A-T		not specified	Uncertain significance (Feb 21, 2025)
3-183718519-G-C		not specified	Uncertain significance (Jun 16, 2024)
3-183718588-C-T		not specified	Uncertain significance (Nov 13, 2023)
3-183721864-T-C		Epilepsy, familial adult myoclonic, 4	Benign/Likely benign (Dec 05, 2021)
3-183721927-C-G		not specified	Uncertain significance (Jul 31, 2024)
3-183721931-C-G		not specified	Uncertain significance (Nov 09, 2022)
3-183721933-A-G		not specified	Uncertain significance (Mar 04, 2025)
3-183722043-C-G		Epilepsy, familial adult myoclonic, 4	Uncertain significance (Aug 20, 2021)
3-183722069-G-A		not specified	Uncertain significance (Sep 01, 2021)
3-183722072-A-G		not specified	Uncertain significance (Jun 28, 2023)
3-183722086-G-C		not specified	Uncertain significance (Aug 12, 2024)
3-183722184-A-AG		Epilepsy, familial adult myoclonic, 4	Benign (Dec 05, 2021)
3-183724420-A-G		not specified	Uncertain significance (Aug 04, 2024)
3-183724428-A-G		not specified	Uncertain significance (Nov 03, 2022)
3-183724438-G-C		not specified	Uncertain significance (Dec 02, 2022)
3-183724444-A-T		not specified	Uncertain significance (Sep 25, 2024)
3-183724451-AG-A		Benign adult familial myoclonic epilepsy	Uncertain significance (Jul 30, 2021)
3-183724456-A-G		YEATS2-related disorder • not specified	Uncertain significance (Jan 10, 2022)
3-183724459-G-A		not specified	Uncertain significance (Jun 06, 2023)
3-183728725-A-G		not specified	Uncertain significance (Apr 08, 2024)
3-183728763-C-T		not specified	Uncertain significance (May 04, 2023)
3-183728764-G-A		not specified	Uncertain significance (Nov 28, 2023)

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

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