YY2

YY2 transcription factor, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): X:21855987-21858740

Links

ENSG00000230797 ∙ NCBI:404281 ∙ OMIM:300570 ∙ HGNC:31684 ∙ Uniprot:O15391 ∙ 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 YY2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YY2 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
missense			21	4		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	22	5	0

Variants in YY2

This is a list of pathogenic ClinVar variants found in the YY2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-21856191-G-C		Osteogenesis imperfecta, type 19 • Keratosis follicularis spinulosa decalvans, X-linked • Olmsted syndrome, X-linked • IFAP syndrome 1, with or without BRESHECK syndrome	Uncertain significance (Jun 22, 2023)
X-21856280-C-G			Uncertain significance (Jul 08, 2024)
X-21856494-A-G		not specified	Uncertain significance (Feb 10, 2025)
X-21856552-A-G		not specified	Uncertain significance (May 03, 2023)
X-21856602-G-A		not specified	Likely benign (Mar 01, 2024)
X-21856611-G-A		not specified	Uncertain significance (May 15, 2024)
X-21856627-A-G		not specified	Likely benign (Dec 04, 2024)
X-21856768-A-G		not specified	Uncertain significance (Apr 22, 2022)
X-21856796-G-T		not specified	Uncertain significance (Dec 18, 2023)
X-21856816-T-G		not specified	Uncertain significance (Jan 20, 2023)
X-21856893-C-T		not specified	Uncertain significance (Jan 26, 2022)
X-21856923-G-A		not specified	Likely benign (Jun 12, 2023)
X-21856959-G-A			Uncertain significance (May 10, 2022)
X-21856988-G-C		not specified	Uncertain significance (May 06, 2024)
X-21856992-G-A		not specified	Uncertain significance (Aug 01, 2022)
X-21857035-C-G		not specified	Uncertain significance (Dec 21, 2022)
X-21857037-G-A		not specified	Uncertain significance (Mar 01, 2023)
X-21857052-C-T		not specified	Uncertain significance (Mar 14, 2023)
X-21857058-G-A		not specified	Uncertain significance (Feb 27, 2023)
X-21857065-A-G		not specified	Uncertain significance (Dec 20, 2022)
X-21857106-C-T		not specified	Uncertain significance (Mar 04, 2025)
X-21857216-A-C		not specified	Uncertain significance (Aug 12, 2024)
X-21857227-G-A		not specified	Likely benign (Jun 06, 2023)
X-21857235-C-T		not specified	Uncertain significance (Dec 03, 2024)
X-21857351-C-T			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YY2	protein_coding	protein_coding	ENST00000429584	1	2741

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.408	0.558	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	121	171	0.710	0.0000148	2486
Missense in Polyphen		16	49.916	0.32054		735
Synonymous	-0.648	91	83.5	1.09	0.00000872	713
Loss of Function	1.69	1	5.12	0.195	4.10e-7	87

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a multifunctional transcription factor that may exhibit positive and negative control on a large number of genes. May antagonize YY1 and function in development and differentiation. {ECO:0000269|PubMed:16260628}.

Recessive Scores

• pRec: 0.0896

Intolerance Scores

• loftool: 0.0712
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.246
• ghis: 0.419

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yy2

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nuclear chromatin;nucleus;transcription factor complex;PcG protein complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;sequence-specific DNA binding;metal ion binding