RYBP

RING1 and YY1 binding protein, the group of Zinc fingers RANBP2-type

Basic information

Region (hg38): 3:72371824-72446621

Links

ENSG00000163602 ∙ NCBI:23429 ∙ OMIM:607535 ∙ HGNC:10480 ∙ Uniprot:Q8N488 ∙ 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 RYBP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RYBP 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
RYBP	protein_coding	protein_coding	ENST00000477973	4	75094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.177	0.811	124437	0	41	124478	0.000165

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.656	147	171	0.859	0.00000861	2029
Missense in Polyphen		14	35.605	0.39321		407
Synonymous	-1.30	84	70.1	1.20	0.00000369	668
Loss of Function	2.18	3	10.7	0.280	4.57e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00110
Ashkenazi Jewish	0.0000996	0.0000995
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000375	0.0000355
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1-like complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility (PubMed:25519132). Component of a PRC1-like complex that mediates monoubiquitination of histone H2A 'Lys-119' on the X chromosome and is required for normal silencing of one copy of the X chromosome in XX females. May stimulate ubiquitination of histone H2A 'Lys-119' by recruiting the complex to target sites (By similarity). Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes (PubMed:19098711). May also regulate the ubiquitin-mediated proteasomal degradation of other proteins like FANK1 to regulate apoptosis (PubMed:14765135, PubMed:27060496). May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1 (PubMed:11953439). May bind to DNA (By similarity). May play a role in the repression of tumor growth and metastasis in breast cancer by down-regulating SRRM3 (PubMed:27748911). {ECO:0000250|UniProtKB:Q8CCI5, ECO:0000269|PubMed:11953439, ECO:0000269|PubMed:14765135, ECO:0000269|PubMed:19098711, ECO:0000269|PubMed:27060496, ECO:0000269|PubMed:27748911}.
• Pathway: Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Transcriptional Regulation by E2F6;Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation by RUNX1;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.142

Haploinsufficiency Scores

• pHI: 0.490
• ghis: 0.606

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Mouse Genome Informatics

• Gene name: Rybp
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system 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); embryo phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;apoptotic process;multicellular organism development;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;histone H2A monoubiquitination;positive regulation of apoptotic process;positive regulation of transcription, DNA-templated;negative regulation of G0 to G1 transition
• Cellular component: nucleus;nucleoplasm;cytoplasm;PcG protein complex
• Molecular function: DNA binding;transcription corepressor activity;protein binding;metal ion binding