RBBP6

RB binding protein 6, ubiquitin ligase, the group of Ring finger proteins

Basic information

Region (hg38): 16:24537693-24572863

Links

ENSG00000122257 ∙ NCBI:5930 ∙ OMIM:600938 ∙ HGNC:9889 ∙ Uniprot:Q7Z6E9 ∙ 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 RBBP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBBP6 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				7		7
missense			81	8		89
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	82	16	0

Variants in RBBP6

This is a list of pathogenic ClinVar variants found in the RBBP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-24546178-A-G		not specified	Uncertain significance (Mar 06, 2023)
16-24548961-G-A		not specified	Uncertain significance (Jun 02, 2023)
16-24553544-C-T		not specified	Uncertain significance (Feb 21, 2024)
16-24553558-G-GTA		not specified	Likely benign (Dec 16, 2022)
16-24555699-A-G		not specified	Uncertain significance (Mar 03, 2022)
16-24555713-T-C		not specified	Likely benign (Jun 07, 2021)
16-24555813-CC-TT		not specified	Uncertain significance (Jun 13, 2022)
16-24555887-A-C		not specified	Likely benign (Mar 01, 2022)
16-24559542-T-C		not specified	Uncertain significance (Oct 05, 2023)
16-24561643-G-C		not specified	Likely benign (Feb 06, 2023)
16-24561840-A-G		not specified	Uncertain significance (Jun 30, 2023)
16-24561871-A-G		not specified	Likely benign (Jul 28, 2022)
16-24561909-C-T		not specified	Uncertain significance (Dec 20, 2022)
16-24561959-T-C		not specified	Uncertain significance (Oct 22, 2021)
16-24561981-T-C		not specified	Uncertain significance (Aug 17, 2021)
16-24562016-C-T		not specified	Uncertain significance (Nov 08, 2022)
16-24562022-A-G		not specified	Uncertain significance (May 18, 2023)
16-24562045-G-C		not specified	Uncertain significance (Sep 22, 2022)
16-24562046-T-G		not specified	Uncertain significance (Sep 22, 2022)
16-24562068-C-T		not specified	Uncertain significance (Jul 25, 2023)
16-24562083-C-T		not specified	Uncertain significance (Aug 22, 2022)
16-24562094-C-T		not specified	Uncertain significance (Oct 12, 2021)
16-24562160-C-T		not specified	Uncertain significance (Feb 06, 2023)
16-24563274-T-G		not specified	Uncertain significance (Feb 13, 2024)
16-24563633-C-T		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBBP6	protein_coding	protein_coding	ENST00000319715	18	35171

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.78e-12	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	809	937	0.863	0.0000502	11707
Missense in Polyphen		34	118.27	0.28747		1446
Synonymous	-1.52	367	332	1.11	0.0000174	3433
Loss of Function	8.00	2	78.4	0.0255	0.00000490	1050

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome (PubMed:18851979). May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth (By similarity). Regulates DNA-replication and the stability of chromosomal common fragile sites (CFSs) in a ZBTB38- and MCM10- dependent manner. Controls ZBTB38 protein stability and abundance via ubiquitination and proteasomal degradation, and ZBTB38 in turn negatively regulates the expression of MCM10 which plays an important role in DNA-replication (PubMed:24726359). {ECO:0000250|UniProtKB:P97868, ECO:0000269|PubMed:18851979, ECO:0000269|PubMed:24726359}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.281
• rvis_EVS: -2.12
• rvis_percentile_EVS: 1.53

Haploinsufficiency Scores

• pHI: 0.757
• hipred: Y
• hipred_score: 0.745
• ghis: 0.678

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.753

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbbp6
• Phenotype: growth/size/body region phenotype; cellular phenotype; embryo 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)

Zebrafish Information Network

• Gene name: rbbp6
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: necrotic

Gene ontology

• Biological process: protein polyubiquitination;in utero embryonic development;DNA replication;regulation of DNA replication;mRNA processing;ubiquitin-dependent protein catabolic process;cellular response to DNA damage stimulus;multicellular organism growth;embryonic organ development;somite development
• Cellular component: chromosome;nucleolus;centrosome;cytosol;nuclear speck;protein-containing complex
• Molecular function: RNA binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding;protein kinase binding;ubiquitin protein ligase activity