RBBP9

RB binding protein 9, serine hydrolase

Basic information

Region (hg38): 20:18486540-18497225

Links

ENSG00000089050 ∙ NCBI:10741 ∙ OMIM:602908 ∙ HGNC:9892 ∙ Uniprot:O75884 ∙ 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 RBBP9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBBP9 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in RBBP9

This is a list of pathogenic ClinVar variants found in the RBBP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-18489793-C-T		not specified	Uncertain significance (Nov 09, 2021)
20-18489806-T-G		not specified	Uncertain significance (Jun 06, 2023)
20-18489810-T-C		not specified	Uncertain significance (Feb 07, 2025)
20-18489875-G-A			Likely benign (Jun 01, 2022)
20-18489907-A-G		not specified	Uncertain significance (Feb 22, 2023)
20-18489960-T-C		not specified	Uncertain significance (Jan 31, 2024)
20-18490400-G-C		not specified	Uncertain significance (Jun 26, 2024)
20-18490403-C-A		not specified	Uncertain significance (Aug 28, 2024)
20-18490403-C-G		not specified	Uncertain significance (Jan 19, 2024)
20-18490436-G-A		not specified	Uncertain significance (May 10, 2023)
20-18493967-G-A		not specified	Uncertain significance (Jul 30, 2024)
20-18493968-C-T		not specified	Uncertain significance (Oct 17, 2023)
20-18493980-A-G		not specified	Uncertain significance (Jan 17, 2025)
20-18493991-A-G		not specified	Uncertain significance (Feb 26, 2025)
20-18494015-T-C		not specified	Uncertain significance (Apr 25, 2022)
20-18494036-G-C		not specified	Uncertain significance (May 24, 2023)
20-18494051-T-C		not specified	Uncertain significance (Dec 02, 2024)
20-18494057-G-C		not specified	Uncertain significance (Jun 26, 2024)
20-18497119-C-A		not specified	Uncertain significance (Mar 24, 2023)
20-18497122-C-T		not specified	Uncertain significance (Jul 02, 2024)
20-18497143-T-C		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBBP9	protein_coding	protein_coding	ENST00000337227	5	10704

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0486	0.931	125715	0	30	125745	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.234	100	107	0.936	0.00000559	1222
Missense in Polyphen		38	44.009	0.86346		500
Synonymous	0.973	33	40.9	0.806	0.00000232	344
Loss of Function	2.01	4	11.3	0.354	6.45e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000261	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the transformation process due to its capacity to confer resistance to the growth-inhibitory effects of TGF-beta1 through interaction with retinoblastoma and the subsequent displacement of E2F-1.

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.389
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.275
• hipred: N
• hipred_score: 0.369
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbbp9

Gene ontology

• Biological process: regulation of cell population proliferation
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: protein binding;hydrolase activity