RBBP9

protein-coding

RB binding protein 9, serine hydrolase

Gene summary

The protein encoded by this gene is a retinoblastoma binding protein that may play a role in the regulation of cell proliferation and differentiation. Two alternatively spliced transcript variants of this gene with identical predicted protein products have been reported, one of which is a nonsense-mediated decay candidate. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006606.3

Inheritance

—

ClinVar variants

U:32B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr20:18,486,540-18,497,225

External References & Databases

Ensembl (ENSG00000089050)

Transcript & Mutation Effects

hg38 • Region Span ~10.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RBBP9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006606.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			31 clinvar			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	32	1	0	33

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006606.3	RefSeq	NP_006597.2	5	MANE Select
ENST00000337227.9	Ensembl	ENSP00000336866.4	5	MANE Select
ENST00000966865.1	Ensembl	ENSP00000636924.1	5	Standard
ENST00000966865.2	Ensembl	ENSP00000636924.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of cell population proliferation

Molecular Function

protein binding
hydrolase activity

Cellular Component

nucleoplasm
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337227
Coding exons: 5
Length: 10704
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125745
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.234	100	107	0.936	0.00000559	1222
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00026	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.973

Gene Damage Prediction

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