RBBP7

Basic information

Region (hg38): X:16839283-16870362

Links

ENSG00000102054

∙ NCBI:5931 ∙ OMIM:300825 ∙ HGNC:9890 ∙ Uniprot:Q16576 ∙ 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 RBBP7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBBP7 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 clinvar	1
missense			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2 clinvar		2
Total	0	0	5	2	1

Variants in RBBP7

This is a list of pathogenic ClinVar variants found in the RBBP7 region.

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

Position	Phenotype	Significance	ClinVar
X-16841437-C-T	not specified	Uncertain significance (Jun 07, 2024)	3330351
X-16841458-C-G	not specified	Uncertain significance (Aug 19, 2024)	2350265
X-16841525-A-G	not specified	Uncertain significance (Jan 16, 2024)	3185124
X-16841526-T-C		Likely benign (Feb 01, 2023)	2660069
X-16841596-G-C	not specified	Uncertain significance (Nov 08, 2024)	3464641
X-16841675-C-T	not specified	Likely benign (Mar 31, 2024)	3330353
X-16841706-A-C		Benign (Nov 15, 2018)	714920
X-16841722-C-T	not specified	Uncertain significance (Nov 11, 2024)	3464637
X-16841726-C-G	not specified	Uncertain significance (Oct 03, 2024)	3464639
X-16841738-C-A	not specified	Uncertain significance (Jan 23, 2024)	3185126
X-16841740-G-C	not specified	Uncertain significance (Jun 06, 2023)	2513139
X-16841756-C-T	not specified	Uncertain significance (Sep 24, 2024)	3464640
X-16841757-G-T		Likely benign (Feb 01, 2023)	2660070
X-16845050-C-G	not specified	Uncertain significance (Aug 26, 2022)	2308947
X-16845071-A-T	not specified	Uncertain significance (Feb 14, 2024)	3152068
X-16845836-A-AT	SPERMATOGENIC FAILURE, X-LINKED, 9	Pathogenic (Jan 08, 2025)	3544365
X-16845886-T-C	not specified	Uncertain significance (Oct 22, 2024)	3431009
X-16852607-G-A	not specified	Uncertain significance (Sep 03, 2024)	3431011
X-16852820-T-C	not specified	Uncertain significance (Apr 13, 2022)	2284233
X-16852835-A-C	not specified	Uncertain significance (Apr 17, 2024)	3313110
X-16852858-T-C	not specified	Uncertain significance (Oct 19, 2024)	3431013
X-16862958-C-T	not specified	Uncertain significance (Oct 07, 2024)	3431012
X-16863002-T-C	not specified	Uncertain significance (Sep 30, 2021)	2411468
X-16869171-G-T		Benign (May 18, 2018)	716899
X-16869191-T-C		Uncertain significance (Jan 01, 2023)	2660071

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBBP7	protein_coding	protein_coding	ENST00000380084	12	31132

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0161	112025	0	1	112026	0.00000446

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.79	72	176	0.409	0.0000132	3090
Missense in Polyphen		18	82.883	0.21717		1392
Synonymous	-0.805	75	66.6	1.13	0.00000531	887
Loss of Function	3.59	1	17.0	0.0590	0.00000113	301

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)	0.0000130	0.00000944
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Core histone-binding subunit that may target chromatin remodeling factors, histone acetyltransferases and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the type B histone acetyltransferase (HAT) complex, which is required for chromatin assembly following DNA replication; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; and the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex. {ECO:0000269|PubMed:10866654}.;
Pathway: Retinoblastoma (RB) in Cancer;Interactome of polycomb repressive complex 2 (PRC2);ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);the prc2 complex sets long-term gene silencing through modification of histone tails;Transcriptional Regulation by E2F6;Generic Transcription Pathway;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Post-translational protein modification;HDACs deacetylate histones;Metabolism of proteins;RNA Polymerase I Promoter Clearance;PKMTs methylate histone lysines;RNA Polymerase II Transcription;RMTs methylate histone arginines;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;Nucleosome assembly;HATs acetylate histones;Cellular responses to external stimuli;Chromosome Maintenance;EGFR1;Regulation of PTEN gene transcription;Neddylation;PTEN Regulation;PIP3 activates AKT signaling;Deposition of new CENPA-containing nucleosomes at the centromere;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle;Intracellular signaling by second messengers;Regulation of Telomerase;Signaling events mediated by HDAC Class I;Hedgehog signaling events mediated by Gli proteins;Regulation of nuclear SMAD2/3 signaling;PRC2 methylates histones and DNA (Consensus)

Recessive Scores

pRec: 0.314

Intolerance Scores

loftool: 0.112
rvis_EVS: -0.14
rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

pHI: 0.970
hipred: Y
hipred_score: 0.776
ghis: 0.636

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.437

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rbbp7
Phenotype: growth/size/body region phenotype; craniofacial phenotype; embryo phenotype; skeleton phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;DNA replication;multicellular organism development;cell population proliferation;histone deacetylation;negative regulation of cell growth;CENP-A containing nucleosome assembly;post-translational protein modification;negative regulation of gene expression, epigenetic;response to steroid hormone;negative regulation of G0 to G1 transition;cellular heat acclimation
Cellular component: nucleus;nucleoplasm;cytosol;NuRD complex;ESC/E(Z) complex
Molecular function: RNA binding;histone deacetylase activity;protein binding