RBBP5

RB binding protein 5, histone lysine methyltransferase complex subunit, the group of WD repeat domain containing|WRAD complex

Basic information

Region (hg38): 1:205086142-205122015

Links

ENSG00000117222 ∙ NCBI:5929 ∙ OMIM:600697 ∙ HGNC:9888 ∙ Uniprot:Q15291 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBBP5 gene.

• not_specified (14 variants)
• not_provided (3 variants)
• RBBP5-related_syndromic_neurodevelopmental_condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBBP5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005057.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense	1		14			15
nonsense	1					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	2	0	14	1	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBBP5	protein_coding	protein_coding	ENST00000264515	14	35874

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000192	125726	0	2	125728	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.59	119	292	0.408	0.0000151	3508
Missense in Polyphen		21	107.25	0.1958		1352
Synonymous	0.804	100	111	0.903	0.00000630	1029
Loss of Function	5.02	2	33.3	0.0601	0.00000195	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In embryonic stem (ES) cells, plays a crucial role in the differentiation potential, particularly along the neural lineage, regulating gene induction and H3 'Lys-4' methylation at key developmental loci, including that mediated by retinoic acid (By similarity). As part of the MLL1/MLL complex, involved in mono-, di- and trimethylation at 'Lys-4' of histone H3. Histone H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. {ECO:0000250, ECO:0000269|PubMed:19556245}.
• Pathway: Cushing,s syndrome - Homo sapiens (human);Signaling by WNT;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;PKMTs methylate histone lysines;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Chromatin modifying enzymes;Neddylation;Chromatin organization;Transcriptional regulation by RUNX1;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.106
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.426
• hipred: Y
• hipred_score: 0.808
• ghis: 0.601

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbbp5

Gene ontology

• Biological process: cellular response to DNA damage stimulus;response to estrogen;post-translational protein modification;regulation of megakaryocyte differentiation;histone H3-K4 methylation;beta-catenin-TCF complex assembly
• Cellular component: nucleus;nucleoplasm;nucleolus;histone methyltransferase complex;MLL3/4 complex;Set1C/COMPASS complex;MLL1 complex
• Molecular function: protein binding;histone-lysine N-methyltransferase activity;methylated histone binding;histone methyltransferase activity (H3-K4 specific);transcription regulatory region DNA binding