RBL1

RB transcriptional corepressor like 1

Basic information

Region (hg38): 20:36996348-37095997

Links

ENSG00000080839 ∙ NCBI:5933 ∙ OMIM:116957 ∙ HGNC:9893 ∙ Uniprot:P28749 ∙ 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 RBL1 gene.

• Inborn genetic diseases (33 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBL1 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			32	1	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	32	1	2

Variants in RBL1

This is a list of pathogenic ClinVar variants found in the RBL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36998805-A-G		not specified	Uncertain significance (Jun 10, 2022)
20-37007537-T-A			Benign (May 25, 2018)
20-37018330-C-A		not specified	Likely benign (Dec 14, 2021)
20-37020697-T-A		not specified	Uncertain significance (Jun 22, 2023)
20-37020730-C-T		not specified	Uncertain significance (Mar 07, 2023)
20-37022736-C-T		not specified	Uncertain significance (Feb 10, 2022)
20-37022748-A-G		not specified	Uncertain significance (Feb 17, 2024)
20-37032835-A-C		not specified	Uncertain significance (Nov 30, 2021)
20-37032855-T-G		not specified	Uncertain significance (Jul 12, 2023)
20-37032865-C-T		not specified	Uncertain significance (Dec 20, 2023)
20-37035236-C-T			Likely benign (May 25, 2018)
20-37035254-T-C		not specified	Uncertain significance (Mar 08, 2024)
20-37035268-C-T		not specified	Uncertain significance (Jun 05, 2023)
20-37035290-C-T		not specified	Uncertain significance (Feb 28, 2023)
20-37035379-C-T		not specified	Uncertain significance (Oct 06, 2022)
20-37040158-C-T		not specified	Uncertain significance (Nov 15, 2021)
20-37040216-T-C		not specified	Uncertain significance (Jan 05, 2022)
20-37040264-C-T		not specified	Uncertain significance (Jan 10, 2023)
20-37044100-G-A		not specified	Uncertain significance (May 05, 2023)
20-37044118-C-A		not specified	Uncertain significance (Feb 14, 2024)
20-37044204-A-G		not specified	Uncertain significance (Jan 17, 2024)
20-37047071-T-G		not specified	Uncertain significance (Nov 09, 2022)
20-37047099-G-C			Benign (Dec 31, 2019)
20-37047150-G-A		not specified	Uncertain significance (Dec 12, 2023)
20-37047163-G-A		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBL1	protein_coding	protein_coding	ENST00000373664	22	99647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.93e-12	1.00	125626	0	122	125748	0.000485

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	492	574	0.857	0.0000301	7006
Missense in Polyphen		167	218.87	0.76301		2679
Synonymous	1.05	178	197	0.905	0.0000100	2027
Loss of Function	3.28	28	54.0	0.518	0.00000297	687

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000735	0.000722
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.0000962	0.0000924
European (Non-Finnish)	0.000729	0.000721
Middle Eastern	0.000490	0.000489
South Asian	0.000165	0.000163
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Key regulator of entry into cell division. Directly involved in heterochromatin formation by maintaining overall chromatin structure and, in particular, that of constitutive heterochromatin by stabilizing histone methylation. Recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. Controls histone H4 'Lys- 20' trimethylation. Probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. Potent inhibitor of E2F-mediated trans-activation. Forms a complex with adenovirus E1A and with SV40 large T antigen. May bind and modulate functionally certain cellular proteins with which T and E1A compete for pocket binding. May act as a tumor suppressor.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Cell cycle - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Cell Cycle;Mitotic G1-G1-S phases;Adipogenesis;TGF-beta Signaling Pathway;G1 to S cell cycle control;ID signaling pathway;Signal Transduction;Gene expression (Transcription);cyclins and cell cycle regulation;mets affect on macrophage differentiation;Generic Transcription Pathway;RNA Polymerase II Transcription;Transcription of E2F targets under negative control by DREAM complex;Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1;G0 and Early G1;Cyclin D associated events in G1;G1 Phase;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Mitotic G1-G1/S phases;TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest;TGF_beta_Receptor;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Cell Cycle;Signaling by TGF-beta Receptor Complex;ID;Signaling by TGF-beta family members;Cell Cycle, Mitotic;Validated targets of C-MYC transcriptional repression;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.208

Intolerance Scores

• loftool: 0.116
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.98

Haploinsufficiency Scores

• pHI: 0.833
• hipred: Y
• hipred_score: 0.706
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.774

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbl1
• Phenotype: craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; reproductive system 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); normal phenotype; vision/eye phenotype; digestive/alimentary phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;cell cycle;regulation of mitotic cell cycle;negative regulation of gene expression;viral process;cell differentiation;regulation of lipid kinase activity;positive regulation of transcription by RNA polymerase II;regulation of cell division;negative regulation of G1/S transition of mitotic cell cycle;negative regulation of cellular senescence
• Cellular component: chromatin;nucleus;nucleoplasm;transcription factor complex
• Molecular function: RNA polymerase II regulatory region DNA binding;RNA polymerase II activating transcription factor binding;protein binding;transcription factor binding;promoter-specific chromatin binding