RGCC

regulator of cell cycle

Basic information

Region (hg38): 13:41457549-41470871

Previous symbols: [ "C13orf15" ]

Links

ENSG00000102760 ∙ NCBI:28984 ∙ OMIM:610077 ∙ HGNC:20369 ∙ Uniprot:Q9H4X1 ∙ 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 RGCC gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

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

Variants in RGCC

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

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

Position	Type	Phenotype	Significance	ClinVar
13-41458311-G-A		not specified	Uncertain significance (Aug 14, 2023)
13-41458345-C-G		not specified	Uncertain significance (Jun 02, 2023)
13-41466825-G-A		not specified	Uncertain significance (Apr 07, 2023)
13-41466888-T-C		not specified	Uncertain significance (Aug 01, 2022)
13-41466897-G-A		not specified	Uncertain significance (Jan 23, 2024)
13-41470478-G-A		not specified	Uncertain significance (Mar 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGCC	protein_coding	protein_coding	ENST00000379359	5	13324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00481	0.705	124786	0	9	124795	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.704	55	71.8	0.766	0.00000315	887
Missense in Polyphen		24	32.222	0.74484		403
Synonymous	0.609	26	30.3	0.859	0.00000141	254
Loss of Function	0.711	4	5.86	0.683	2.47e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000483	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates the activity of cell cycle-specific kinases. Enhances CDK1 activity. May contribute to the regulation of the cell cycle. May inhibit growth of glioma cells by promoting arrest of mitotic progression at the G2/M transition. Fibrogenic factor contributing to the pathogenesis of renal fibrosis through fibroblast activation. {ECO:0000269|PubMed:11687586, ECO:0000269|PubMed:17146433, ECO:0000269|PubMed:19158077, ECO:0000269|PubMed:22163048}.
• Pathway: TP53 Regulates Transcription of Cell Cycle Genes;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.101

Haploinsufficiency Scores

• pHI: 0.419
• hipred: N
• hipred_score: 0.346
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rgcc
• Phenotype: growth/size/body region phenotype; embryo 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); 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)

Gene ontology

• Biological process: negative regulation of exit from mitosis;negative regulation of endothelial cell proliferation;positive regulation of extracellular matrix constituent secretion;complement activation;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;negative regulation of cell population proliferation;positive regulation of gene expression;positive regulation of epithelial to mesenchymal transition;negative regulation of angiogenesis;activation of protein kinase activity;positive regulation of collagen biosynthetic process;negative regulation of blood vessel endothelial cell migration;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of mitotic nuclear division;positive regulation of transcription by RNA polymerase II;negative regulation of cytokine secretion;positive regulation of cytokine secretion;positive regulation of DNA-binding transcription factor activity;positive regulation of stress fiber assembly;positive regulation of cell cycle arrest;cellular response to hypoxia;mitotic cell cycle arrest;fibroblast activation;negative regulation of fibroblast growth factor production;positive regulation of extracellular matrix assembly;negative regulation of mitotic cell cycle phase transition;negative regulation of cell-cell adhesion mediated by cadherin;positive regulation of endothelial cell apoptotic process;positive regulation of DNA biosynthetic process
• Cellular component: nucleus;nucleolus;cytoplasm;centrosome;cytosol
• Molecular function: protein binding;protein kinase binding;protein kinase activator activity;R-SMAD binding