RB1CC1
RB1 inducible coiled-coil 1, the group of Protein phosphatase 1 regulatory subunits|Autophagy related
Basic information
Region (hg38): 8:52622458-52745843
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Schizophrenia | AD | General | Evidence or clinical applicability is unclear | Neurologic | 21822266 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (165 variants)
- not_provided (20 variants)
- Familial_cancer_of_breast (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RB1CC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014781.5. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 14 | |||||
| missense | 155 | 10 | 165 | |||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 156 | 16 | 8 |
Highest pathogenic variant AF is 7.17637e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RB1CC1 | protein_coding | protein_coding | ENST00000025008 | 22 | 123388 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 2.61e-9 | 125725 | 0 | 20 | 125745 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.812 | 709 | 772 | 0.918 | 0.0000376 | 10522 |
| Missense in Polyphen | 210 | 320.61 | 0.655 | 4464 | ||
| Synonymous | -1.65 | 307 | 272 | 1.13 | 0.0000136 | 2841 |
| Loss of Function | 7.57 | 5 | 76.4 | 0.0654 | 0.00000404 | 1030 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000188 | 0.000181 |
| Ashkenazi Jewish | 0.000100 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000937 | 0.0000924 |
| European (Non-Finnish) | 0.0000892 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000337 | 0.0000327 |
| Other | 0.000356 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in autophagy (PubMed:21775823). Regulates early events but also late events of autophagosome formation through direct interaction with Atg16L1 (PubMed:23392225). Required for the formation of the autophagosome-like double-membrane structure that surrounds the Salmonella-containing vacuole (SCV) during S.typhimurium infection and subsequent xenophagy (By similarity). Involved in repair of DNA damage caused by ionizing radiation, which subsequently improves cell survival by decreasing apoptosis (By similarity). Inhibits PTK2/FAK1 and PTK2B/PYK2 kinase activity, affecting their downstream signaling pathways (PubMed:10769033, PubMed:12221124). Plays a role as a modulator of TGF-beta-signaling by restricting substrate specificity of RNF111 (By similarity). Functions as a DNA-binding transcription factor (PubMed:12095676). Is a potent regulator of the RB1 pathway through induction of RB1 expression (PubMed:14533007). Plays a crucial role in muscular differentiation (PubMed:12163359). Plays an indispensable role in fetal hematopoiesis and in the regulation of neuronal homeostasis (By similarity). {ECO:0000250|UniProtKB:Q9ESK9, ECO:0000269|PubMed:10769033, ECO:0000269|PubMed:12095676, ECO:0000269|PubMed:12163359, ECO:0000269|PubMed:12221124, ECO:0000269|PubMed:14533007, ECO:0000269|PubMed:21775823, ECO:0000269|PubMed:23392225}.;
- Pathway
- Autophagy - animal - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);PI3K-AKT-mTOR signaling pathway and therapeutic opportunities;Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli;mTOR signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.215
Intolerance Scores
- loftool
- 0.345
- rvis_EVS
- -1.59
- rvis_percentile_EVS
- 3.11
Haploinsufficiency Scores
- pHI
- 0.820
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.607
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.251
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rb1cc1
- Phenotype
- immune system phenotype; digestive/alimentary 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); normal phenotype; 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); liver/biliary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; 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);
Zebrafish Information Network
- Gene name
- rb1cc1
- Affected structure
- optic cup
- Phenotype tag
- abnormal
- Phenotype quality
- decreased frequency
Gene ontology
- Biological process
- autophagosome assembly;autophagy of mitochondrion;liver development;positive regulation of protein phosphorylation;autophagy;cell cycle;heart development;macroautophagy;regulation of macroautophagy;autophagy of peroxisome;piecemeal microautophagy of the nucleus;positive regulation of cell size;positive regulation of JNK cascade;reticulophagy;glycophagy;negative regulation of extrinsic apoptotic signaling pathway
- Cellular component
- phagophore assembly site;lysosome;endoplasmic reticulum membrane;cytosol;extrinsic component of membrane;nuclear membrane;phagophore assembly site membrane;Atg1/ULK1 kinase complex
- Molecular function
- protein binding;protein kinase binding;protein-containing complex scaffold activity