RCC2
regulator of chromosome condensation 2
Basic information
Region (hg38): 1:17406760-17439677
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCC2 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 | |||||
| missense | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 19 | 1 | 0 |
Variants in RCC2
This is a list of pathogenic ClinVar variants found in the RCC2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-17409147-A-T | not specified | Uncertain significance (Dec 18, 2023) | ||
| 1-17413566-T-C | not specified | Uncertain significance (Apr 12, 2022) | ||
| 1-17413689-A-G | not specified | Uncertain significance (May 10, 2024) | ||
| 1-17413696-G-C | not specified | Uncertain significance (Aug 08, 2023) | ||
| 1-17416566-T-C | not specified | Uncertain significance (Nov 27, 2023) | ||
| 1-17416577-C-T | not specified | Uncertain significance (Nov 06, 2023) | ||
| 1-17420746-T-C | not specified | Uncertain significance (May 07, 2024) | ||
| 1-17420791-C-G | Malignant tumor of prostate | Uncertain significance (-) | ||
| 1-17425613-G-A | not specified | Uncertain significance (Sep 07, 2022) | ||
| 1-17425618-C-T | not specified | Uncertain significance (Nov 17, 2022) | ||
| 1-17425679-A-G | not specified | Uncertain significance (Jan 19, 2022) | ||
| 1-17429142-C-T | not specified | Uncertain significance (Feb 28, 2024) | ||
| 1-17438276-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
| 1-17438277-C-A | not specified | Uncertain significance (Dec 27, 2022) | ||
| 1-17438318-C-T | not specified | Uncertain significance (Apr 09, 2024) | ||
| 1-17438319-C-A | not specified | Uncertain significance (May 05, 2023) | ||
| 1-17438391-A-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 1-17438419-C-T | Likely benign (Sep 01, 2022) | |||
| 1-17438423-G-A | not specified | Uncertain significance (Jan 16, 2024) | ||
| 1-17438469-A-C | not specified | Uncertain significance (Nov 29, 2021) | ||
| 1-17438476-C-G | not specified | Uncertain significance (Jun 22, 2024) | ||
| 1-17438484-A-G | not specified | Uncertain significance (Mar 29, 2023) | ||
| 1-17438495-G-C | not specified | Uncertain significance (Nov 09, 2023) | ||
| 1-17438498-G-A | not specified | Uncertain significance (Mar 29, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RCC2 | protein_coding | protein_coding | ENST00000375436 | 12 | 32965 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.956 | 0.0443 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.09 | 139 | 286 | 0.486 | 0.0000171 | 3331 |
| Missense in Polyphen | 24 | 84.188 | 0.28508 | 924 | ||
| Synonymous | -0.664 | 123 | 114 | 1.08 | 0.00000721 | 1037 |
| Loss of Function | 4.14 | 4 | 27.4 | 0.146 | 0.00000149 | 299 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000551 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.0000551 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Multifunctional protein that may effect its functions by regulating the activity of small GTPases, such as RAC1 and RALA (PubMed:12919680, PubMed:25074804, PubMed:26158537, PubMed:28869598). Required for normal progress through the cell cycle, both during interphase and during mitosis (PubMed:23388455, PubMed:12919680, PubMed:26158537). Required for the presence of normal levels of MAD2L1, AURKB and BIRC5 on inner centromeres during mitosis, and for normal attachment of kinetochores to mitotic spindles (PubMed:12919680, PubMed:26158537). Required for normal organization of the microtubule cytoskeleton in interphase cells (PubMed:23388455). Functions as guanine nucleotide exchange factor (GEF) for RALA (PubMed:26158537). Interferes with the activation of RAC1 by guanine nucleotide exchange factors (PubMed:25074804). Prevents accumulation of active, GTP-bound RAC1, and suppresses RAC1-mediated reorganization of the actin cytoskeleton and formation of membrane protrusions (PubMed:25074804, PubMed:28869598). Required for normal cellular responses to contacts with the extracellular matrix of adjacent cells, and for directional cell migration in response to a fibronectin gradient (in vitro) (PubMed:25074804, PubMed:28869598). {ECO:0000269|PubMed:12919680, ECO:0000269|PubMed:23388455, ECO:0000269|PubMed:25074804, ECO:0000269|PubMed:26158537, ECO:0000269|PubMed:28869598}.;
- Pathway
- Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic
(Consensus)
Intolerance Scores
- loftool
- 0.225
- rvis_EVS
- -0.67
- rvis_percentile_EVS
- 15.62
Haploinsufficiency Scores
- pHI
- 0.503
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.644
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rcc2
- 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); homeostasis/metabolism phenotype; vision/eye phenotype; hematopoietic system phenotype; pigmentation 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);
Zebrafish Information Network
- Gene name
- rcc2
- Affected structure
- pharyngeal arch 1
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- cell cycle;integrin-mediated signaling pathway;regulation of fibroblast migration;positive regulation of G2/M transition of mitotic cell cycle;regulation of cell migration;negative regulation of GTPase activity;establishment of protein localization;focal adhesion assembly;cell division;negative regulation of focal adhesion assembly;positive regulation of attachment of spindle microtubules to kinetochore;chromosome passenger complex localization to kinetochore;activation of GTPase activity;negative regulation of substrate adhesion-dependent cell spreading;regulation of ruffle assembly
- Cellular component
- nucleolus;cytosol;microtubule;plasma membrane;membrane;midbody;early endosome membrane;chromosome, centromeric core domain;mitotic spindle midzone
- Molecular function
- RNA binding;guanyl-nucleotide exchange factor activity;protein binding;microtubule binding;protein kinase binding;protein domain specific binding;small GTPase binding;Rac GTPase binding