RCC1
Basic information
Region (hg38): 1:28505943-28539300
Previous symbols: [ "CHC1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- See_cases (7 variants)
- INFECTION-INDUCED_ACUTE-ONSET_AXONAL_NEUROPATHY (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001381865.2. 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 | 0 | |||||
| missense | 35 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 3 | 35 | 1 | 0 |
Highest pathogenic variant AF is 0.000017348697
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RCC1 | protein_coding | protein_coding | ENST00000373831 | 10 | 33358 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.931 | 0.0689 | 124495 | 0 | 3 | 124498 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.68 | 201 | 280 | 0.717 | 0.0000168 | 2910 |
| Missense in Polyphen | 42 | 79.063 | 0.53122 | 766 | ||
| Synonymous | 0.390 | 110 | 115 | 0.954 | 0.00000723 | 936 |
| Loss of Function | 3.72 | 3 | 21.7 | 0.138 | 0.00000111 | 243 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Guanine-nucleotide releasing factor that promotes the exchange of Ran-bound GDP by GTP, and thereby plays an important role in RAN-mediated functions in nuclear import and mitosis (PubMed:1944575, PubMed:17435751, PubMed:20668449, PubMed:22215983, PubMed:11336674). Contributes to the generation of high levels of chromosome-associated, GTP-bound RAN, which is important for mitotic spindle assembly and normal progress through mitosis (PubMed:12194828, PubMed:17435751, PubMed:22215983). Via its role in maintaining high levels of GTP-bound RAN in the nucleus, contributes to the release of cargo proteins from importins after nuclear import (PubMed:22215983). Involved in the regulation of onset of chromosome condensation in the S phase (PubMed:3678831). Binds both to the nucleosomes and double- stranded DNA (PubMed:17435751, PubMed:18762580). {ECO:0000269|PubMed:11336674, ECO:0000269|PubMed:12194828, ECO:0000269|PubMed:17435751, ECO:0000269|PubMed:18762580, ECO:0000269|PubMed:1944575, ECO:0000269|PubMed:20668449, ECO:0000269|PubMed:22215983, ECO:0000269|PubMed:3678831}.;
- Pathway
- Disease;role of ran in mitotic spindle regulation;cycling of ran in nucleocytoplasmic transport;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;Infectious disease;mechanism of protein import into the nucleus;Nuclear import of Rev protein;Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.371
Intolerance Scores
- loftool
- 0.121
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.54
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.736
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rcc1
- Phenotype
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;mitotic spindle organization;chromosome segregation;regulation of mitotic nuclear division;viral process;spindle assembly;protein heterotetramerization;cell division
- Cellular component
- chromatin;nuclear chromatin;condensed nuclear chromosome;nucleus;nucleoplasm;cytoplasm;nuclear membrane;protein-containing complex
- Molecular function
- chromatin binding;Ran guanyl-nucleotide exchange factor activity;protein binding;Ran GTPase binding;nucleosome binding;nucleosomal DNA binding;histone binding;sulfate binding;protein heterodimerization activity