RRM2
ribonucleotide reductase regulatory subunit M2
Basic information
Region (hg38): 2:10120698-10211725
Previous symbols: [ "C2orf48" ]
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 RRM2 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 1 |
Variants in RRM2
This is a list of pathogenic ClinVar variants found in the RRM2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-10122769-C-G | not specified | Uncertain significance (Feb 01, 2025) | ||
| 2-10122775-G-T | not specified | Uncertain significance (Jun 02, 2023) | ||
| 2-10122837-C-G | not specified | Uncertain significance (Dec 26, 2023) | ||
| 2-10122846-G-A | Benign (Jan 22, 2018) | |||
| 2-10122887-A-G | not specified | Uncertain significance (May 08, 2024) | ||
| 2-10123390-A-G | not specified | Uncertain significance (Apr 20, 2023) | ||
| 2-10123478-A-G | not specified | Uncertain significance (Dec 28, 2022) | ||
| 2-10123851-T-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 2-10124766-A-G | not specified | Uncertain significance (Jan 01, 2025) | ||
| 2-10124835-A-G | not specified | Uncertain significance (Jan 22, 2024) | ||
| 2-10126888-A-G | not specified | Uncertain significance (Jan 01, 2025) | ||
| 2-10126894-A-G | not specified | Uncertain significance (Dec 05, 2024) | ||
| 2-10126901-C-T | not specified | Uncertain significance (Aug 23, 2021) | ||
| 2-10142258-A-T | Inborn genetic diseases | Uncertain significance (Oct 19, 2021) | ||
| 2-10210386-C-A | not specified | Uncertain significance (Aug 10, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RRM2 | protein_coding | protein_coding | ENST00000360566 | 10 | 9091 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.745 | 0.255 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.34 | 146 | 250 | 0.584 | 0.0000119 | 2938 |
| Missense in Polyphen | 28 | 95.848 | 0.29213 | 1229 | ||
| Synonymous | -1.12 | 106 | 92.3 | 1.15 | 0.00000458 | 831 |
| Loss of Function | 3.56 | 4 | 22.1 | 0.181 | 0.00000104 | 258 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000112 | 0.0000906 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. Inhibits Wnt signaling.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Gemcitabine Pathway, Pharmacodynamics;Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Pyrimidine Metabolism;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);Gemcitabine Action Pathway;MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gemcitabine Metabolism Pathway;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Fluoropyrimidine Activity;Mitotic G1-G1-S phases;Retinoblastoma (RB) in Cancer;Hepatitis C and Hepatocellular Carcinoma;Pyrimidine metabolism;Nucleotide Metabolism;pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;RNA Polymerase II Transcription;Metabolism;Activation of E2F1 target genes at G1/S;G1/S-Specific Transcription;Mitotic G1-G1/S phases;Purine nucleotides nucleosides metabolism;superpathway of purine nucleotide salvage;Pyrimidine nucleotides nucleosides metabolism;G1/S Transition;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;pyrimidine deoxyribonucleotides biosynthesis from CTP;guanosine deoxyribonucleotides <i>de novo</i> biosynthesis;Cell Cycle;Cell Cycle, Mitotic;guanosine nucleotides <i>de novo</i> biosynthesis;adenosine deoxyribonucleotides <i>de novo</i> biosynthesis;purine nucleotides <i>de novo</i> biosynthesis;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.216
Intolerance Scores
- loftool
- 0.164
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.75
Haploinsufficiency Scores
- pHI
- 0.984
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.707
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.990
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rrm2
- Phenotype
- skeleton 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);
Zebrafish Information Network
- Gene name
- rrm2
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- necrotic
Gene ontology
- Biological process
- regulation of transcription involved in G1/S transition of mitotic cell cycle;DNA replication;deoxyribonucleotide biosynthetic process;oxidation-reduction process;negative regulation of G0 to G1 transition
- Cellular component
- cytosol
- Molecular function
- ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor;protein binding;metal ion binding