RRM1
Basic information
Region (hg38): 11:4094706-4138932
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 6 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Biochemical; Musculoskeletal | 35617047 |
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 RRM1 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 | 2 | |||||
missense | 26 | 27 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 26 | 1 | 2 |
Variants in RRM1
This is a list of pathogenic ClinVar variants found in the RRM1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-4102031-T-C | Uncertain significance (Jun 01, 2024) | |||
11-4106058-A-G | not specified | Uncertain significance (Jan 02, 2024) | ||
11-4106068-T-C | not specified | Uncertain significance (Jun 05, 2024) | ||
11-4107452-T-C | not specified | Uncertain significance (Sep 07, 2022) | ||
11-4107453-A-G | not specified | Uncertain significance (Feb 13, 2024) | ||
11-4107509-T-C | Benign (Dec 31, 2019) | |||
11-4107515-A-G | not specified | Uncertain significance (Sep 29, 2023) | ||
11-4109644-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
11-4109687-A-G | not specified | Uncertain significance (Dec 20, 2023) | ||
11-4111632-A-G | not specified | Uncertain significance (Jan 31, 2024) | ||
11-4111955-A-C | not specified | Uncertain significance (Dec 12, 2023) | ||
11-4112041-C-G | not specified | Uncertain significance (Jan 02, 2024) | ||
11-4119881-A-G | not specified | Uncertain significance (Nov 08, 2022) | ||
11-4123205-C-T | Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 6 | Pathogenic (Dec 07, 2023) | ||
11-4123206-G-A | RRM1-related disorder • Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 6 | Uncertain significance (Feb 23, 2023) | ||
11-4123302-G-A | not specified | Uncertain significance (Oct 05, 2023) | ||
11-4126684-G-A | not specified | Uncertain significance (Jul 31, 2023) | ||
11-4126787-G-A | not specified | Uncertain significance (Jun 16, 2024) | ||
11-4127053-C-T | not specified | Uncertain significance (Sep 20, 2023) | ||
11-4127054-G-A | Likely benign (Dec 31, 2019) | |||
11-4127105-T-G | not specified | Uncertain significance (Apr 23, 2024) | ||
11-4127116-C-T | not specified | Uncertain significance (Oct 25, 2023) | ||
11-4127117-C-G | not specified | Uncertain significance (Mar 01, 2024) | ||
11-4127126-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
11-4127204-C-G | not specified | Uncertain significance (Feb 23, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RRM1 | protein_coding | protein_coding | ENST00000300738 | 19 | 44170 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 2.87e-7 | 125738 | 0 | 5 | 125743 | 0.0000199 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.99 | 196 | 429 | 0.457 | 0.0000219 | 5249 |
Missense in Polyphen | 31 | 169.41 | 0.18299 | 2108 | ||
Synonymous | -0.286 | 150 | 146 | 1.03 | 0.00000721 | 1442 |
Loss of Function | 6.16 | 1 | 46.2 | 0.0216 | 0.00000252 | 544 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000443 | 0.0000440 |
Middle Eastern | 0.00 | 0.00 |
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.;
- Pathway
- Pyrimidine metabolism - 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;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;Gemcitabine Action Pathway;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gemcitabine Metabolism Pathway;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Fluoropyrimidine Activity;Retinoblastoma (RB) in Cancer;Pyrimidine metabolism;Nucleotide Metabolism;pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Metabolism;Purine nucleotides nucleosides metabolism;superpathway of purine nucleotide salvage;Pyrimidine nucleotides nucleosides metabolism;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;pyrimidine deoxyribonucleotides biosynthesis from CTP;guanosine deoxyribonucleotides <i>de novo</i> biosynthesis;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
- 0.352
Intolerance Scores
- loftool
- 0.149
- rvis_EVS
- -0.64
- rvis_percentile_EVS
- 16.53
Haploinsufficiency Scores
- pHI
- 0.991
- hipred
- Y
- hipred_score
- 0.859
- ghis
- 0.699
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.982
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rrm1
- 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
- rrm1
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- sigmoid
Gene ontology
- Biological process
- mitotic cell cycle;pyrimidine nucleobase metabolic process;DNA replication;male gonad development;deoxyribonucleotide biosynthetic process;response to ionizing radiation;cell proliferation in forebrain;protein heterotetramerization;oxidation-reduction process;retina development in camera-type eye
- Cellular component
- nuclear envelope;cytosol;ribonucleoside-diphosphate reductase complex;cell projection;neuronal cell body
- Molecular function
- ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor;protein binding;ATP binding;identical protein binding;disordered domain specific binding