GeneBe

RRM1

ribonucleotide reductase catalytic subunit M1

Basic information

Region (hg38): 11:4094707-4138932

Links

ENSG00000167325 ∙ NCBI:6240 ∙ OMIM:180410 ∙ HGNC:10451 ∙ Uniprot:P23921 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 6ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Musculoskeletal35617047

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RRM1 gene.

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
clinvar
 2
missense
26
clinvar
1
clinvar
 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)2672455
11-4102062-A-G not specified Uncertain significance (Sep 08, 2024)3435572
11-4106058-A-G not specified Uncertain significance (Jan 02, 2024)3156447
11-4106068-T-C not specified Uncertain significance (Jun 05, 2024)3315431
11-4106088-G-A not specified Uncertain significance (Aug 05, 2024)3435574
11-4107452-T-C not specified Uncertain significance (Sep 07, 2022)2311341
11-4107453-A-G not specified Uncertain significance (Feb 13, 2024)3156453
11-4107509-T-C Benign (Dec 31, 2019)731616
11-4107515-A-G not specified Uncertain significance (Sep 29, 2023)3156454
11-4109644-C-T not specified Uncertain significance (Oct 12, 2021)2338175
11-4109687-A-G not specified Uncertain significance (Dec 20, 2023)3156455
11-4111632-A-G not specified Uncertain significance (Jan 31, 2024)3156456
11-4111955-A-C not specified Uncertain significance (Dec 12, 2023)3156457
11-4112041-C-G not specified Uncertain significance (Jan 02, 2024)3156458
11-4119881-A-G not specified Uncertain significance (Nov 08, 2022)2209447
11-4123205-C-T Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 6 Pathogenic (Dec 07, 2023)2664486
11-4123206-G-A RRM1-related disorder • Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 6 Conflicting classifications of pathogenicity (Dec 19, 2024)2444243
11-4123302-G-A not specified Uncertain significance (Oct 05, 2023)3156449
11-4126684-G-A not specified Uncertain significance (Jul 31, 2023)2599706
11-4126787-G-A not specified Uncertain significance (Jun 16, 2024)3315432
11-4126790-A-G not specified Uncertain significance (Dec 03, 2024)3435578
11-4127053-C-T not specified Uncertain significance (Sep 20, 2023)3156450
11-4127054-G-A Likely benign (Dec 31, 2019)776564
11-4127105-T-G not specified Uncertain significance (Apr 23, 2024)3315430
11-4127116-C-T not specified Uncertain significance (Oct 25, 2023)3156451

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RRM1protein_codingprotein_codingENST00000300738 1944170
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.002.87e-7125738051257430.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.991964290.4570.00002195249
Missense in Polyphen31169.410.182992108
Synonymous-0.2861501461.030.000007211442
Loss of Function6.16146.20.02160.00000252544

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00004430.0000440
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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