RRM1

ribonucleotide reductase catalytic subunit M1

Basic information

Region (hg38): 11:4094706-4138932

Links

ENSG00000167325

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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Inborn genetic diseases (8 variants)
not provided (3 variants)
RRM1-related disorder (1 variants)

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding						0
Total	0	0	9	1	2

Variants in RRM1

This is a list of pathogenic ClinVar variants found in the RRM1 region.

Position	Phenotype	Significance	ClinVar
11-4107452-T-C	Inborn genetic diseases	Uncertain significance (Sep 07, 2022)	link
11-4107509-T-C		Benign (Dec 31, 2019)	link
11-4109644-C-T	Inborn genetic diseases	Uncertain significance (Oct 12, 2021)	link
11-4119881-A-G	Inborn genetic diseases	Uncertain significance (Nov 08, 2022)	link
11-4123206-G-A	RRM1-related disorder	Uncertain significance (Feb 23, 2023)	link
11-4126684-G-A	Inborn genetic diseases	Uncertain significance (Jul 31, 2023)	link
11-4127054-G-A		Likely benign (Dec 31, 2019)	link
11-4127126-G-A	Inborn genetic diseases	Uncertain significance (Jan 26, 2022)	link
11-4127204-C-G	Inborn genetic diseases	Uncertain significance (Feb 23, 2023)	link
11-4127223-C-T		Benign (Jan 02, 2019)	link
11-4127245-G-C	Inborn genetic diseases	Uncertain significance (Jun 13, 2023)	link
11-4129084-A-G	Inborn genetic diseases	Uncertain significance (Sep 06, 2022)	link
11-4129128-G-T	Inborn genetic diseases	Uncertain significance (Jul 15, 2021)	link
11-4133621-T-C	Inborn genetic diseases	Uncertain significance (Oct 27, 2022)	link
11-4135094-A-G	Inborn genetic diseases	Uncertain significance (Oct 26, 2021)	link
11-4135149-C-G	Inborn genetic diseases	Uncertain significance (Feb 15, 2023)	link
11-4138265-A-C	Inborn genetic diseases	Uncertain significance (Jun 07, 2023)	link

GnomAD

Source: gnomAD

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: 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 de novo 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 de novo biosynthesis;pyrimidine deoxyribonucleotides biosynthesis from CTP;guanosine deoxyribonucleotides de novo biosynthesis;guanosine nucleotides de novo biosynthesis;adenosine deoxyribonucleotides de novo biosynthesis;purine nucleotides de novo 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