NT5M Gene (Protein Coding)

5',3'-Nucleotidase, Mitochondrial

GC17P017303
GIFtS:
38
This gene encodes a 5' nucleotidase that localizes to the mitochondrial matrix. This enzyme dephosphorylates the 5'- and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides. The gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008] See more...

Aliases for NT5M Gene

Aliases for NT5M Gene

  • 5',3'-Nucleotidase, Mitochondrial 2 3 4 5
  • DNT-2 2 3 4
  • DNT2 2 3 4
  • 5'(3')-Deoxyribonucleotidase, Mitochondrial 3 4
  • 5' Nucleotidase, Mitochondrial 2 3
  • Deoxy-5'-Nucleotidase 2 3 4
  • MdN 2 3
  • Mitochondrial 5' Nucleotidase 3
  • 5(3)-Deoxyribonucleotidase 3
  • EC 3.1.3.- 4
  • EC 3.1.3 51
  • NT5M 5

External Ids for NT5M Gene

Previous GeneCards Identifiers for NT5M Gene

  • GC17P017521
  • GC17P018565
  • GC17P017149
  • GC17P017407
  • GC17P017147
  • GC17P016959
  • GC17P017206

Summaries for NT5M Gene

Entrez Gene Summary for NT5M Gene

  • This gene encodes a 5' nucleotidase that localizes to the mitochondrial matrix. This enzyme dephosphorylates the 5'- and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides. The gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]

GeneCards Summary for NT5M Gene

NT5M (5',3'-Nucleotidase, Mitochondrial) is a Protein Coding gene. Diseases associated with NT5M include Methemoglobinemia and Thumb Deformity. Among its related pathways are Metabolism of nucleotides and NAD metabolism. Gene Ontology (GO) annotations related to this gene include nucleotide binding and nucleotidase activity. An important paralog of this gene is NT5C.

UniProtKB/Swiss-Prot Summary for NT5M Gene

  • Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.

Additional gene information for NT5M Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NT5M Gene

Genomics for NT5M Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for NT5M Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NT5M on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NT5M

Top Transcription factor binding sites by QIAGEN in the NT5M gene promoter:
  • CUTL1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • GCNF-2
  • p53
  • POU3F1

Genomic Locations for NT5M Gene

Latest Assembly
chr17:17,303,335-17,347,663
(GRCh38/hg38)
Size:
44,329 bases
Orientation:
Plus strand

Previous Assembly
chr17:17,206,687-17,250,977
(GRCh37/hg19 by Entrez Gene)
Size:
44,291 bases
Orientation:
Plus strand

chr17:17,206,649-17,250,977
(GRCh37/hg19 by Ensembl)
Size:
44,329 bases
Orientation:
Plus strand

Genomic View for NT5M Gene

Genes around NT5M on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NT5M Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NT5M Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for NT5M Gene

Proteins for NT5M Gene

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  • Protein details for NT5M Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NPB1-NT5M_HUMAN
    Recommended name:
    5'(3')-deoxyribonucleotidase, mitochondrial
    Protein Accession:
    Q9NPB1

    Protein attributes for NT5M Gene

    Size:
    228 amino acids
    Molecular mass:
    25862 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for NT5M Gene

neXtProt entry for NT5M Gene

Selected DME Specific Peptides for NT5M Gene

Q9NPB1:
  • GVLADFE
  • DLLIDDRP

Post-translational modifications for NT5M Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NT5M Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for NT5M Gene

Gene Families for NT5M Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NT5M Gene

InterPro:
Blocks:
  • 5 nucleotidase, deoxy, cytosolic type C
ProtoNet:

Suggested Antigen Peptide Sequences for NT5M Gene

GenScript: Design optimal peptide antigens:
  • Deoxy-5'-nucleotidase 2 (NT5M_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NPB1

UniProtKB/Swiss-Prot:

NT5M_HUMAN :
  • Belongs to the 5'(3')-deoxyribonucleotidase family.
Family:
  • Belongs to the 5'(3')-deoxyribonucleotidase family.
genes like me logo Genes that share domains with NT5M: view

Function for NT5M Gene

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  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
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  6. Cell Lines for research

Molecular function for NT5M Gene

UniProtKB/Swiss-Prot Function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.

Enzyme Numbers (IUBMB) for NT5M Gene

Phenotypes From GWAS Catalog for NT5M Gene

Gene Ontology (GO) - Molecular Function for NT5M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0008252 nucleotidase activity TAS 10899995
GO:0008253 5'-nucleotidase activity IBA 21873635
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with NT5M: view
genes like me logo Genes that share phenotypes with NT5M: view

Animal Models for research

miRNA for NT5M Gene

miRTarBase miRNAs that target NT5M

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NT5M

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NT5M Gene

Localization for NT5M Gene

Subcellular locations from UniProtKB/Swiss-Prot for NT5M Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NT5M gene
Compartment Confidence
mitochondrion 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for NT5M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion TAS 10899995
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with NT5M: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NT5M Gene

Pathways & Interactions for NT5M Gene

genes like me logo Genes that share pathways with NT5M: view

Pathways by source for NT5M Gene

1 GeneGo (Thomson Reuters) pathway for NT5M Gene
  • NAD metabolism

Gene Ontology (GO) - Biological Process for NT5M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication TAS 10899995
GO:0009117 nucleotide metabolic process IEA --
GO:0009223 pyrimidine deoxyribonucleotide catabolic process TAS,IBA 21873635
GO:0009264 deoxyribonucleotide catabolic process IEA --
GO:0016311 dephosphorylation IEA --
genes like me logo Genes that share ontologies with NT5M: view

No data available for SIGNOR curated interactions for NT5M Gene

Drugs & Compounds for NT5M Gene

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(21) Drugs for NT5M Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine Approved, Investigational Pharma 659
Magnesium Approved, Experimental, Investigational Pharma 0
Water Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0
Cyclic 3',5'-thymidine monophosphate Experimental Pharma Target 0

(9) Additional Compounds for NT5M Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
deoxyadenosine
  • (2R,3S,5R)-5-(6-Amino-9H-purin-9-yl)-2-(hydroxymethyl)tetrahydrofuran-3-ol
  • 5-(6-AMINO-purin-9-yl)-2-hydroxymethyl-tetrahydro-furan-3-ol
  • 9-(2-Deoxy-beta-D-erythro-pentofuranosyl)adenine
  • 9-(2-Deoxy-beta-D-ribofuranosyl)-9H-purin-6-amine
  • Adenine deoxyribonucleoside
 958-09-8
Deoxyadenosine monophosphate
  • 2'-dAMP
  • 2'-Deoxy-5'-adenosine monophosphate
  • 2'-Deoxy-AMP
  • 2'-Deoxyadenosine 5'-(dihydrogen phosphate)
  • 2'-Deoxyadenosine 5'-phosphate
 653-63-4
deoxyguanosine
  • 2-Amino-9-(2-deoxy-9-beta-D-ribofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-beta-D-erythro-pentofuranosyl)-guanine
  • dG
  • Guanine deoxy nucleoside
  • 2'-Deoxyguanosine
 961-07-9
dIMP
  • 2'-Deoxy-5'-inosinic acid
  • 2'-Deoxyinosine 5'-monophosphate
  • 2'-Deoxyinosine 5'-monophosphoric acid
  • 2'-Deoxyinosine 5'-phosphate
  • 9-(2-Deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purin-6-ol
 3393-18-8
Nicotinamide ribotide
  • b-Nicotinamide D-ribonucleotide
  • β-Nicotinamide D-ribonucleotide
  • Mononucleotide, nicotinamide
  • Nicotinamide mononucleotide
  • 3-(Aminocarbonyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridinium
 75414-16-3
genes like me logo Genes that share compounds with NT5M: view

Transcripts for NT5M Gene

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mRNA/cDNA for NT5M Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NT5M

Alternative Splicing Database (ASD) splice patterns (SP) for NT5M Gene

No ASD Table

Relevant External Links for NT5M Gene

GeneLoc Exon Structure for
NT5M

Expression for NT5M Gene

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  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NT5M Gene

mRNA expression in normal human tissues for NT5M Gene
mRNA expression by BioGPS for NT5M GenemRNA expression by GTEx for NT5M Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NT5M

SOURCE GeneReport for Unigene cluster for NT5M Gene:

Hs.513977

mRNA Expression by UniProt/SwissProt for NT5M Gene:

Q9NPB1-NT5M_HUMAN
Tissue specificity: Highly expressed in heart, brain and skeletal muscle. Detected at very low levels in kidney and pancreas.

Evidence on tissue expression from TISSUES for NT5M Gene

  • Nervous system(4.3)
  • Muscle(4.3)
genes like me logo Genes that share expression patterns with NT5M: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NT5M Gene

Orthologs for NT5M Gene

This gene was present in the common ancestor of chordates.

Orthologs for NT5M Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia NT5M 30 31
  • 99.56 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Nt5m 30 17 31
  • 90.83 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia NT5M 30 31
  • 90.01 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia NT5M 30 31
  • 88.69 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Nt5m 30
  • 85.25 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia NT5M 31
  • 63 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia NT5M 31
  • 61 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves NT5M 30 31
  • 80.95 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia NT5M 31
  • 65 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia nt5m 30
  • 74.96 (n)
Species where no ortholog for NT5M was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for NT5M Gene

ENSEMBL:
Gene Tree for NT5M (if available)
TreeFam:
Gene Tree for NT5M (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NT5M: view image

Paralogs for NT5M Gene

Paralogs for NT5M Gene

(1) SIMAP similar genes for NT5M Gene using alignment to 4 proteins:

  • NT5M_HUMAN
  • J3QLR5_HUMAN
  • J3QRN4_HUMAN
  • K7EPW8_HUMAN
genes like me logo Genes that share paralogs with NT5M: view

Variants for NT5M Gene

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dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NT5M Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for NT5M Gene

Variant ID Type Subtype PubMed ID
esv1198553 CNV deletion 17803354
esv26411 CNV loss 19812545
esv2659771 CNV deletion 23128226
esv2673352 CNV deletion 23128226
esv2813 CNV loss 18987735
esv3161567 CNV deletion 24192839
esv33859 CNV loss 17666407
esv3554215 CNV deletion 23714750
esv3640127 CNV loss 21293372
esv3640128 CNV loss 21293372
esv5295 CNV loss 18987735
esv6568 CNV loss 19470904
nsv1061186 CNV gain 25217958
nsv112007 CNV deletion 16902084
nsv1125206 CNV deletion 24896259
nsv1146229 CNV deletion 26484159
nsv155 OTHER inversion 15895083
nsv469777 CNV gain 16826518
nsv499114 OTHER inversion 21111241
nsv833380 CNV loss 17160897
nsv833382 CNV loss 17160897
nsv9500 CNV loss 18304495
nsv954571 CNV deletion 24416366
nsv955407 CNV deletion 24416366

Variation tolerance for NT5M Gene

Residual Variation Intolerance Score: 65.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.81; 17.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NT5M Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NT5M

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NT5M Gene

Disorders for NT5M Gene

MalaCards: The human disease database

(14) MalaCards diseases for NT5M Gene - From: CVR, COP, and GCD

Disorder Aliases PubMed IDs
methemoglobinemia
thumb deformity
  • thumb absent or hypoplastic
smith-magenis syndrome
  • sms
potocki-lupski syndrome
  • ptls
sleep disorder
  • non-organic sleep disorder
- elite association - COSMIC cancer census association via MalaCards
Search NT5M in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NT5M

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with NT5M: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NT5M Gene

Publications for NT5M Gene

  1. Crystal structure of a human mitochondrial deoxyribonucleotidase. (PMID: 12352955) Rinaldo-Matthis A … Nordlund P (Nature structural biology 2002) 3 4 23
  2. A deoxyribonucleotidase in mitochondria: involvement in regulation of dNTP pools and possible link to genetic disease. (PMID: 10899995) Rampazzo C … Bianchi V (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Human mitochondrial 5'-deoxyribonucleotidase. Overproduction in cultured cells and functional aspects. (PMID: 12124385) Gallinaro L … Bianchi V (The Journal of biological chemistry 2002) 3 23

ExternalLinks

View latest publications for NT5M gene in Mastermind

Products for NT5M Gene

Sources for NT5M Gene