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DNPH1 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [ Homo sapiens (human) ]

Gene ID: 10591, updated on 10-Dec-2024

Summary

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Official Symbol
DNPH1provided by HGNC
Official Full Name
2'-deoxynucleoside 5'-phosphate N-hydrolase 1provided by HGNC
Primary source
HGNC:HGNC:21218
See related
Ensembl:ENSG00000112667 MIM:618762; AllianceGenome:HGNC:21218
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RCL; C6orf108; dJ330M21.3
Summary
This gene was identified on the basis of its stimulation by c-Myc protein. The latter is a transcription factor that participates in the regulation of cell proliferation, differentiation, and apoptosis. The exact function of this gene is not known but studies in rat suggest a role in cellular proliferation and c-Myc-mediated transformation. Two alternative transcripts encoding different proteins have been described. [provided by RefSeq, Jul 2008]
Expression
Broad expression in kidney (RPKM 65.7), duodenum (RPKM 28.6) and 23 other tissues See more
Orthologs
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Genomic context

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See DNPH1 in Genome Data Viewer
Location:
6p21.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (43225629..43229481, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (43054425..43058274, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (43193367..43197219, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17219 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43139967-43140935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43145601-43146102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43146103-43146602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17220 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17221 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:43154118-43155317 Neighboring gene serum response factor Neighboring gene cullin 9 Neighboring gene MPRA-validated peak5812 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43190560-43191097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:43197001-43197500 Neighboring gene tau tubulin kinase 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:43239819-43240068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43245015-43245670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43245671-43246325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43254414-43255266 Neighboring gene Sharpr-MPRA regulatory region 10500 Neighboring gene uncharacterized LOC124901319 Neighboring gene solute carrier family 22 member 7

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80. Carberry AE, et al. Chembiochem, 2024 Apr 2. PMID 38350003
  2. An enzyme-coupled microplate assay for activity and inhibition of hmdUMP hydrolysis by DNPH1. Wagner AG, et al. Anal Biochem, 2023 Jul 1. PMID 37142196, Free PMC Article
  3. Targeting the nucleotide salvage factor DNPH1 sensitizes BRCA-deficient cells to PARP inhibitors. Fugger K, et al. Science, 2021 Apr 9. PMID 33833118, Free PMC Article
  4. Probing the active site of the deoxynucleotide N-hydrolase Rcl encoded by the rat gene c6orf108. Dupouy C, et al. J Biol Chem, 2010 Dec 31. PMID 20962348, Free PMC Article
  5. 6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: synthesis, structural studies and cytotoxic activities. Amiable C, et al. Eur J Med Chem, 2014 Oct 6. PMID 25108359

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80.
    Title: Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80.
  2. Targeting the nucleotide salvage factor DNPH1 sensitizes BRCA-deficient cells to PARP inhibitors.
    Title: Targeting the nucleotide salvage factor DNPH1 sensitizes BRCA-deficient cells to PARP inhibitors.
  3. analysis of human deoxynucleotide N-hydrolase Rcl and rat gene c6orf108
    Title: Probing the active site of the deoxynucleotide N-hydrolase Rcl encoded by the rat gene c6orf108.
  4. characterization of the human Rcl gene, we cloned its promoter, Rcl is a bona fide target gene of ETV1.
    Title: Rcl is a novel ETV1/ER81 target gene upregulated in breast tumors.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5-hydroxymethyl-dUMP N-hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5-hydroxymethyl-dUMP N-hydrolase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 5-hydroxymethyl-dUMP N-hydrolase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables 5-hydroxymethyl-dUMP N-hydrolase activity TAS
Traceable Author Statement
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in deoxyribonucleoside monophosphate catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in deoxyribonucleoside monophosphate catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in deoxyribonucleoside monophosphate catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in epithelial cell differentiation IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in nucleoside salvage IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell growth ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in purine nucleotide catabolic process TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
5-hydroxymethyl-dUMP N-hydrolase
Names
c-Myc-responsive protein RCL
deoxyribonucleoside 5'-monophosphate N-glycosidase
putative c-Myc-responsive
NP_006434.1
NP_954653.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_006443.3 → NP_006434.1  5-hydroxymethyl-dUMP N-hydrolase isoform 1

    See identical proteins and their annotated locations for NP_006434.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL133375, BC011683, BM747628
    Consensus CDS
    CCDS4891.1
    UniProtKB/Swiss-Prot
    B2LUJ9, O43598
    Related
    ENSP00000230431.7, ENST00000230431.11
    Conserved Domains (1) summary
    cl23749
    Location:23 → 126
    TIR_2; TIR domain

  2. NM_199184.2 → NP_954653.1  5-hydroxymethyl-dUMP N-hydrolase isoform 2

    See identical proteins and their annotated locations for NP_954653.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an additional segment in the 3' coding region, compared to variant 1, that causes a frameshift. The resulting protein (isoform 2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AF040105, AL133375, BC011683, BQ052226
    Consensus CDS
    CCDS43465.1
    UniProtKB/Swiss-Prot
    O43598
    Related
    ENSP00000377556.2, ENST00000393987.2
    Conserved Domains (1) summary
    cl23749
    Location:23 → 141
    TIR_2; TIR domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    43225629..43229481 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    43054425..43058274 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43598.1 GenPept UniProtKB/Swiss-Prot:O43598

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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