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NTHL1 Gene(Protein Coding)

Nth-Like DNA Glycosylase 1

GCID:
GC16M002041
GIFtS:
60
Genes Participants
UDN Logo

Aliases for NTHL1 Gene

Aliases for NTHL1 Gene

  • Nth-Like DNA Glycosylase 1 2 3 5
  • Bifunctional DNA N-Glycoslyase/DNA-(Apurinic Or Apyrimidinic Site) Lyase 3 4
  • DNA Glycoslyase/AP Lyase 3 4
  • OCTS3 3 4
  • HNTH1 3 4
  • NTH1 3 4
  • Nth Endonuclease III-Like 1 (E. Coli) 2
  • Nth (E.Coli Endonuclease III)-Like 1 2
  • Nth Endonuclease III-Like 1 3
  • EC 4.2.99.18 4
  • EC 3.2.2.- 4
  • FAP3 3

External Ids for NTHL1 Gene

Previous GeneCards Identifiers for NTHL1 Gene

  • GC16M002107
  • GC16M002030
  • GC16M002031
  • GC16M002032
  • GC16M002089
  • GC16M002014

Summaries for NTHL1 Gene

Entrez Gene Summary for NTHL1 Gene

  • The protein encoded by this gene is a DNA N-glycosylase of the endonuclease III family. Like a similar protein in E. coli, the encoded protein has DNA glycosylase activity on DNA substrates containing oxidized pyrimidine residues and has apurinic/apyrimidinic lyase activity. [provided by RefSeq, Oct 2008]

GeneCards Summary for NTHL1 Gene

NTHL1 (Nth-Like DNA Glycosylase 1) is a Protein Coding gene. Diseases associated with NTHL1 include Familial Adenomatous Polyposis 3. Among its related pathways are Chks in Checkpoint Regulation and DNA Double-Strand Break Repair. GO annotations related to this gene include double-stranded DNA binding and 4 iron, 4 sulfur cluster binding.

UniProtKB/Swiss-Prot for NTHL1 Gene

  • Bifunctional DNA N-glycosylase with associated apurinic/apyrimidinic (AP) lyase function that catalyzes the first step in base excision repair (BER), the primary repair pathway for the repair of oxidative DNA damage. The DNA N-glycosylase activity releases the damaged DNA base from DNA by cleaving the N-glycosidic bond, leaving an AP site. The AP-lyase activity cleaves the phosphodiester bond 3 to the AP site by a beta-elimination. Primarily recognizes and repairs oxidative base damage of pyrimidines. Has also 8-oxo-7,8-dihydroguanine (8-oxoG) DNA glycosylase activity. Acts preferentially on DNA damage opposite guanine residues in DNA. Is able to process lesions in nucleosomes without requiring or inducing nucleosome disruption.

Gene Wiki entry for NTHL1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NTHL1 Gene

Genomics for NTHL1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for NTHL1 Gene

Enhancers for NTHL1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around NTHL1 on UCSC Golden Path with GeneCards custom track

Promoters for NTHL1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around NTHL1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the NTHL1 gene promoter:

Genomic Location for NTHL1 Gene

Chromosome:
16
Start:
2,039,815 bp from pter
End:
2,047,866 bp from pter
Size:
8,052 bases
Orientation:
Minus strand

Genomic View for NTHL1 Gene

Genes around NTHL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NTHL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NTHL1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for NTHL1 Gene

Proteins for NTHL1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for NTHL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78549-NTH_HUMAN
    Recommended name:
    Endonuclease III-like protein 1
    Protein Accession:
    P78549
    Secondary Accessions:
    • Q1MVR1
    • Q99566
    • Q99794
    • Q9BPX2

    Protein attributes for NTHL1 Gene

    Size:
    312 amino acids
    Molecular mass:
    34390 Da
    Cofactor:
    Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
    Quaternary structure:
    • Interacts with YBX1.

    Alternative splice isoforms for NTHL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NTHL1 Gene

Proteomics data for NTHL1 Gene at MOPED

Protein Expression for NTHL1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for NTHL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NTHL1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NTHL1 Gene

Domains & Families for NTHL1 Gene

Gene Families for NTHL1 Gene

HGNC:

Protein Domains for NTHL1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for NTHL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P78549

UniProtKB/Swiss-Prot:

NTH_HUMAN :
  • Contains 1 HhH domain.
  • Belongs to the Nth/MutY family.
Domain:
  • Contains 1 HhH domain.
Family:
  • Belongs to the Nth/MutY family.
genes like me logo Genes that share domains with NTHL1: view

Function for NTHL1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for NTHL1 Gene

GENATLAS Biochemistry:
nth (E coli endonuclease III)-like 1,34.3 kDa,with lyase activity,involved in the excision of damaged pyrimidines
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=371 nM for 5-hydroxy-6-hydrothymine containing duplex oligonucleotides (N-glycosylase activity) {ECO:0000269 PubMed:11380260, ECO:0000269 PubMed:9890904}; KM=1093 nM for 5-hydroxyuracil containing duplex oligonucleotides (N-glycosylase activity) {ECO:0000269 PubMed:11380260, ECO:0000269 PubMed:9890904}; KM=548 nM for 5-hydroxycytosine containing duplex oligonucleotides (N-glycosylase activity) {ECO:0000269 PubMed:11380260, ECO:0000269 PubMed:9890904}; KM=1101 nM for thymine glycol containing duplex oligonucleotides (N-glycosylase activity) {ECO:0000269 PubMed:11380260, ECO:0000269 PubMed:9890904}; KM=718 nM for 5,6-dihydroxycytosine containing duplex oligonucleotides (N-glycosylase activity) {ECO:0000269 PubMed:11380260, ECO:0000269 PubMed:9890904}; KM=0.05 nM for 5-hydroxycytosine-G containing duplex oligonucleotides (N-glycosylase activity) {ECO:0000269 PubMed:11380260, ECO:0000269 PubMed:9890904}; KM=0.2 nM for 5-hydroxycytosine-A containing duplex oligonucleotides (N-glycosylase activity) {ECO:0000269 PubMed:11380260, ECO:0000269 PubMed:9890904};
UniProtKB/Swiss-Prot CatalyticActivity:
The C-O-P bond 3 to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3-terminal unsaturated sugar and a product with a terminal 5-phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
APE1 displaces NTHL1 from the N-glycosylase-generated AP site in DNA, thereby increasing the turnover of the DNA N-glycosylase activity. AP lyase activity is stimulated by YBX1.
UniProtKB/Swiss-Prot Function:
Bifunctional DNA N-glycosylase with associated apurinic/apyrimidinic (AP) lyase function that catalyzes the first step in base excision repair (BER), the primary repair pathway for the repair of oxidative DNA damage. The DNA N-glycosylase activity releases the damaged DNA base from DNA by cleaving the N-glycosidic bond, leaving an AP site. The AP-lyase activity cleaves the phosphodiester bond 3 to the AP site by a beta-elimination. Primarily recognizes and repairs oxidative base damage of pyrimidines. Has also 8-oxo-7,8-dihydroguanine (8-oxoG) DNA glycosylase activity. Acts preferentially on DNA damage opposite guanine residues in DNA. Is able to process lesions in nucleosomes without requiring or inducing nucleosome disruption.

Enzyme Numbers (IUBMB) for NTHL1 Gene

Gene Ontology (GO) - Molecular Function for NTHL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity TAS --
GO:0003690 double-stranded DNA binding IDA 15358233
GO:0003824 catalytic activity IEA --
GO:0005515 protein binding IPI 15358233
GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity TAS --
genes like me logo Genes that share ontologies with NTHL1: view

Phenotypes for NTHL1 Gene

MGI mutant phenotypes for NTHL1:
inferred from 2 alleles
GenomeRNAi human phenotypes for NTHL1:
genes like me logo Genes that share phenotypes with NTHL1: view

Human Phenotype Ontology for NTHL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NTHL1 Gene

MGI Knock Outs for NTHL1:

Animal Model Products

  • Taconic Biosciences Mouse Models for NTHL1

CRISPR Products

miRNA for NTHL1 Gene

miRTarBase miRNAs that target NTHL1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for NTHL1 Gene

Localization for NTHL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NTHL1 Gene

Nucleus. Mitochondrion.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NTHL1 Gene COMPARTMENTS Subcellular localization image for NTHL1 gene
Compartment Confidence
nucleus 5
mitochondrion 4
cytosol 1
peroxisome 1

No data available for Gene Ontology (GO) - Cellular Components for NTHL1 Gene

Pathways & Interactions for NTHL1 Gene

genes like me logo Genes that share pathways with NTHL1: view

Pathways by source for NTHL1 Gene

1 KEGG pathway for NTHL1 Gene
1 GeneGo (Thomson Reuters) pathway for NTHL1 Gene
1 Qiagen pathway for NTHL1 Gene

Gene Ontology (GO) - Biological Process for NTHL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006296 nucleotide-excision repair, DNA incision, 5-to lesion IEA,IDA 8990169
GO:0098792 xenophagy IMP 22020285
genes like me logo Genes that share ontologies with NTHL1: view

No data available for SIGNOR curated interactions for NTHL1 Gene

Drugs & Compounds for NTHL1 Gene

Products:

  1. Drug

(2) Additional Compounds for NTHL1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NTHL1: view

Transcripts for NTHL1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for NTHL1 Gene

(4) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(12) Selected AceView cDNA sequences:
(10) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NTHL1 Gene

Nth endonuclease III-like 1 (E. coli):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NTHL1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c · 6d
SP1: - - -
SP2: - -
SP3: - - -
SP4: - - -
SP5: -
SP6:

Relevant External Links for NTHL1 Gene

GeneLoc Exon Structure for
NTHL1
ECgene alternative splicing isoforms for
NTHL1

Expression for NTHL1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for NTHL1 Gene

mRNA expression in normal human tissues for NTHL1 Gene
mRNA expression by BioGPS for NTHL1 GenemRNA expression by GTEx for NTHL1 Gene

Protein differential expression in normal tissues from HIPED for NTHL1 Gene

This gene is overexpressed in Colon muscle (26.9) and Pancreas (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for NTHL1 Gene



SOURCE GeneReport for Unigene cluster for NTHL1 Gene Hs.66196

mRNA Expression by UniProt/SwissProt for NTHL1 Gene

P78549-NTH_HUMAN
Tissue specificity: Widely expressed with highest levels in heart and lowest levels in lung and liver.
genes like me logo Genes that share expression patterns with NTHL1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for NTHL1 Gene

Orthologs for NTHL1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NTHL1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia NTHL1 35
  • 83.11 (n)
  • 82.89 (a)
NTHL1 36
  • 83 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia NTHL1 35
  • 82.04 (n)
  • 80 (a)
NTHL1 36
  • 79 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Nthl1 35
  • 81.02 (n)
  • 82.03 (a)
Nthl1 16
Nthl1 36
  • 81 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Nthl1 35
  • 81.36 (n)
  • 82.37 (a)
oppossum
(Monodelphis domestica)
 Mammalia NTHL1 36
  • 67 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia NTHL1 36
  • 55 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia NTHL1 36
  • 98 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves NTHL1 35
  • 71.39 (n)
  • 72.05 (a)
CHNTHL1 36
  • 66 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia NTHL1 36
  • 75 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia nthl1 35
  • 66.93 (n)
  • 66.54 (a)
Str.11448 35
zebrafish
(Danio rerio)
 Actinopterygii nthl1 35
  • 69.37 (n)
  • 73.42 (a)
nthl1 36
  • 45 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta CG9272 37
  • 50 (a)
CG9272 35
  • 54.86 (n)
  • 50.19 (a)
CG9272 36
  • 35 (a)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea R10E4.5 37
  • 51 (a)
nth-1 35
  • 53.86 (n)
  • 51.39 (a)
nth-1 36
  • 38 (a)
 OneToOne
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes NTG1 36
  • 27 (a)
 OneToMany
NTG2 36
  • 26 (a)
 OneToMany
NTG1 38
bread mold
(Neurospora crassa)
 Ascomycetes NCU06654 35
  • 54.53 (n)
  • 48.68 (a)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes nth1 35
  • 49.39 (n)
  • 49.08 (a)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.720 36
  • 46 (a)
 OneToOne
Species with no ortholog for NTHL1:
  • A. gosspyii yeast (Ashbya 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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 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)

Evolution for NTHL1 Gene

ENSEMBL:
Gene Tree for NTHL1 (if available)
TreeFam:
Gene Tree for NTHL1 (if available)

Paralogs for NTHL1 Gene

No data available for Paralogs for NTHL1 Gene

Variants for NTHL1 Gene

Sequence variations from dbSNP and Humsavar for NTHL1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
VAR_016125 -
VAR_016126 -
rs1805378 - 2,044,652(-) GCTCA(C/T)CTACC intron-variant, reference, missense
rs3087468 - 2,040,233(-) CAGTG(G/T)ACACG reference, missense
rs3211977 - 2,043,575(-) TGTGT(C/T)AGGCA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for NTHL1 Gene

Variant ID Type Subtype PubMed ID
esv2422427 CNV Duplication 17116639
dgv2540n71 CNV Loss 21882294
dgv2544n71 CNV Loss 21882294
dgv2545n71 CNV Loss 21882294
nsv905048 CNV Loss 21882294
dgv2546n71 CNV Loss 21882294
dgv2547n71 CNV Loss 21882294
dgv2548n71 CNV Gain 21882294
dgv2549n71 CNV Loss 21882294
dgv2550n71 CNV Loss 21882294
dgv2552n71 CNV Gain+Loss 21882294
nsv523037 CNV Loss 19592680
nsv471072 CNV Loss 18288195
dgv2555n71 CNV Gain+Loss 21882294
nsv905095 CNV Gain 21882294
nsv905101 CNV Loss 21882294
nsv905102 CNV Loss 21882294
dgv2556n71 CNV Loss 21882294
dgv2557n71 CNV Loss 21882294

Variation tolerance for NTHL1 Gene

Residual Variation Intolerance Score: 84.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.69; 32.22% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NTHL1 Gene

Human Gene Mutation Database (HGMD)
NTHL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NTHL1 Gene

Disorders for NTHL1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NTHL1 Gene - From: OMIM, ClinVar, and GeneCards

Disorder Aliases PubMed IDs
familial adenomatous polyposis 3
  • fap3
- elite association - COSMIC cancer census association via MalaCards
Search NTHL1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NTH_HUMAN
  • Familial adenomatous polyposis 3 (FAP3) [MIM:616415]: A form of familial adenomatous polyposis, a condition characterized by the development of multiple colorectal adenomatous polyps, benign neoplasms derived from glandular epithelium. Some affected individuals may develop colorectal carcinoma. {ECO:0000269 PubMed:25938944}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for NTHL1

Genetic Association Database (GAD)
NTHL1
Human Genome Epidemiology (HuGE) Navigator
NTHL1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NTHL1
genes like me logo Genes that share disorders with NTHL1: view

No data available for Genatlas for NTHL1 Gene

Publications for NTHL1 Gene

  1. Cloning and characterization of a functional human homolog of Escherichia coli endonuclease III. (PMID: 8990169) Aspinwall R. … Hickson I.D. (Proc. Natl. Acad. Sci. U.S.A. 1997) 2 3 4 23 67
  2. Altered expression of the human base excision repair gene NTH1 in gastric cancer. (PMID: 19414504) Goto M. … Sugimura H. (Carcinogenesis 2009) 3 23
  3. Inherited predisposition to colorectal adenomas caused by multiple rare alleles of MUTYH but not OGG1, NUDT1, NTH1 or NEIL 1, 2 or 3. (PMID: 18515411) Dallosso A.R. … Sampson J.R. (Gut 2008) 3 23
  4. Substrate specificity of human endonuclease III (hNTH1). Effect of human APE1 on hNTH1 activity. (PMID: 12519758) Marenstein D.R. … Teebor G.W. (J. Biol. Chem. 2003) 3 23
  5. Genomic structure and sequence of a human homologue (NTHL1/NTH1) of Escherichia coli endonuclease III with those of the adjacent parts of TSC2 and SLC9A3R2 genes. (PMID: 9831664) Imai K. … Seki S. (Gene 1998) 3 23

Products for NTHL1 Gene

Sources for NTHL1 Gene

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