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    NTHL1 nth like DNA glycosylase 1 [ Homo sapiens (human) ]

    Gene ID: 4913, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NTHL1provided by HGNC
    Official Full Name
    nth like DNA glycosylase 1provided by HGNC
    Primary source
    HGNC:HGNC:8028
    See related
    Ensembl:ENSG00000065057 MIM:602656; AllianceGenome:HGNC:8028
    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
    FAP3; NTH1; OCTS3; hNTH1
    Summary
    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]
    Expression
    Ubiquitous expression in spleen (RPKM 7.3), ovary (RPKM 6.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NTHL1 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (2039820..2047834, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (2059629..2067643, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2089821..2097835, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2092 Neighboring gene CRISPRi-validated cis-regulatory element chr16.496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2082560-2083144 Neighboring gene neuropeptide W Neighboring gene NHERF family PDZ scaffold protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2086649-2087231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2097239-2097738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7024 Neighboring gene TSC complex subunit 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:2119055-2119286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2128423-2129132 Neighboring gene microRNA 1225 Neighboring gene polycystin 1, transient receptor potential channel interacting

    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. Altered expression of the human base excision repair gene NTH1 in gastric cancer. Goto M, et al. Carcinogenesis, 2009 Aug. PMID 19414504
    2. Monoallelic NTHL1 Loss-of-Function Variants and Risk of Polyposis and Colorectal Cancer. Elsayed FA, et al. Gastroenterology, 2020 Dec. PMID 32860789, Free PMC Article
    3. NTHL1 Tumor Syndrome. Adam MP, et al. , 1993. PMID 32239880
    4. An Excimer Clamp for Measuring Damaged-Base Excision by the DNA Repair Enzyme NTH1. Jun YW, et al. Angew Chem Int Ed Engl, 2020 May 4. PMID 32109332, Free PMC Article
    5. NTHL1 biallelic mutations seldom cause colorectal cancer, serrated polyposis or a multi-tumor phenotype, in absence of colorectal adenomas. Belhadj S, et al. Sci Rep, 2019 Jun 21. PMID 31227763, Free PMC Article

    See all (96) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Enhanced Sampling for Conformational Changes and Molecular Mechanisms of Human NTHL1.
      Title: Enhanced Sampling for Conformational Changes and Molecular Mechanisms of Human NTHL1.
    2. NTHL1 is a recessive cancer susceptibility gene.
      Title: NTHL1 is a recessive cancer susceptibility gene.
    3. Concurrent Reduced Expression of Contiguous PKD1, TSC2 and NTHL1 Leading to Kidney Diseases and Multiple Diverse Renal Cancers.
      Title: Concurrent Reduced Expression of Contiguous PKD1, TSC2 and NTHL1 Leading to Kidney Diseases and Multiple Diverse Renal Cancers.
    4. Human endonuclease III/NTH1: focusing on the [4Fe-4S] cluster and the N-terminal domain.
      Title: Human endonuclease III/NTH1: focusing on the [4Fe-4S] cluster and the N-terminal domain.
    5. Prevalence and Characterization of Biallelic and Monoallelic NTHL1 and MSH3 Variant Carriers From a Pan-Cancer Patient Population.
      Title: Prevalence and Characterization of Biallelic and Monoallelic NTHL1 and MSH3 Variant Carriers From a Pan-Cancer Patient Population.
    6. Further delineation of the NTHL1 associated syndrome: A report from the French Oncogenetic Consortium.
      Title: Further delineation of the NTHL1 associated syndrome: A report from the French Oncogenetic Consortium.
    7. Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis.
      Title: Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis.
    8. Evaluating the role of NTHL1 p.Q90* allele in inherited breast cancer predisposition.
      Title: Evaluating the role of NTHL1 p.Q90* allele in inherited breast cancer predisposition.
    9. Monoallelic NTHL1 Loss-of-Function Variants and Risk of Polyposis and Colorectal Cancer.
      Title: Monoallelic NTHL1 Loss-of-Function Variants and Risk of Polyposis and Colorectal Cancer.
    10. NTHL1 in genomic integrity, aging and cancer.
      Title: NTHL1 in genomic integrity, aging and cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (42)

    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

    Associated conditions

    Description Tests
    Familial adenomatous polyposis 3
    MedGen: C4225157 OMIM: 616415 GeneReviews: NTHL1 Tumor Syndrome
    		Compare labs

    EBI GWAS Catalog

    Description
    Joint influence of small-effect genetic variants on human longevity.
    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 4 iron, 4 sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA N-glycosylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-(apurinic or apyrimidinic site) endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables class I DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables damaged DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables endonuclease activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidized purine nucleobase lesion DNA N-glycosylase activity TAS
    Traceable Author Statement
    more info
    		  
    enables oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in base-excision repair, AP site formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in base-excision repair, AP site formation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in depyrimidination TAS
    Traceable Author Statement
    more info
    		  
    involved_in nucleotide-excision repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nucleotide-excision repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    endonuclease III-like protein 1
    Names
    DNA glycoslyase/AP lyase
    DNA glycosylase/AP lyase
    bifunctional DNA N-glycoslyase/DNA-(apurinic or apyrimidinic site) lyase
    bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase
    nth endonuclease III-like 1
    NP_001305122.2
    NP_001305123.1
    NP_002519.2
    XP_047290127.1
    XP_054236381.1

    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.

    Genomic

    1. NG_008412.1 RefSeqGene

      Range
      5033..13047
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1366

    mRNA and Protein(s)

    1. NM_001318193.2 → NP_001305122.2  endonuclease III-like protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
      Source sequence(s)
      BC003014, BE900738, U79718
      UniProtKB/TrEMBL
      H3BPD5
      Related
      ENSP00000498821.1, ENST00000651583.1
      Conserved Domains (1) summary
      cl27658
      Location:117 → 245
      HHH; Helix-hairpin-helix motif

    2. NM_001318194.2 → NP_001305123.1  endonuclease III-like protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 3, which has a distinct N-terminus, and is shorter, compared to isoform 1.
      Source sequence(s)
      BC003014, BG468617, HY094895
      UniProtKB/TrEMBL
      A0A494BZZ6
      Conserved Domains (3) summary
      smart00525
      Location:171 → 191
      FES; iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
      smart00478
      Location:20 → 169
      ENDO3c; endonuclease III
      COG0177
      Location:11 → 192
      Nth; Endonuclease III [Replication, recombination and repair]

    3. NM_002528.7 → NP_002519.2  endonuclease III-like protein 1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      U79718, U81285
      Consensus CDS
      CCDS10457.2
      UniProtKB/Swiss-Prot
      P78549, Q1MVR1, Q99566, Q99794, Q9BPX2
      UniProtKB/TrEMBL
      E5KTI5
      Related
      ENSP00000498421.1, ENST00000651570.2
      Conserved Domains (1) summary
      COG0177
      Location:121 → 302
      Nth; Endonuclease III [Replication, recombination and repair]

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      2039820..2047834 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434171.1 → XP_047290127.1  endonuclease III-like protein 1 isoform X1

      Related
      ENSP00000498290.1, ENST00000651522.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      2059629..2067643 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380406.1 → XP_054236381.1  endonuclease III-like protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P78549.3 GenPept UniProtKB/Swiss-Prot:P78549

    Gene LinkOut

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

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