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

Gene ID: 4913, updated on 11-Apr-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
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Genomic context

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Location:
16p13.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (2039820..2047834, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (2059629..2067643, complement)
105.20220307 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. Human endonuclease III/NTH1: focusing on the [4Fe-4S] cluster and the N-terminal domain. Moe E, et al. Chem Commun (Camb), 2022 Nov 10. PMID 36279116
  2. Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis. Carroll BL, et al. Nucleic Acids Res, 2021 Dec 16. PMID 34871433, Free PMC Article
  3. Further delineation of the NTHL1 associated syndrome: A report from the French Oncogenetic Consortium. Boulouard F, et al. Clin Genet, 2021 May. PMID 33454955
  4. NTHL1 in genomic integrity, aging and cancer. Das L, et al. DNA Repair (Amst), 2020 Sep. PMID 33087284, Free PMC Article
  5. Evaluating the role of NTHL1 p.Q90* allele in inherited breast cancer predisposition. Kumpula T, et al. Mol Genet Genomic Med, 2020 Nov. PMID 32949222, Free PMC Article

See all (89) 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)

Genotypes

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 IEA
Inferred from Electronic Annotation
more info
  
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_2023_10

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
P78549.2 GenPept UniProtKB/Swiss-Prot:P78549

Gene LinkOut

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