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DCLRE1B DNA cross-link repair 1B [ Homo sapiens (human) ]

Gene ID: 64858, updated on 6-May-2024

Summary

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Official Symbol
DCLRE1Bprovided by HGNC
Official Full Name
DNA cross-link repair 1Bprovided by HGNC
Primary source
HGNC:HGNC:17641
See related
Ensembl:ENSG00000118655 MIM:609683; AllianceGenome:HGNC:17641
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
DKCB8; SNM1B; SNMIB; APOLLO
Summary
DNA interstrand cross-links prevent strand separation, thereby physically blocking transcription, replication, and segregation of DNA. DCLRE1B is one of several evolutionarily conserved genes involved in repair of interstrand cross-links (Dronkert et al., 2000 [PubMed 10848582]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 3.3), appendix (RPKM 3.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1p13.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (113904619..113914086)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (113916281..113925748)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114447241..114456708)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene AP4B1 antisense RNA 1 Neighboring gene protein tyrosine phosphatase non-receptor type 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1538 Neighboring gene BCL2 like 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1541 Neighboring gene adaptor related protein complex 4 subunit beta 1 Neighboring gene GATA motif-containing MPRA enhancer 196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1217 Neighboring gene HIPK1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114480377-114480904 Neighboring gene homeodomain interacting protein kinase 1 Neighboring gene MPRA-validated peak375 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:114519457-114520034 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:114521340-114522173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114523841-114524673 Neighboring gene olfactomedin like 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family. Baddock HT, et al. Nucleic Acids Res, 2021 Sep 20. PMID 34387694, Free PMC Article
  2. The SNM1B/APOLLO DNA nuclease functions in resolution of replication stress and maintenance of common fragile site stability. Mason JM, et al. Hum Mol Genet, 2013 Dec 15. PMID 23863462, Free PMC Article
  3. Snm1B/Apollo functions in the Fanconi anemia pathway in response to DNA interstrand crosslinks. Mason JM, et al. Hum Mol Genet, 2011 Jul 1. PMID 21478198, Free PMC Article
  4. Apollo, an Artemis-related nuclease, interacts with TRF2 and protects human telomeres in S phase. van Overbeek M, et al. Curr Biol, 2006 Jul 11. PMID 16730176
  5. Human SNM1B is required for normal cellular response to both DNA interstrand crosslink-inducing agents and ionizing radiation. Demuth I, et al. Oncogene, 2004 Nov 11. PMID 15467758

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DCLRE1B/Apollo germline mutations associated with renal cell carcinoma impair telomere protection.
    Title: DCLRE1B/Apollo germline mutations associated with renal cell carcinoma impair telomere protection.
  2. DCLRE1B promotes tumor progression and predicts immunotherapy response through METTL3-mediated m6A modification in pancreatic cancer.
    Title: DCLRE1B promotes tumor progression and predicts immunotherapy response through METTL3-mediated m6A modification in pancreatic cancer.
  3. Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition.
    Title: Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition.
  4. A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family.
    Title: A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family.
  5. Different charge distributions along the DNA binding groove may account for the drastic difference in processivity and DNA digestion efficiency, including that of damaged substrates, between SNM1A and SNM1B.
    Title: The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities.
  6. The SNM1B/APOLLO DNA nuclease functions in resolution of replication stress and maintenance of common fragile site stability.
    Title: The SNM1B/APOLLO DNA nuclease functions in resolution of replication stress and maintenance of common fragile site stability.
  7. the N-terminal region of Snm1B forms a complex containing PSF2 and Mus81, while the C-terminal region is important for PSF2-mediated chromatin association.
    Title: Snm1B interacts with PSF2.
  8. The nuclease hSNM1B/Apollo is linked to the Fanconi anemia pathway via its interaction with FANCP/SLX4.
    Title: The nuclease hSNM1B/Apollo is linked to the Fanconi anemia pathway via its interaction with FANCP/SLX4.
  9. differences in the substrate selectivities of SNM1A and SNM1B are likely to be relevant to their in vivo roles
    Title: Characterization of the human SNM1A and SNM1B/Apollo DNA repair exonucleases.
  10. SNM1B functions epistatically to the central Fanconi anemia factor, FANCD2, in cellular survival after interstrand crosslinks damage and homology-directed repair of DNA double-strand breaks
    Title: Snm1B/Apollo functions in the Fanconi anemia pathway in response to DNA interstrand crosslinks.
Submit: New GeneRIF Correction See all GeneRIFs (20)

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
Dyskeratosis congenita, autosomal recessive 8
MedGen: C5774257 OMIM: 620133 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
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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Homology

Clone Names

  • FLJ12810, FLJ13998, DKFZp686C24187

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-3' DNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-3' exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables beta-lactamase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein-containing complex binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in double-strand break repair via nonhomologous end joining IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in interstrand cross-link repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in interstrand cross-link repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protection from non-homologous end joining at telomere IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomere capping IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomere maintenance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in telomere maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomere maintenance via telomere lengthening IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomeric 3' overhang formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in telomeric loop formation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome, telomeric region HDA PubMed 
colocalizes_with chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
5' exonuclease Apollo
Names
DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)
PSO2 homolog
SNM1 homolog B
beta-lactamase DCLRE1B
NP_001306875.1
NP_001306876.1
NP_001350619.1
NP_001350620.1
NP_073747.1

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_057565.1 RefSeqGene

    Range
    5708..14468
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1219

mRNA and Protein(s)

  1. NM_001319946.2 → NP_001306875.1  5' exonuclease Apollo isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate 5' exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AI669133, CR936679, DR005221
    Conserved Domains (3) summary
    cd11662
    Location:370 → 403
    apollo_TRF2_binding; TRF2-binding region of apollo and similar proteins
    pfam07522
    Location:90 → 173
    DRMBL; DNA repair metallo-beta-lactamase
    cl23716
    Location:1 → 25
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

  2. NM_001319947.2 → NP_001306876.1  5' exonuclease Apollo isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AI669133, BC029687, DA414122
    UniProtKB/Swiss-Prot
    Q9H816
    Conserved Domains (3) summary
    cd11662
    Location:370 → 403
    apollo_TRF2_binding; TRF2-binding region of apollo and similar proteins
    pfam07522
    Location:90 → 173
    DRMBL; DNA repair metallo-beta-lactamase
    cl23716
    Location:1 → 25
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

  3. NM_001363690.2 → NP_001350619.1  5' exonuclease Apollo isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) includes alternate splicing in the 3' coding region, which results in a frameshift compared to variant 1. The encoded isoform (c) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AL137856
    Conserved Domains (2) summary
    cd16273
    Location:6 → 151
    SNM1A-1C-like_MBL-fold; SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain
    pfam07522
    Location:216 → 299
    DRMBL; DNA repair metallo-beta-lactamase

  4. NM_001363691.2 → NP_001350620.1  5' exonuclease Apollo isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' and 3' coding regions, compared to variant 1. The encoded isoform (d) has a shorter N-terminus and a shorter distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AF306691, AI669133, AL137856
    Conserved Domains (2) summary
    pfam07522
    Location:90 → 173
    DRMBL; DNA repair metallo-beta-lactamase
    cl23716
    Location:1 → 25
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

  5. NM_022836.4 → NP_073747.1  5' exonuclease Apollo isoform a

    See identical proteins and their annotated locations for NP_073747.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AI669133, BC029687, DR005221
    Consensus CDS
    CCDS866.1
    UniProtKB/Swiss-Prot
    Q9H816, Q9H9E5
    UniProtKB/TrEMBL
    A0A3B3ITQ0
    Related
    ENSP00000498042.1, ENST00000650450.2
    Conserved Domains (3) summary
    cd11662
    Location:496 → 529
    apollo_TRF2_binding; TRF2-binding region of apollo and similar proteins
    cd16273
    Location:6 → 151
    SNM1A-1C-like_MBL-fold; SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain
    pfam07522
    Location:216 → 299
    DRMBL; DNA repair metallo-beta-lactamase

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    113904619..113914086
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    113916281..113925748
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H816.1 GenPept UniProtKB/Swiss-Prot:Q9H816

Gene LinkOut

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

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