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SPRTN SprT-like N-terminal domain [ Homo sapiens (human) ]

Gene ID: 83932, updated on 13-Apr-2024

Summary

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Official Symbol
SPRTNprovided by HGNC
Official Full Name
SprT-like N-terminal domainprovided by HGNC
Primary source
HGNC:HGNC:25356
See related
Ensembl:ENSG00000010072 MIM:616086; AllianceGenome:HGNC:25356
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
DVC1; PRO4323; spartan; C1orf124
Summary
The protein encoded by this gene may play a role in DNA repair during replication of damaged DNA. This protein recruits valosin containing protein (p97) to stalled DNA replication forks where it may prevent excessive translesional DNA synthesis and limit the number of DNA-damage induced mutations. It may also be involved in replication-related G2/M-checkpoint regulation. Deficiency of a similar protein in mouse causes chromosomal instability and progeroid phenotypes. Mutations in this gene have been associated with Ruijs-Aalfs syndrome (RJALS). Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2015]
Expression
Broad expression in testis (RPKM 6.8), bone marrow (RPKM 3.1) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1q42.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (231338293..231355023)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (230721543..230738274)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (231474039..231490769)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:231420145-231420646 Neighboring gene RNA, 5S ribosomal pseudogene 80 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:231472900-231473775 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:231473776-231474650 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:231474651-231475525 Neighboring gene exocyst complex component 8 Neighboring gene uncharacterized LOC107985360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2729 Neighboring gene egl-9 family hypoxia inducible factor 1 Neighboring gene Sharpr-MPRA regulatory region 11665 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:231538414-231538617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2730 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:231558174-231558498 Neighboring gene small nuclear ribonucleoprotein D2 pseudogene 2

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. SPRTN patient variants cause global-genome DNA-protein crosslink repair defects. Weickert P, et al. Nat Commun, 2023 Jan 21. PMID 36681662, Free PMC Article
  2. The protease SPRTN and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability. Ruggiano A, et al. Cell Rep, 2021 Dec 7. PMID 34879279, Free PMC Article
  3. A ubiquitin switch controls autocatalytic inactivation of the DNA-protein crosslink repair protease SPRTN. Zhao S, et al. Nucleic Acids Res, 2021 Jan 25. PMID 33348378, Free PMC Article
  4. DNA Structure-Specific Cleavage of DNA-Protein Crosslinks by the SPRTN Protease. Reinking HK, et al. Mol Cell, 2020 Oct 1. PMID 32853547, Free PMC Article
  5. Structural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan. Li F, et al. Cell Rep, 2019 Mar 19. PMID 30893605

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SPRTN is involved in hepatocellular carcinoma development through the ER stress response.
    Title: SPRTN is involved in hepatocellular carcinoma development through the ER stress response.
  2. SPRTN patient variants cause global-genome DNA-protein crosslink repair defects.
    Title: SPRTN patient variants cause global-genome DNA-protein crosslink repair defects.
  3. Ubiquitin-directed AAA+ ATPase p97/VCP unfolds stable proteins crosslinked to DNA for proteolysis by SPRTN.
    Title: Ubiquitin-directed AAA+ ATPase p97/VCP unfolds stable proteins crosslinked to DNA for proteolysis by SPRTN.
  4. The protease SPRTN and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability.
    Title: The protease SPRTN and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability.
  5. Replication-dependent cytotoxicity and Spartan-mediated repair of trapped PARP1-DNA complexes.
    Title: Replication-dependent cytotoxicity and Spartan-mediated repair of trapped PARP1-DNA complexes.
  6. SPRTN protease-cleaved MRE11 decreases DNA repair and radiosensitises cancer cells.
    Title: SPRTN protease-cleaved MRE11 decreases DNA repair and radiosensitises cancer cells.
  7. USP11 mediates repair of DNA-protein cross-links by deubiquitinating SPRTN metalloprotease.
    Title: USP11 mediates repair of DNA-protein cross-links by deubiquitinating SPRTN metalloprotease.
  8. A ubiquitin switch controls autocatalytic inactivation of the DNA-protein crosslink repair protease SPRTN.
    Title: A ubiquitin switch controls autocatalytic inactivation of the DNA-protein crosslink repair protease SPRTN.
  9. DNA Structure-Specific Cleavage of DNA-Protein Crosslinks by the SPRTN Protease.
    Title: DNA Structure-Specific Cleavage of DNA-Protein Crosslinks by the SPRTN Protease.
  10. TEX264 recognises both unmodified and SUMO1-modifed TOP1 and initiates TOP1cc repair by recruiting p97 and SPRTN.
    Title: TEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts.
Submit: New GeneRIF Correction See all GeneRIFs (26)

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
Progeroid features-hepatocellular carcinoma predisposition syndrome
MedGen: C4015461 OMIM: 616200 GeneReviews: Not available
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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

Clone Names

  • dJ876B10.3, DKFZp547N043

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables K63-linked polyubiquitin modification-dependent protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metalloendopeptidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables polyubiquitin modification-dependent protein binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein autoprocessing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein-DNA covalent cross-linking repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteolysis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to UV IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in translesion synthesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in translesion synthesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
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
DNA-dependent metalloprotease SPRTN
Names
DNA damage protein targeting VCP
DNA damage-targeting VCP (p97) adaptor
zinc finger RAD18 domain-containing protein
NP_001010984.1
NP_001248391.1
NP_114407.3
XP_006711881.1
XP_054194986.1

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_042052.1 RefSeqGene

    Range
    5358..22088
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001010984.4 → NP_001010984.1  DNA-dependent metalloprotease SPRTN isoform b

    See identical proteins and their annotated locations for NP_001010984.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate segment in the 3' end which results in the introduction of an early stop codon, compared to variant 1. This variant encodes a protein (isoform B) with a shorter C-terminus which lacks a Rad18-like CCHC zinc finger domain, compared to isoform A.
    Source sequence(s)
    AL117352, AY358611, BC068478, BU630543
    Consensus CDS
    CCDS31054.1
    UniProtKB/Swiss-Prot
    Q9H040
    Related
    ENSP00000375731.4, ENST00000391858.8
    Conserved Domains (1) summary
    pfam10263
    Location:45 → 213
    SprT-like; SprT-like family

  2. NM_001261462.3 → NP_001248391.1  DNA-dependent metalloprotease SPRTN isoform c

    See identical proteins and their annotated locations for NP_001248391.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks a coding exon and has an alternate segment in the 3' end which results in the introduction of an early stop codon, compared to variant 1. This variant encodes a protein (isoform C) with a shorter C-terminus which lacks a Rad18-like CCHC zinc finger domain, compared to isoform A.
    Source sequence(s)
    AL117352, AY358611, BC068478, BU630543
    Consensus CDS
    CCDS58066.1
    UniProtKB/Swiss-Prot
    Q9H040
    Related
    ENSP00000008440.9, ENST00000008440.9
    Conserved Domains (1) summary
    pfam10263
    Location:45 → 170
    SprT-like; SprT-like family

  3. NM_032018.7 → NP_114407.3  DNA-dependent metalloprotease SPRTN isoform a

    See identical proteins and their annotated locations for NP_114407.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (A).
    Source sequence(s)
    AL117352, BC068478, BU630543
    Consensus CDS
    CCDS1594.1
    UniProtKB/Swiss-Prot
    B1AKT0, B5MEF7, Q5TE78, Q6UWW6, Q96BC5, Q96KA0, Q9H040
    Related
    ENSP00000295050.7, ENST00000295050.12
    Conserved Domains (2) summary
    smart00734
    Location:453 → 476
    ZnF_Rad18; Rad18-like CCHC zinc finger
    pfam10263
    Location:45 → 213
    SprT-like; SprT-like family

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
    231338293..231355023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006711818.4 → XP_006711881.1  DNA-dependent metalloprotease SPRTN isoform X1

    Conserved Domains (2) summary
    smart00734
    Location:410 → 433
    ZnF_Rad18; Rad18-like CCHC zinc finger
    smart00731
    Location:43 → 169
    SprT; SprT homologues

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    230721543..230738274
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339011.1 → XP_054194986.1  DNA-dependent metalloprotease SPRTN isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H040.2 GenPept UniProtKB/Swiss-Prot:Q9H040

Gene LinkOut

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