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XPC XPC complex subunit, DNA damage recognition and repair factor [ Homo sapiens (human) ]

Gene ID: 7508, updated on 3-Apr-2024

Summary

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Official Symbol
XPCprovided by HGNC
Official Full Name
XPC complex subunit, DNA damage recognition and repair factorprovided by HGNC
Primary source
HGNC:HGNC:12816
See related
Ensembl:ENSG00000154767 MIM:613208; AllianceGenome:HGNC:12816
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
XP3; RAD4; XPCC; p125
Summary
The protein encoded by this gene is a key component of the XPC complex, which plays an important role in the early steps of global genome nucleotide excision repair (NER). The encoded protein is important for damage sensing and DNA binding, and shows a preference for single-stranded DNA. Mutations in this gene or some other NER components can result in Xeroderma pigmentosum, a rare autosomal recessive disorder characterized by increased sensitivity to sunlight with the development of carcinomas at an early age. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017]
Expression
Ubiquitous expression in ovary (RPKM 17.1), kidney (RPKM 15.8) and 25 other tissues See more
Orthologs
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Genomic context

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See XPC in Genome Data Viewer
Location:
3p25.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (14145147..14178601, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (14147095..14180465, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (14186647..14220101, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:14163053-14163787 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:14163788-14164523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14088 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14165995-14166729 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14166730-14167464 Neighboring gene transmembrane protein 43 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14185247-14185934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19499 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14190053-14190737 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14192355-14192855 Neighboring gene XPC antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19501 Neighboring gene LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14251094-14251594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14251595-14252095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14092 Neighboring gene uncharacterized LOC105376958

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. Association between polymorphisms rs2228001 and rs2228000 in XPC and genetic susceptibility to preeclampsia: a case control study. Wang J, et al. BMC Pregnancy Childbirth, 2021 Nov 22. PMID 34802422, Free PMC Article
  2. Loss of Function Variants in the XPC Causes Severe Xeroderma Pigmentosum in Three Large Consanguineous Families. Nawal W, et al. Klin Padiatr, 2022 May. PMID 34544175
  3. Genetic variations in nucleotide excision repair pathway genes and hepatoblastoma susceptibility. Zhuo Z, et al. Int J Cancer, 2021 Nov 1. PMID 34196959
  4. Association of DNA repair gene XPC Ala499Val (rs2228000 C>T) and Lys939Gln (rs2228001 A>C) polymorphisms with the risk of chronic myeloid leukemia: A case-control study in a South Indian population. Lakkireddy S, et al. J Gene Med, 2021 Jul. PMID 33829606
  5. XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature. Yurchenko AA, et al. Nat Commun, 2020 Nov 17. PMID 33203900, Free PMC Article

See all (429) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic Polymorphisms of XPC, XPD, XPG Genes and their Association with Radiotherapy Induced Toxicity among Head and Neck Cancer Patients: A Hospital Based Study from Maharashtra.
    Title: Genetic Polymorphisms of XPC, XPD, XPG Genes and their Association with Radiotherapy Induced Toxicity among Head and Neck Cancer Patients: A Hospital Based Study from Maharashtra.
  2. Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein.
    Title: Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein.
  3. A Significant Increasing Risk Association between Cigarette Smoking and XPA and XPC Genes Polymorphisms.
    Title: A Significant Increasing Risk Association between Cigarette Smoking and XPA and XPC Genes Polymorphisms.
  4. Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
    Title: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
  5. Regulation of XPC Binding Dynamics and Global Nucleotide Excision Repair by p63 and Vitamin D Receptor.
    Title: Regulation of XPC Binding Dynamics and Global Nucleotide Excision Repair by p63 and Vitamin D Receptor.
  6. Joint effects of polycyclic aromatic hydrocarbons, smoking, and XPC polymorphisms on damage in exon 2 of KRAS gene among young coke oven workers.
    Title: Joint effects of polycyclic aromatic hydrocarbons, smoking, and XPC polymorphisms on damage in exon 2 of KRAS gene among young coke oven workers.
  7. Loss of Function Variants in the XPC Causes Severe Xeroderma Pigmentosum in Three Large Consanguineous Families.", trans "Loss-of-Function-Varianten im XPC als Ursache schwerer Xeroderma pigmentosum in drei grossen konsanguinen Familien.
    Title: Loss of Function Variants in the XPC Causes Severe Xeroderma Pigmentosum in Three Large Consanguineous Families.
  8. Association of DNA repair gene XPC Ala499Val (rs2228000 C>T) and Lys939Gln (rs2228001 A>C) polymorphisms with the risk of chronic myeloid leukemia: A case-control study in a South Indian population.
    Title: Association of DNA repair gene XPC Ala499Val (rs2228000 C>T) and Lys939Gln (rs2228001 A>C) polymorphisms with the risk of chronic myeloid leukemia: A case-control study in a South Indian population.
  9. Hsa_circ_0069244 acts as the sponge of miR-346 to inhibit non-small cell lung cancer progression by regulating XPC expression.
    Title: Hsa_circ_0069244 acts as the sponge of miR-346 to inhibit non-small cell lung cancer progression by regulating XPC expression.
  10. Increased H2O2 levels and p53 stabilization lead to mitochondrial dysfunction in XPC-deficient cells.
    Title: Increased H2O2 levels and p53 stabilization lead to mitochondrial dysfunction in XPC-deficient cells.
Submit: New GeneRIF Correction See all GeneRIFs (247)

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
Xeroderma pigmentosum, group C
MedGen: C2752147 OMIM: 278720 GeneReviews: Xeroderma Pigmentosum
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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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA damage sensor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA damage sensor activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding IEA
Inferred from Electronic Annotation
more info
  
enables bubble DNA binding TAS
Traceable Author Statement
more info
 PubMed 
enables damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables damaged DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables heteroduplex DNA loop binding TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables single-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA repair TAS
Traceable Author Statement
more info
 PubMed 
involved_in UV-damage excision repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mismatch repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitotic intra-S DNA damage checkpoint signaling IEA
Inferred from Electronic Annotation
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 
involved_in nucleotide-excision repair ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in pyrimidine dimer repair by nucleotide-excision repair IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of mitotic cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to UV-B IEA
Inferred from Electronic Annotation
more info
  
involved_in response to auditory stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in response to xenobiotic stimulus IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of XPC complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of XPC complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in nucleolus 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
  
part_of nucleotide-excision repair complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of nucleotide-excision repair factor 2 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
located_in site of DNA damage IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
DNA repair protein complementing XP-C cells
Names
mutant xeroderma pigmentosum group C
xeroderma pigmentosum, complementation group C

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_011763.1 RefSeqGene

    Range
    5001..38526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_472

mRNA and Protein(s)

  1. NM_001354726.2 → NP_001341655.1  DNA repair protein complementing XP-C cells isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC093495, FJ695191, FJ695192
    Conserved Domains (1) summary
    TIGR00605
    Location:1 → 674
    rad4; DNA repair protein rad4

  2. NM_001354727.2 → NP_001341656.1  DNA repair protein complementing XP-C cells isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon and contains another alternate exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC093495, FJ695192
    UniProtKB/TrEMBL
    D9I4E1
    Conserved Domains (1) summary
    TIGR00605
    Location:147 → 865
    rad4; DNA repair protein rad4

  3. NM_001354729.2 → NP_001341658.1  DNA repair protein complementing XP-C cells isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice junction in the 5' end compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC093495, FJ695191, FJ695192
    UniProtKB/TrEMBL
    D9I4E1
    Conserved Domains (1) summary
    TIGR00605
    Location:141 → 861
    rad4; DNA repair protein rad4

  4. NM_001354730.2 → NP_001341659.1  DNA repair protein complementing XP-C cells isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (6) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC093495, FJ695191, FJ695192
    UniProtKB/TrEMBL
    D9I4E1
    Conserved Domains (1) summary
    cl26537
    Location:147 → 785
    BHD_3; Rad4 beta-hairpin domain 3

  5. NM_004628.5 → NP_004619.3  DNA repair protein complementing XP-C cells isoform 1

    See identical proteins and their annotated locations for NP_004619.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC093495, FJ695191, FJ695192
    Consensus CDS
    CCDS46763.1
    UniProtKB/Swiss-Prot
    B4DIP3, E9PB96, E9PH69, Q01831, Q53GT7, Q96AX0
    UniProtKB/TrEMBL
    D9I4E1, X5DRB1
    Related
    ENSP00000285021.8, ENST00000285021.12
    Conserved Domains (1) summary
    TIGR00605
    Location:147 → 867
    rad4; DNA repair protein rad4

RNA

  1. NR_148950.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC093495, FJ695192

  2. NR_148951.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC093495, FJ695192

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    14145147..14178601 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047448864.1 → XP_047304820.1  DNA repair protein complementing XP-C cells isoform X1

  2. XM_047448865.1 → XP_047304821.1  DNA repair protein complementing XP-C cells isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    14147095..14180465 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347761.1 → XP_054203736.1  DNA repair protein complementing XP-C cells isoform X1

  2. XM_054347762.1 → XP_054203737.1  DNA repair protein complementing XP-C cells isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001145769.1: Suppressed sequence

    Description
    NM_001145769.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q01831.4 GenPept UniProtKB/Swiss-Prot:Q01831

Gene LinkOut

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