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

Summary

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
Title: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
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.
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.
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.
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.
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.
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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

XPC_1288 (e-PCR)
- UniSTS:277867

XPC_v388 (e-PCR)
- UniSTS:277867

D3S1440 (e-PCR)
- UniSTS:148117

D3S1441 (e-PCR)
- UniSTS:148118

RH69460 (e-PCR)
- UniSTS:62148

STS-X65024 (e-PCR)
- UniSTS:83407

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

NG_011763.1 RefSeqGene

Range

5001..38526

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_472

mRNA and Protein(s)

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
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
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
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
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

NR_148950.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC093495, FJ695192
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

14145147..14178601 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047448864.1 → XP_047304820.1 DNA repair protein complementing XP-C cells isoform X1
XM_047448865.1 → XP_047304821.1 DNA repair protein complementing XP-C cells isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

14147095..14180465 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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.