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

Summary

Official Symbol: XPAprovided by HGNC
Official Full Name: XPA, DNA damage recognition and repair factorprovided by HGNC
Primary source: HGNC:HGNC:12814
See related: Ensembl:ENSG00000136936 MIM:611153; AllianceGenome:HGNC:12814
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: XP1; XPAC
Summary: This gene encodes a zinc finger protein plays a central role in nucleotide excision repair (NER), a specialized type of DNA repair. NER is responsible for repair of UV radiation-induced photoproducts and DNA adducts induced by chemical carcinogens and chemotherapeutic drugs. The encoded protein interacts with DNA and several NER proteins, acting as a scaffold to assemble the NER incision complex at sites of DNA damage. Mutations in this gene cause Xeroderma pigmentosum complementation group A (XP-A), an autosomal recessive skin disorder featuring hypersensitivity to sunlight and increased risk for skin cancer. [provided by RefSeq, Aug 2017]
Expression: Ubiquitous expression in thyroid (RPKM 6.2), fat (RPKM 4.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q22.33

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (97654398..97697340, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (109826339..109869281, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (100437191..100459622, complement)

Chromosome 9 - NC_000009.12 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?

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.
A disease-associated XPA allele interferes with TFIIH binding and primarily affects transcription-coupled nucleotide excision repair.
Title: A disease-associated XPA allele interferes with TFIIH binding and primarily affects transcription-coupled nucleotide excision repair.
Homozygous CRISPR/Cas9 Knockout Generated a Novel Functionally Active Exon 1 Skipping XPA Variant in Melanoma Cells.
Title: Homozygous CRISPR/Cas9 Knockout Generated a Novel Functionally Active Exon 1 Skipping XPA Variant in Melanoma Cells.
XPA Enhances Temozolomide Resistance of Glioblastoma Cells by Promoting Nucleotide Excision Repair.
Title: XPA Enhances Temozolomide Resistance of Glioblastoma Cells by Promoting Nucleotide Excision Repair.
Nucleotide Excision Repair Pathway Activity Is Inhibited by Airborne Particulate Matter (PM10) through XPA Deregulation in Lung Epithelial Cells.
Title: Nucleotide Excision Repair Pathway Activity Is Inhibited by Airborne Particulate Matter (PM(10)) through XPA Deregulation in Lung Epithelial Cells.
Probing Protein-DNA Conformational Dynamics in DNA Damage Recognition: Xeroderma Pigmentosum Group A Stabilizes the Damaged DNA-RPA14 Complex by Controlling Conformational Fluctuation Dynamics.
Title: Probing Protein-DNA Conformational Dynamics in DNA Damage Recognition: Xeroderma Pigmentosum Group A Stabilizes the Damaged DNA-RPA14 Complex by Controlling Conformational Fluctuation Dynamics.
XPA is susceptible to proteolytic cleavage by cathepsin L during lysis of quiescent cells.
Title: XPA is susceptible to proteolytic cleavage by cathepsin L during lysis of quiescent cells.
Xeroderma pigmentosum A homolog from Hydra partially complements DNA repair defect in human XPA-deficient cells.
Title: Xeroderma pigmentosum A homolog from Hydra partially complements DNA repair defect in human XPA-deficient cells.
Regulation of XPA could play a role in inhibition of radiation-induced bystander effects in QU-DB cells at high doses.
Title: Regulation of XPA could play a role in inhibition of radiation-induced bystander effects in QU-DB cells at high doses.

Submit: New GeneRIF Correction See all GeneRIFs (140)

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 A MedGen: C0268135 OMIM: 278700 GeneReviews: Xeroderma Pigmentosum	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study identifies a novel susceptibility gene for serum TSH levels in Chinese populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed
The FOXE1 locus is a major genetic determinant for radiation-related thyroid carcinoma in Chernobyl. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

STS-D14533 (e-PCR)
- UniSTS:82198

XPA_1273 (e-PCR)
- UniSTS:277866

XPA_v374 (e-PCR)
- UniSTS:277866

RH46402 (e-PCR)
- UniSTS:31083

D9S1714 (e-PCR)
- UniSTS:57979

RH65875 (e-PCR)
- UniSTS:76725

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in UV protection	IDA Inferred from Direct Assay more info	PubMed
involved_in UV protection	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in UV-damage excision repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in base-excision repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in nucleotide-excision repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleotide-excision repair involved in interstrand cross-link repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in nucleotide-excision repair, DNA damage recognition	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein localization to nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to auditory stimulus	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of DNA replication factor A complex	IDA Inferred from Direct Assay more info	PubMed
located_in intercellular bridge	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 factor 1 complex	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 repair protein complementing XP-A cells

Names: xeroderma pigmentosum group A-complementing protein; xeroderma pigmentosum, complementation group A

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_011642.1 RefSeqGene

Range

5001..27501

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_471

mRNA and Protein(s)

NM_000380.4 → NP_000371.1 DNA repair protein complementing XP-A cells isoform 1

See identical proteins and their annotated locations for NP_000371.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

BC014965, CB155090

Consensus CDS

CCDS6729.1

UniProtKB/Swiss-Prot

P23025, Q5T1U9, Q6LCW7, Q6LD02

UniProtKB/TrEMBL

F2Z2T2

Related

ENSP00000364270.5, ENST00000375128.5

Conserved Domains (1) summary

TIGR00598
Location:105 → 273

rad14; DNA repair protein
NM_001354975.2 → NP_001341904.1 DNA repair protein complementing XP-A cells isoform 2

Status: REVIEWED

Source sequence(s)

AL445531

Conserved Domains (1) summary

TIGR00598
Location:63 → 231

rad14; DNA repair protein

RNA

NR_027302.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an additional exon in the CDS, which includes an upstream stop codon, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, so is unlikely to make a functional protein.

Source sequence(s)

AI961077, AL531629, BC014965, CB155090

Related

ENST00000462523.5
NR_149091.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL445531
NR_149092.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL445531
NR_149093.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL445531
NR_149094.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL445531

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_000009.12 Reference GRCh38.p14 Primary Assembly

Range

97654398..97697340 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006717278.2 → XP_006717341.1 DNA repair protein complementing XP-A cells isoform X1

UniProtKB/TrEMBL

F2Z2T2

Conserved Domains (3) summary

TIGR00598
Location:105 → 257

rad14; DNA repair protein

pfam01286
Location:104 → 133

XPA_N; XPA protein N-terminal

pfam05181
Location:135 → 186

XPA_C; XPA protein C-terminus