Gene Gene information from NCBI Gene database.
Entrez ID 7507
Gene name XPA, DNA damage recognition and repair factor
Gene symbol XPA
Synonyms (NCBI Gene)
XP1XPAC
Chromosome 9
Chromosome location 9q22.33
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 che
SNPs SNP information provided by dbSNP.
50
SNP ID Visualize variation Clinical significance Consequence
rs104894131 C>A,T Likely-pathogenic, uncertain-significance Coding sequence variant, non coding transcript variant, missense variant, intron variant
rs104894132 G>A Pathogenic Coding sequence variant, non coding transcript variant, stop gained
rs104894133 G>A Pathogenic Coding sequence variant, non coding transcript variant, stop gained
rs104894134 A>G,T Pathogenic, likely-benign Non coding transcript variant, synonymous variant, intron variant, stop gained, coding sequence variant
rs149226993 G>A Likely-pathogenic, pathogenic Non coding transcript variant, stop gained, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
44
miRTarBase ID miRNA Experiments Reference
MIRT004137 hsa-miR-192-5p Microarray 16822819
MIRT003917 hsa-miR-210-3p Western blot 19141645
MIRT003918 hsa-miR-373-3p Western blot 19141645
MIRT1496078 hsa-miR-1296 CLIP-seq
MIRT1496079 hsa-miR-2909 CLIP-seq
Transcription factors Transcription factors information provided by TRRUST V2 database.
3
Transcription factor Regulation Reference
DDB2 Unknown 24953096
ERCC2 Unknown 24953096
HMGA1 Repression 17616660
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
41
GO ID Ontology Definition Evidence Reference
GO:0000110 Component Nucleotide-excision repair factor 1 complex IBA
GO:0000715 Process Nucleotide-excision repair, DNA damage recognition IBA
GO:0003677 Function DNA binding IEA
GO:0003684 Function Damaged DNA binding IBA
GO:0003684 Function Damaged DNA binding IDA 7700386
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
611153 12814 ENSG00000136936
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P23025
Protein name DNA repair protein complementing XP-A cells (Xeroderma pigmentosum group A-complementing protein)
Protein function Involved in DNA nucleotide excision repair (NER). Initiates repair by binding to damaged sites with various affinities, depending on the photoproduct and the transcriptional state of the region. Required for UV-induced CHEK1 phosphorylation and
PDB 1D4U , 1XPA , 2JNW , 6J44 , 6LAE , 6RO4 , 7AD8 , 8EBT , 8EBU , 8EBX , 8EBY
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01286 XPA_N 102 133 XPA protein N-terminal Domain
PF05181 XPA_C 135 186 XPA protein C-terminus Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in various cell lines and in skin fibroblasts. {ECO:0000269|PubMed:1918083, ECO:0000269|PubMed:8543191}.
Sequence
MAAADGALPEAAALEQPAELPASVRASIERKRQRALMLRQARLAARPYSATAAAATGGMA
NVKAAPKIIDTGGGFILEEEEEEEQKIGKVVHQPGPVMEFDYVICEECGKEFMDSYLMNH
FDLPTCDNCRDAD
DKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGDMKL
YLKLQI
VKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETI
VHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM
Sequence length 273
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Platinum drug resistance
Nucleotide excision repair
  Formation of Incision Complex in GG-NER
Dual Incision in GG-NER
Formation of TC-NER Pre-Incision Complex
Dual incision in TC-NER
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
13
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Thyroid cancer, nonmedullary, 1 Pathogenic rs1587755557 RCV005887150
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Xeroderma pigmentosum Pathogenic; Likely pathogenic rs2131379218, rs104894131, rs1200172747, rs104894132, rs104894133, rs2131393093, rs2490184373, rs777372873, rs750218942, rs2490237534, rs1057519018, rs1554701103, rs1554701540, rs149226993, rs746617574
View all (4 more)
RCV004526164
RCV005055500
RCV000780797
RCV000781924
RCV001420782
View all (14 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Xeroderma pigmentosum group A Likely pathogenic; Pathogenic rs757098056, rs746824252, rs2131379218, rs2131396482, rs104894131, rs1200172747, rs104894132, rs104894133, rs104894134, rs1587755557, rs2490221098, rs777372873, rs1405271436, rs786205205, rs750218942
View all (51 more)
RCV003462882
RCV005040424
RCV005050485
RCV003464313
RCV000001048
View all (64 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
XPA-related disorder Likely pathogenic; Pathogenic rs746617574 RCV003403537
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
CARCINOMA, BASAL CELL CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
INTESTINAL NEOPLASMS CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
LIVER NEOPLASMS CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Actinic keratosis Actinic keratosis CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 15598786
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma LHGDN 18645534
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 15598786
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 9864090
★☆☆☆☆
Found in Text Mining only
Adenoma of large intestine Colorectal adenoma BEFREE 29871536
★☆☆☆☆
Found in Text Mining only
Alopecia Alopecia HPO_DG
★☆☆☆☆
Found in Text Mining only
Alternating hemiplegia of childhood Alternating hemiplegia of childhood Pubtator 28398700 Associate
★☆☆☆☆
Found in Text Mining only
Apraxias Apraxia CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Ataxia Telangiectasia Ataxia Telangiectasia BEFREE 27197874
★☆☆☆☆
Found in Text Mining only