Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
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

Show/Hide all (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
rs746617574	C>G	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, intron variant
rs748286715	CA>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant
rs750218942	C>G	Pathogenic	Intron variant, splice acceptor variant
rs752573039	->A	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained, splice donor variant
rs755803064	A>C,G	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant, stop gained
rs759052378	->TT	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs761978351	G>A	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs764582394	->TTTC	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs769255883	C>A,G,T	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, stop gained, missense variant
rs778543124	AGTCTTACGGTACA>-	Pathogenic-likely-pathogenic	Coding sequence variant, non coding transcript variant, splice donor variant, frameshift variant, intron variant
rs779161471	C>-	Likely-pathogenic, pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, frameshift variant
rs781195170	CTCT>-,CT	Likely-pathogenic	Coding sequence variant, intron variant, non coding transcript variant, frameshift variant
rs786205205	->TA	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, frameshift variant
rs886039226	ATAA>TTTCTTATG	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, stop gained
rs1019535182	A>G	Likely-pathogenic	Splice donor variant
rs1057519018	CT>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1200172747	TAAGA>-	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, frameshift variant
rs1240801740	CA>-	Likely-pathogenic	Inframe indel, intron variant, coding sequence variant, stop gained, non coding transcript variant
rs1253496792	A>G	Likely-pathogenic	Initiator codon variant, missense variant, non coding transcript variant, 5 prime UTR variant
rs1326841833	->T	Likely-pathogenic	Coding sequence variant, intron variant, frameshift variant, non coding transcript variant
rs1554699296	->A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1554699334	A>T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1554701103	->T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1554701129	->G	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1554701139	CT>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1554701144	AA>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1554701152	T>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1554701478	A>T	Likely-pathogenic	Splice donor variant, intron variant
rs1554701481	C>T	Likely-pathogenic	Splice donor variant, intron variant
rs1554701488	T>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant
rs1554701520	->T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant
rs1554701532	T>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained, intron variant
rs1554701540	CT>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant
rs1554701563	C>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant
rs1554701931	C>T	Likely-pathogenic	Splice donor variant, intron variant
rs1554701945	->TAAATTCTTTCCCA	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant
rs1554701985	AAGGAAAATGAACTCTAGTTTCCT>GAC	Likely-pathogenic	Intron variant
rs1554702597	TTACCT>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, splice donor variant, intron variant
rs1554702608	C>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1554702629	G>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1554703119	C>A,T	Likely-pathogenic	5 prime UTR variant, splice donor variant
rs1554703183	AAAGCCCCGTCGGCCGCCGCCATCTCTGGC>-	Likely-pathogenic	5 prime UTR variant, non coding transcript variant, inframe deletion, initiator codon variant
rs1564045331	ATTCTT>-	Likely-pathogenic	Inframe indel, non coding transcript variant, coding sequence variant, intron variant
rs1587744218	C>-	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1587755557	A>C	Pathogenic	Splice donor variant, 5 prime UTR variant

Show/Hide all (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
MIRT1496080	hsa-miR-3119	CLIP-seq
MIRT1496081	hsa-miR-3158-3p	CLIP-seq
MIRT1496082	hsa-miR-3163	CLIP-seq
MIRT1496083	hsa-miR-3180-5p	CLIP-seq
MIRT1496084	hsa-miR-4420	CLIP-seq
MIRT1496085	hsa-miR-4446-3p	CLIP-seq
MIRT1496086	hsa-miR-4446-5p	CLIP-seq
MIRT1496087	hsa-miR-4494	CLIP-seq
MIRT1496088	hsa-miR-4539	CLIP-seq
MIRT1496089	hsa-miR-4724-5p	CLIP-seq
MIRT1496090	hsa-miR-4755-5p	CLIP-seq
MIRT1496091	hsa-miR-499a-5p	CLIP-seq
MIRT1496092	hsa-miR-544	CLIP-seq
MIRT1496093	hsa-miR-642a	CLIP-seq
MIRT1496094	hsa-miR-653	CLIP-seq
MIRT2663398	hsa-miR-300	CLIP-seq
MIRT2663399	hsa-miR-3140-3p	CLIP-seq
MIRT2663400	hsa-miR-381	CLIP-seq
MIRT2663401	hsa-miR-4503	CLIP-seq
MIRT2663402	hsa-miR-4666-3p	CLIP-seq
MIRT1496089	hsa-miR-4724-5p	CLIP-seq
MIRT2663403	hsa-miR-4738-3p	CLIP-seq
MIRT2663404	hsa-miR-4789-5p	CLIP-seq
MIRT2663405	hsa-miR-4803	CLIP-seq
MIRT2663406	hsa-miR-556-3p	CLIP-seq
MIRT2663407	hsa-miR-944	CLIP-seq
MIRT2695369	hsa-miR-1298	CLIP-seq
MIRT2663398	hsa-miR-300	CLIP-seq
MIRT2663399	hsa-miR-3140-3p	CLIP-seq
MIRT2663400	hsa-miR-381	CLIP-seq
MIRT2663401	hsa-miR-4503	CLIP-seq
MIRT2663402	hsa-miR-4666-3p	CLIP-seq
MIRT1496089	hsa-miR-4724-5p	CLIP-seq
MIRT2663403	hsa-miR-4738-3p	CLIP-seq
MIRT2663404	hsa-miR-4789-5p	CLIP-seq
MIRT2663405	hsa-miR-4803	CLIP-seq
MIRT2663406	hsa-miR-556-3p	CLIP-seq
MIRT2695370	hsa-miR-624	CLIP-seq
MIRT2663407	hsa-miR-944	CLIP-seq

Show/Hide all (3)

Transcription factor	Regulation	Reference
DDB2	Unknown	24953096
ERCC2	Unknown	24953096
HMGA1	Repression	17616660

Show/Hide all (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
GO:0003684	Function	Damaged DNA binding	IEA
GO:0003684	Function	Damaged DNA binding	TAS	10946233
GO:0005515	Function	Protein binding	IPI	7700386, 8197175, 8999876, 9013642, 10944529, 10982866, 11058119, 12527904, 16491090, 17948053, 20304803, 20670893, 25416956, 28514442, 32296183, 33961781
GO:0005634	Component	Nucleus	IDA	1601884
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005662	Component	DNA replication factor A complex	IDA	7700386
GO:0005829	Component	Cytosol	IDA
GO:0006281	Process	DNA repair	IDA	1601884
GO:0006281	Process	DNA repair	IEA
GO:0006281	Process	DNA repair	IEA
GO:0006281	Process	DNA repair	IMP	1601884
GO:0006284	Process	Base-excision repair	IBA
GO:0006289	Process	Nucleotide-excision repair	IEA
GO:0006289	Process	Nucleotide-excision repair	IEA
GO:0006289	Process	Nucleotide-excision repair	IMP	21148310
GO:0006974	Process	DNA damage response	IEA
GO:0006979	Process	Response to oxidative stress	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008630	Process	Intrinsic apoptotic signaling pathway in response to DNA damage	IEA
GO:0009411	Process	Response to UV	IEA
GO:0009636	Process	Response to toxic substance	IEA
GO:0009650	Process	UV protection	IDA	1601884
GO:0009650	Process	UV protection	IMP	1601884
GO:0010506	Process	Regulation of autophagy	IEA
GO:0016604	Component	Nuclear body	IDA
GO:0019904	Function	Protein domain specific binding	IPI	17720715
GO:0034504	Process	Protein localization to nucleus	IMP	1601884
GO:0035264	Process	Multicellular organism growth	IEA
GO:0042803	Function	Protein homodimerization activity	IPI	8197175
GO:0046872	Function	Metal ion binding	IEA
GO:0060261	Process	Positive regulation of transcription initiation by RNA polymerase II	IEA
GO:0070914	Process	UV-damage excision repair	IBA
GO:1901255	Process	Nucleotide-excision repair involved in interstrand cross-link repair	IBA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

MIM	HGNC	e!Ensembl
611153	12814	ENSG00000136936

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
FDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGDMKL
YLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETI
VHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM

Sequence length

273

Interactions

View interactions

	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

206

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Thyroid cancer, nonmedullary, 1	Pathogenic	rs1587755557	RCV005887150
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 RCV002266270 RCV002281808 RCV003111575 RCV001255518 RCV005063025 RCV002265751 RCV000781922 RCV002255500 RCV000781923 RCV001174635 RCV002256462 RCV001194216 RCV003403540 RCV001585956
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 RCV000001049 RCV000001050 RCV000001051 RCV000001052 RCV000001053 RCV002289322 RCV002472010 RCV002472019 RCV000170428 RCV000246304 RCV001172311 RCV001172312 RCV003464890 RCV003464891 RCV003464892 RCV005047687 RCV004574099 RCV004573252 RCV004573874 RCV004573875 RCV004573876 RCV004573877 RCV004573878 RCV000415712 RCV000667095 RCV000754105 RCV003459478 RCV000667814 RCV000668902 RCV000674093 RCV000670038 RCV000674552 RCV000674742 RCV000670791 RCV000668826 RCV000674401 RCV000669338 RCV000666956 RCV000671796 RCV000668662 RCV000670923 RCV000665444 RCV000665796 RCV000673845 RCV000671391 RCV000670444 RCV000668799 RCV000670391 RCV000671795 RCV000670364 RCV000670758 RCV000673546 RCV000673551 RCV000674100 RCV000672997 RCV000672862 RCV000666994 RCV000674229 RCV000672325 RCV000669539 RCV000666137 RCV000671257 RCV000667207 RCV003467782
XPA-related disorder	Likely pathogenic; Pathogenic	rs746617574	RCV003403537

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Malignant tumor of esophagus	Likely benign	rs528443906	RCV005936592
Ovarian cancer	Conflicting classifications of pathogenicity	rs1477700804, rs1339290732	RCV003154192 RCV003154666
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	rs562768588	RCV005890482

Show/Hide Text Mining Associations (98)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acrocephalosyndactylia	Associate	18567921, 31478152
Adenocarcinoma	Associate	19270000
Alcoholic Neuropathy	Stimulate	24252196
Alternating hemiplegia of childhood	Associate	28398700
Ataxia Telangiectasia	Associate	27197874
Atrophy	Stimulate	24252196
Breast Neoplasms	Associate	18990233, 21751184, 24642895, 27768589, 33184404
Breast Neoplasms	Stimulate	21751184
Cachexia	Associate	24252196
Carcinogenesis	Associate	28222669
Carcinoma Basal Cell	Associate	30089811
Carcinoma Hepatocellular	Associate	26967386
Carcinoma Non Small Cell Lung	Associate	15882455, 19430706, 23617284, 26159902
Carcinoma Renal Cell	Associate	18711149
Carcinoma Squamous Cell	Associate	23335232, 25491297, 30089811
Cerebellar Ataxia	Associate	36893274
Chorea	Associate	38040034
Choroidal Effusions	Associate	15844177
Chromosome Aberrations	Associate	28222669
Cockayne Syndrome	Associate	11710928
Cognition Disorders	Associate	38040034
Cognitive Dysfunction	Associate	18567921
Colorectal Neoplasms	Associate	29568775, 29675892
Colorectal Neoplasms	Stimulate	31988591
Death	Associate	23617284, 26159902
DNA Repair Deficiency Disorders	Associate	10102040
DNA Virus Infections	Associate	6357782
Drug Hypersensitivity	Associate	27197874
Dystonia	Associate	38040034
Endometrial Neoplasms	Associate	21750170
Esophageal Neoplasms	Associate	19270000
Esophageal Squamous Cell Carcinoma	Associate	17653764, 26831662
Gastrointestinal Neoplasms	Associate	17653764
Gastrointestinal Stromal Tumors	Associate	27460091
Genetic Diseases Inborn	Associate	25913378
Glioblastoma	Stimulate	35536165
Glioma	Associate	35536165
Gliosis	Associate	24252196
Graft vs Host Disease	Associate	29513361
Granulosa cell tumor of the ovary	Associate	31906898
Hearing Loss Sensorineural	Associate	24252196, 34627174
Hematologic Diseases	Associate	28472728
Heredodegenerative Disorders Nervous System	Stimulate	18567921
Hypoxia	Associate	22467238
Immunologic Deficiency Syndromes	Associate	31455402
Infertility	Associate	28704716
Intellectual Disability	Associate	25566891
Intestinal Pseudo Obstruction	Stimulate	31906898
Keratosis Actinic	Associate	24636351
Laminopathies	Associate	28515154
Leukemia Myeloid Acute	Associate	16507781
Lung Neoplasms	Associate	22467238, 26159902, 26317794
Lupus Erythematosus Systemic	Associate	27492607
Lymphoma B Cell	Associate	23818366
Margins of Excision	Associate	27197874, 28704716
Melanoma	Associate	26880244, 27197874, 36232946
Muscular Disorders Atrophic	Associate	24252196
Myelodysplastic Syndromes	Associate	28472728
Nasopharyngeal Carcinoma	Associate	26156020
Neoplasm Metastasis	Stimulate	31906898
Neoplasms	Associate	15844177, 18567921, 25491297, 26156020, 26831662, 27307058, 27460091, 30089811, 32364878, 32859265, 33827469, 37240218, 38300970, 39237917, 6577447, 8040325, 8755929 View all (2 more)
Neoplasms	Inhibit	22182450
Neoplasms Germ Cell and Embryonal	Inhibit	10074455
Neoplasms Germ Cell and Embryonal	Associate	31906898
Neoplasms Radiation Induced	Inhibit	33380655
Neoplastic Syndromes Hereditary	Associate	33827469
Nerve Degeneration	Stimulate	24252196
Nervous System Diseases	Associate	24252196, 25913378, 34627174
Neuroblastoma	Associate	22182450
Neurodegenerative Diseases	Associate	10759556, 12177298, 24252196
Neurologic Manifestations	Associate	25566891, 31478152, 34627174, 38040034
Neurologic Manifestations	Stimulate	9284095
Ovarian Neoplasms	Inhibit	15844177
Ovarian Neoplasms	Associate	37240218, 38300970, 8040325
Pallor	Associate	24252196
Pena Shokeir syndrome type 1	Associate	38040034
Progeria	Associate	17848622, 28515154
Progeroid syndrome neonatal	Associate	17848622
Prostatic Neoplasms	Associate	36509750
Pterygium	Associate	20431719
Pulmonary Disease Chronic Obstructive	Associate	29506519
Rectal Neoplasms	Associate	29675892
Reflex Abnormal	Associate	38040034
Sensorimotor neuropathy with ataxia autosomal dominant	Stimulate	34627174
Skin Abnormalities	Associate	25913378
Skin Diseases	Associate	24063568, 8105686
Skin Neoplasms	Associate	17687452, 27197874, 30089811, 36893274, 9284095
Skin Neoplasms	Stimulate	24252196
Smoke Inhalation Injury	Associate	27622501
Squamous Cell Carcinoma of Head and Neck	Associate	27622501, 33714009, 35390246, 36118674
Squamous Cell Carcinoma of Head and Neck	Inhibit	29528139
Stomach Neoplasms	Associate	27340861
Testicular Neoplasms	Associate	10074455
Trichothiodystrophy Syndromes	Associate	11710928
Urinary Bladder Neoplasms	Inhibit	28222669
Xeroderma Pigmentosum	Associate	1188925, 18470933, 18927284, 1918083, 19917958, 23755135, 24063568, 25056193, 25491297, 25566891, 25913378, 26874523, 27413738, 28704716, 28719581 View all (11 more)
Xeroderma Pigmentosum	Inhibit	2168562
Xeroderma Pigmentosum Complementation Group B	Associate	10102040, 8105686

XPA (XPA, DNA damage recognition and repair factor)