WRAP53 (WD repeat containing antisense to TP53)

Gene

• Entrez ID: 55135
• Gene name: WD repeat containing antisense to TP53
• Gene symbol: WRAP53
• Synonyms (NCBI Gene): DKCB3, TCAB1, WDR79
• Chromosome: 17
• Chromosome location: 17p13.1
• Summary: This gene encodes an essential component of the telomerase holoenzyme complex, a ribonucleoprotein complex required for telomere synthesis. This protein is enriched in Cajal bodies, nuclear sites of RNP processing that are important for telomerase functio

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs116535684	G>A,T	Conflicting-interpretations-of-pathogenicity, benign	Coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs281865548	C>T	Pathogenic	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, missense variant
rs281865549	C>T	Pathogenic	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, missense variant
rs281865550	G>A	Pathogenic	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, missense variant
rs968150359	G>A	Risk-factor	Missense variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant, 3 prime UTR variant
rs1597422298	T>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022742	hsa-miR-124-3p	Proteomics	18668037
MIRT038551	hsa-miR-106b-3p	CLASH	23622248
MIRT037886	hsa-miR-455-3p	CLASH	23622248
MIRT734576	hsa-miR-302a-3p	qRT-PCR	33123477

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000781	Component	Chromosome, telomeric region	IEA
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IDA	19179534
GO:0003723	Function	RNA binding	IEA
GO:0003723	Function	RNA binding	IPI	20351177
GO:0005515	Function	Protein binding	IPI	19179534, 21072240, 25467444, 32296183
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005697	Component	Telomerase holoenzyme complex	IDA	19179534, 26170453, 29695869, 29804836
GO:0005829	Component	Cytosol	IDA
GO:0006281	Process	DNA repair	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0007004	Process	Telomere maintenance via telomerase	IDA	29695869, 29804836
GO:0007004	Process	Telomere maintenance via telomerase	TAS	25467444
GO:0015030	Component	Cajal body	IBA
GO:0015030	Component	Cajal body	IDA	19179534, 19285445, 21072240, 22547674, 26170453
GO:0015030	Component	Cajal body	IEA
GO:0015030	Component	Cajal body	IMP	25467444
GO:0016604	Component	Nuclear body	IDA
GO:0030576	Process	Cajal body organization	IBA
GO:0030576	Process	Cajal body organization	IMP	21072240
GO:0031625	Function	Ubiquitin protein ligase binding	IPI	25512560, 27715493
GO:0032203	Process	Telomere formation via telomerase	IMP	19179534
GO:0032212	Process	Positive regulation of telomere maintenance via telomerase	IDA	23685356
GO:0034337	Process	RNA folding	IDA	29804836
GO:0035861	Component	Site of double-strand break	IDA	25512560, 26734725, 27715493
GO:0042393	Function	Histone binding	IPI	26734725, 27715493
GO:0042802	Function	Identical protein binding	IPI	21072240
GO:0044877	Function	Protein-containing complex binding	IDA	25467444
GO:0045739	Process	Positive regulation of DNA repair	IDA	25512560
GO:0051087	Function	Protein-folding chaperone binding	IPI	25467444
GO:0070034	Function	Telomerase RNA binding	IDA	22547674, 26170453, 29695869, 29804836
GO:0070034	Function	Telomerase RNA binding	IPI	20351177, 25467444
GO:0090666	Process	ScaRNA localization to Cajal body	IDA	19285445
GO:0090666	Process	ScaRNA localization to Cajal body	IMP	25467444
GO:0090671	Process	Telomerase RNA localization to Cajal body	IMP	25467444
GO:0140597	Function	Protein carrier chaperone	IMP	25467444
GO:0140691	Function	RNA folding chaperone	IDA	19179534, 29804836
GO:0140691	Function	RNA folding chaperone	IEA
GO:1904851	Process	Positive regulation of establishment of protein localization to telomere	IMP	25467444
GO:1904867	Process	Protein localization to Cajal body	IDA	22547674, 25467444
GO:1905168	Process	Positive regulation of double-strand break repair via homologous recombination	IDA	25512560
GO:2000781	Process	Positive regulation of double-strand break repair	IDA	27715493
GO:2001034	Process	Positive regulation of double-strand break repair via nonhomologous end joining	IDA	25512560

Other IDs

• MIM: 612661
• HGNC: 25522
• e!Ensembl: ENSG00000141499

Protein

• UniProt ID: Q9BUR4
• Protein name: Telomerase Cajal body protein 1 (WD repeat-containing protein 79) (WD40 repeat-containing protein antisense to TP53 gene) (WRAP53beta)
• Protein function: RNA chaperone that plays a key role in telomere maintenance and RNA localization to Cajal bodies (PubMed:29695869, PubMed:29804836). Specifically recognizes and binds the Cajal body box (CAB box) present in both small Cajal body RNAs (scaRNAs) a
• PDB: 7BGB, 7TRC, 7V9A, 8OUE, 8OUF
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00400	WD40	263 → 304	WD domain, G-beta repeat	Repeat
  PF00400	WD40	357 → 396	WD domain, G-beta repeat	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Expressed in all tissues and cell lines examined. {ECO:0000269|PubMed:19250907}.
• Sequence:

  MKTLETQPLAPDCCPSDQDPAPAHPSPHASPMNKNADSELMPPPPERGDPPRLSPDPVAG
  SAVSQELREGDPVSLSTPLETEFGSPSELSPRIEEQELSENTSLPAEEANGSLSEEEANG
  PELGSGKAMEDTSGEPAAEDEGDTAWNYSFSQLPRFLSGSWSEFSTQPENFLKGCKWAPD
  GSCILTNSADNILRIYNLPPELYHEGEQVEYAEMVPVLRMVEGDTIYDYCWYSLMSSAQP
  DTSYVASSSRENPIHIWDAFTGELRASFRAYNHLDELTAAHSLCFSPDGSQLFCGFNRTV
  RVFSTARPGRDCEVRATFAKKQGQSGIISCIAFSPAQPLYACGSYGRSLGLYAWDDGSPL
  ALLGGHQGGITHLCFHPDGNRFFSGARKDAELLCWDLRQSGYPLWSLGREVTTNQRIYFD
  LDPTGQFLVSGSTSGAVSVWDTDGPGNDGKPEPVLSFLPQKDCTNGVSLHPSLPLLATAS
  GQRVFPEPTESGDEGEELGLPLLSTRHVHLECRLQLWWCGGAPDSSIPDDHQGEKGQGGT
  EGGVGELI

• Sequence length: 548

Pathways

Reactome:

Telomere Extension By Telomerase

Associated diseases

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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Dyskeratosis congenita, autosomal recessive 3	Pathogenic; Likely pathogenic	rs281865549, rs281865547, rs1597422298	RCV000023967 RCV000034152 RCV000791190	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hereditary cancer-predisposing syndrome	Pathogenic	rs1206472792	RCV003445471	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BODY WEIGHT	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dyskeratosis congenita	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar ClinGen, Disgenet, GenCC, Orphanet ClinGen, Disgenet, GenCC, Orphanet ClinGen, Disgenet, GenCC, Orphanet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Dyskeratosis Congenita, Recessive	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Germ cell tumor of testis	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LI-FRAUMENI SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LI-FRAUMENI SYNDROME 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of breast	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TELOMERE SYNDROME	—	ClinGen, Disgenet ClinGen, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UTERINE FIBROID	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WRAP53-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alopecia	Alopecia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ataxia Telangiectasia	Ataxia Telangiectasia	BEFREE	28607398		★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	30552426	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	17683073, 23886136, 25134915, 31387111		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	23886136, 26460974, 31387111, 36975842	Associate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	28347242	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	23192612		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Chronic Disease	Chronic disease	Pubtator	37299586	Associate	★☆☆☆☆ Found in Text Mining only
Cirrhosis	Cirrhosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Classical Lissencephalies and Subcortical Band Heterotopias	Lissencephaly	Pubtator	25467444	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Bone Marrow Failure Syndromes	Congenital bone marrow failure syndrome	Pubtator	31664887	Associate	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	30552426	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dyskeratosis congenita	Dyskeratosis Congenita	Orphanet			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Dyskeratosis Congenita	Dyskeratosis Congenita	CLINGEN_DG	21072240, 21205863, 21602826, 25467444		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Dyskeratosis Congenita	Dyskeratosis Congenita	BEFREE	21205863, 21981348, 22814958, 30472699, 31664887		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Dyskeratosis Congenita	Dyskeratosis Congenita	GENOMICS_ENGLAND_DG	21205863, 21602826, 28297620		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Dyskeratosis Congenita	Dyskeratosis congenita	Pubtator	21602826, 29514627, 31664887, 36116037	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Dyskeratosis Congenita	Dyskeratosis Congenita	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
DYSKERATOSIS CONGENITA, AUTOSOMAL RECESSIVE, 3	Dyskeratosis Congenita	UNIPROT_DG	21205863, 21602826		★☆☆☆☆ Found in Text Mining only
DYSKERATOSIS CONGENITA, AUTOSOMAL RECESSIVE, 3	Dyskeratosis Congenita	GENOMICS_ENGLAND_DG	21205863, 22285015		★☆☆☆☆ Found in Text Mining only
DYSKERATOSIS CONGENITA, AUTOSOMAL RECESSIVE, 3	Dyskeratosis Congenita	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
DYSKERATOSIS CONGENITA, AUTOSOMAL RECESSIVE, 3	Dyskeratosis Congenita	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Dystrophia unguium	Nail dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Epileptic Encephalopathy Early Infantile 3	Developmental and epileptic encephalopathy	Pubtator	30552426	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	24626331	Stimulate	★☆☆☆☆ Found in Text Mining only
Esophageal Stenosis	Esophageal Stenosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Head and Neck Carcinoma	Head And Neck Carcinoma	BEFREE	21368886		★☆☆☆☆ Found in Text Mining only
Hoyeraal Hreidarsson syndrome	Hoyeraal hreidarsson syndrome	Pubtator	32303682	Associate	★☆☆☆☆ Found in Text Mining only
Hypodontia	Hypodontia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of the maxilla	Hypoplasia of the maxilla	HPO_DG			★☆☆☆☆ Found in Text Mining only
Inherited bone marrow failure syndrome	Inherited Bone Marrow Failure Syndrome	BEFREE	31664887		★☆☆☆☆ Found in Text Mining only
Keratoderma, Palmoplantar	Palmoplantar keratoderma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Laryngeal Squamous Cell Carcinoma	Laryngeal Carcinoma	BEFREE	25854392		★☆☆☆☆ Found in Text Mining only
Leukoplakia, Oral	Leukoplakia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	26551349		★☆☆☆☆ Found in Text Mining only
Liver Failure	Liver failure	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	24626331	Stimulate	★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malabsorption Syndrome	Malabsorption Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant Head and Neck Neoplasm	Head and neck cancer	BEFREE	21368886		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	17683073, 23886136, 25134915, 31387111		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	23192612		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	21368886, 23192612, 24626331, 25134915, 27525856, 28607398, 31281482		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	23886136		★☆☆☆☆ Found in Text Mining only
Muscular Atrophy Spinal	Spinal muscular atrophy	Pubtator	21072240	Associate	★☆☆☆☆ Found in Text Mining only
NAIL DISORDER, NONSYNDROMIC CONGENITAL, 9	Nail Diseases	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nail dysplasia	Nail dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	28607398		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	24626331, 25854392, 28180319		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	25512560, 26460974	Associate	★☆☆☆☆ Found in Text Mining only
Neutropenia, Severe Congenital, X-Linked	Neutropenia	GENOMICS_ENGLAND_DG	21205863		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	26849396, 28406480, 29516630, 31281482		★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	22471498		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	22471498	Associate	★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	23192612		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	23192612	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasm	Pancreatic Neoplasm	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pancytopenia	Pancytopenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	31051499	Stimulate	★☆☆☆☆ Found in Text Mining only
Periodontitis	Periodontitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Seminoma	Seminoma	BEFREE	29579225		★☆☆☆☆ Found in Text Mining only
Spinal Muscular Atrophy	Spinal Muscular Atrophy	BEFREE	28502804		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	24626331		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	25854392	Associate	★☆☆☆☆ Found in Text Mining only
Taurodontism	Taurodontism	HPO_DG			★☆☆☆☆ Found in Text Mining only