UBAP1 (ubiquitin associated protein 1)

Gene

• Entrez ID: 51271
• Gene name: Ubiquitin associated protein 1
• Gene symbol: UBAP1
• Synonyms (NCBI Gene): NAG20, SPG80, UAP, UBAP, UBAP-1
• Chromosome: 9
• Chromosome location: 9p13.3
• Summary: This gene is a member of the UBA domain family, whose members include proteins having connections to ubiquitin and the ubiquitination pathway. The ubiquitin associated domain is thought to be a non-covalent ubiquitin binding domain consisting of a compact

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1563919973	->CCAGA	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1563920000	->G	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1563920132	->C	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1563920172	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1563920268	->TGAG	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1587878722	->GTGAATTC	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1587878961	A>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1587879449	G>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT003280	hsa-miR-141-3p	Luciferase reporter assay, Western blot	20053927
MIRT003280	hsa-miR-141-3p	Luciferase reporter assay, Western blot	20053927
MIRT003280	hsa-miR-141-3p	Reporter assay;Western blot;Other	20053927
MIRT1466675	hsa-miR-1266	CLIP-seq
MIRT1466676	hsa-miR-1587	CLIP-seq
MIRT1466677	hsa-miR-1909	CLIP-seq
MIRT1466678	hsa-miR-2278	CLIP-seq
MIRT1466679	hsa-miR-2467-3p	CLIP-seq
MIRT1466680	hsa-miR-3132	CLIP-seq
MIRT1466681	hsa-miR-3135b	CLIP-seq
MIRT1466682	hsa-miR-3169	CLIP-seq
MIRT1466683	hsa-miR-3179	CLIP-seq
MIRT1466684	hsa-miR-3202	CLIP-seq
MIRT1466685	hsa-miR-3652	CLIP-seq
MIRT1466686	hsa-miR-3664-3p	CLIP-seq
MIRT1466687	hsa-miR-3685	CLIP-seq
MIRT1466688	hsa-miR-384	CLIP-seq
MIRT1466689	hsa-miR-4271	CLIP-seq
MIRT1466690	hsa-miR-4283	CLIP-seq
MIRT1466691	hsa-miR-4289	CLIP-seq
MIRT1466692	hsa-miR-4292	CLIP-seq
MIRT1466693	hsa-miR-4318	CLIP-seq
MIRT1466694	hsa-miR-4417	CLIP-seq
MIRT1466695	hsa-miR-4422	CLIP-seq
MIRT1466696	hsa-miR-4428	CLIP-seq
MIRT1466697	hsa-miR-4430	CLIP-seq
MIRT1466698	hsa-miR-4492	CLIP-seq
MIRT1466699	hsa-miR-4498	CLIP-seq
MIRT1466700	hsa-miR-4518	CLIP-seq
MIRT1466701	hsa-miR-4519	CLIP-seq
MIRT1466702	hsa-miR-452	CLIP-seq
MIRT1466703	hsa-miR-4656	CLIP-seq
MIRT1466704	hsa-miR-4675	CLIP-seq
MIRT1466705	hsa-miR-4676-3p	CLIP-seq
MIRT1466706	hsa-miR-4694-5p	CLIP-seq
MIRT1466707	hsa-miR-4716-3p	CLIP-seq
MIRT1466708	hsa-miR-4725-3p	CLIP-seq
MIRT1466709	hsa-miR-4741	CLIP-seq
MIRT1466710	hsa-miR-4747-5p	CLIP-seq
MIRT1466711	hsa-miR-4773	CLIP-seq
MIRT1466712	hsa-miR-4793-5p	CLIP-seq
MIRT1466713	hsa-miR-548aa	CLIP-seq
MIRT1466714	hsa-miR-548g	CLIP-seq
MIRT1466715	hsa-miR-592	CLIP-seq
MIRT1466716	hsa-miR-597	CLIP-seq
MIRT1466717	hsa-miR-599	CLIP-seq
MIRT1466718	hsa-miR-625	CLIP-seq
MIRT1466719	hsa-miR-664	CLIP-seq
MIRT1466720	hsa-miR-762	CLIP-seq
MIRT1466721	hsa-miR-1258	CLIP-seq
MIRT1466722	hsa-miR-141	CLIP-seq
MIRT1466723	hsa-miR-199a-5p	CLIP-seq
MIRT1466724	hsa-miR-199b-5p	CLIP-seq
MIRT1466725	hsa-miR-200a	CLIP-seq
MIRT739255	hsa-miR-2355-5p	CLIP-seq
MIRT1466726	hsa-miR-25	CLIP-seq
MIRT1466727	hsa-miR-298	CLIP-seq
MIRT739256	hsa-miR-3189-5p	CLIP-seq
MIRT1466728	hsa-miR-32	CLIP-seq
MIRT1466729	hsa-miR-363	CLIP-seq
MIRT1466730	hsa-miR-367	CLIP-seq
MIRT1466731	hsa-miR-3672	CLIP-seq
MIRT1466732	hsa-miR-3678-3p	CLIP-seq
MIRT1466733	hsa-miR-3919	CLIP-seq
MIRT1466734	hsa-miR-4712-3p	CLIP-seq
MIRT739254	hsa-miR-4749-3p	CLIP-seq
MIRT1466735	hsa-miR-4756-3p	CLIP-seq
MIRT1466736	hsa-miR-507	CLIP-seq
MIRT1466737	hsa-miR-557	CLIP-seq
MIRT1466738	hsa-miR-92a	CLIP-seq
MIRT1466739	hsa-miR-92b	CLIP-seq
MIRT2361034	hsa-miR-2681	CLIP-seq
MIRT2361035	hsa-miR-3136-5p	CLIP-seq
MIRT2361036	hsa-miR-4439	CLIP-seq
MIRT2361037	hsa-miR-4533	CLIP-seq
MIRT1466710	hsa-miR-4747-5p	CLIP-seq
MIRT2361038	hsa-miR-943	CLIP-seq
MIRT1466721	hsa-miR-1258	CLIP-seq
MIRT1466722	hsa-miR-141	CLIP-seq
MIRT1466725	hsa-miR-200a	CLIP-seq
MIRT1466731	hsa-miR-3672	CLIP-seq
MIRT2361039	hsa-miR-4266	CLIP-seq
MIRT2361040	hsa-miR-4695-5p	CLIP-seq
MIRT1466734	hsa-miR-4712-3p	CLIP-seq
MIRT2361041	hsa-miR-4779	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000813	Component	ESCRT I complex	IBA
GO:0000813	Component	ESCRT I complex	IDA	21757351
GO:0000813	Component	ESCRT I complex	IEA
GO:0000813	Component	ESCRT I complex	IPI	21757351
GO:0005515	Function	Protein binding	IPI	25416956
GO:0005737	Component	Cytoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IEA
GO:0005829	Component	Cytosol	IDA	21757351
GO:0005829	Component	Cytosol	IEA
GO:0005886	Component	Plasma membrane	IDA
GO:0010008	Component	Endosome membrane	NAS	32424346
GO:0010008	Component	Endosome membrane	TAS
GO:0015031	Process	Protein transport	IEA
GO:0036258	Process	Multivesicular body assembly	NAS	32424346
GO:0043130	Function	Ubiquitin binding	IBA
GO:0043130	Function	Ubiquitin binding	IDA	21757351
GO:0043130	Function	Ubiquitin binding	IEA
GO:0043162	Process	Ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IBA
GO:0043162	Process	Ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IEA
GO:0043162	Process	Ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IMP	21757351
GO:0043328	Process	Protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	NAS	32424346
GO:0090148	Process	Membrane fission	NAS	32424346

Other IDs

• MIM: 609787
• HGNC: 12461
• e!Ensembl: ENSG00000165006

Protein

• UniProt ID: Q9NZ09
• Protein name: Ubiquitin-associated protein 1 (UBAP-1) (Nasopharyngeal carcinoma-associated gene 20 protein)
• Protein function: Component of the ESCRT-I complex, a regulator of vesicular trafficking process (PubMed:21757351, PubMed:22405001, PubMed:31203368). Binds to ubiquitinated cargo proteins and is required for the sorting of endocytic ubiquitinated cargos into mult
• PDB: 1WGN, 4AE4, 5LM1
• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous. Highly expressed in heart, brain, placenta, lung, liver, skeletal muscle and pancreas. {ECO:0000269|PubMed:11599797}.
• Sequence:

  MASKKLGADFHGTFSYLDDVPFKTGDKFKTPAKVGLPIGFSLPDCLQVVREVQYDFSLEK
  KTIEWAEEIKKIEEAEREAECKIAEAEAKVNSKSGPEGDSKMSFSKTHSTATMPPPINPI
  LASLQHNSILTPTRVSSSATKQKVLSPPHIKADFNLADFECEEDPFDNLELKTIDEKEEL
  RNILVGTTGPIMAQLLDNNLPRGGSGSVLQDEEVLASLERATLDFKPLHKPNGFITLPQL
  GNCEKMSLSSKVSLPPIPAVSNIKSLSFPKLDSDDSNQKTAKLASTFHSTSCLRNGTFQN
  SLKPSTQSSASELNGHHTLGLSALNLDSGTEMPALTSSQMPSLSVLSVCTEESSPPNTGP
  TVTPPNFSVSQVPNMPSCPQAYSELQMLSPSERQCVETVVNMGYSYECVLRAMKKKGENI
  EQILDYLFAHGQLCEKGFDPLLVEEALEMHQCSEEKMMEFLQLMSKFKEMGFELKDIKEV
  LLLHNNDQDNALEDLMARAGAS

• Sequence length: 502

Pathways

Reactome:

Budding and maturation of HIV virion
Membrane binding and targetting of GAG proteins
Endosomal Sorting Complex Required For Transport (ESCRT)
HCMV Late Events

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
Hereditary spastic paraplegia	Pathogenic	rs1563920252	RCV005626202	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spastic paraplegia 80, autosomal dominant	Likely pathogenic; Pathogenic	rs1227081826, rs2131620305, rs2491080250, rs1563920268, rs1563920252, rs1563920172, rs1563919973, rs1563920000, rs1563920132, rs1587878722, rs1587879449, rs1587878961, rs1833955862	RCV002226873 RCV002246801 RCV003388179 RCV000770927 RCV000770928 RCV000770929 RCV000770930 RCV000770931 RCV000770932 RCV000850170 RCV000850171 RCV001027715 RCV001199970	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTOSOMAL DOMINANT SPASTIC PARAPLEGIA TYPE 12	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL DOMINANT SPASTIC PARAPLEGIA TYPE 80	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BRCAX BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GILLES DE LA TOURETTE SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA 12, AUTOSOMAL DOMINANT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UBAP1-related disorder	Benign; Uncertain significance; Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Angina, Unstable	Intermediate coronary syndrome	BEFREE	19094431		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	16891930		★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	38402586	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Ovarian Epithelial	Epithelial ovarian carcinoma	Pubtator	28423358	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	28423358	Associate	★☆☆☆☆ Found in Text Mining only
Congestive heart failure	Congestive Heart Failure	BEFREE	30819182		★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	BEFREE	19094431		★☆☆☆☆ Found in Text Mining only
Frontotemporal Dementia	Frontotemporal dementia	Pubtator	25239657	Associate	★☆☆☆☆ Found in Text Mining only
Frontotemporal Lobar Degeneration	Frontotemporal dementia	BEFREE	19217189		★☆☆☆☆ Found in Text Mining only
Gout	Gout	Pubtator	32630231	Associate	★☆☆☆☆ Found in Text Mining only
Heart failure	Heart Failure	BEFREE	30819182		★☆☆☆☆ Found in Text Mining only
Henoch-Schoenlein Purpura	Henoch-Schonlein Nephritis	BEFREE	30929741, 31515522		★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	Pubtator	38402586	Associate	★☆☆☆☆ Found in Text Mining only
Learning Disabilities	Learning disorders	Pubtator	32934340	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	16891930		★☆☆☆☆ Found in Text Mining only
Motor Neuron Disease	Motor neuron disease	Pubtator	25239657	Associate	★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	16226037, 20053927		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	11599797, 20053927		★☆☆☆☆ Found in Text Mining only
Neurofibrosarcoma	Neurofibrosarcoma	Pubtator	32590748	Associate	★☆☆☆☆ Found in Text Mining only
Parkinson Disease Secondary	Secondary parkinson disease	Pubtator	32934340	Associate	★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia	Spastic Paraplegia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spastic paraplegia 10, autosomal dominant	Spondylometaphyseal dysplasia	BEFREE	31203368		★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia Hereditary	Hereditary spastic paraplegia	Pubtator	31696996, 32934340, 35347897, 36739287	Associate	★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia, Hereditary	Spastic paraplegia	BEFREE	30929741, 31203368, 31515522, 31696996		★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia, Hereditary	Spastic paraplegia	GENOMICS_ENGLAND_DG	30929741		★☆☆☆☆ Found in Text Mining only
Stable angina	Stable Angina	BEFREE	19094431		★☆☆☆☆ Found in Text Mining only