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    UBAP1 ubiquitin associated protein 1 [ Homo sapiens (human) ]

    Gene ID: 51271, updated on 3-Apr-2024

    Summary

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    Official Symbol
    UBAP1provided by HGNC
    Official Full Name
    ubiquitin associated protein 1provided by HGNC
    Primary source
    HGNC:HGNC:12461
    See related
    Ensembl:ENSG00000165006 MIM:609787; AllianceGenome:HGNC:12461
    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
    UAP; UBAP; NAG20; SPG80; UBAP-1
    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 three helix bundle. This particular protein originates from a gene locus in a refined region on chromosome 9 undergoing loss of heterozygosity in nasopharyngeal carcinoma (NPC). Taking into account its cytogenetic location, this UBA domain family member is being studies as a putative target for mutation in nasopharyngeal carcinomas. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]
    Expression
    Ubiquitous expression in bone marrow (RPKM 39.6), testis (RPKM 26.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See UBAP1 in Genome Data Viewer
    Location:
    9p13.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (34179005..34252523)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (34197963..34271456)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (34179003..34252521)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene DDB1 and CUL4 associated factor 12 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:34118233-34118334 Neighboring gene TUBB4B pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:34126245-34126946 Neighboring gene tubulin beta pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:34143547-34143738 Neighboring gene inosine monophosphate dehydrogenase 1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34169067-34169709 Neighboring gene Sharpr-MPRA regulatory region 9718 Neighboring gene hESC enhancers GRCh37_chr9:34178090-34179048 and GRCh37_chr9:34179049-34180005 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34180006-34180963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28306 Neighboring gene uncharacterized LOC114224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34197642-34198592 Neighboring gene ribosomal protein L35a pseudogene 2 Neighboring gene RNA, 5S ribosomal pseudogene 282 Neighboring gene MPRA-validated peak7226 silencer Neighboring gene ribosomal protein S8 pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19843 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:34254397-34255596 Neighboring gene kinesin family member 24 Neighboring gene RNA, U2 small nuclear 50, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34318623-34319288 Neighboring gene serpin family H member 1 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. A novel UBAP1 truncated variant in a Chinese family with hereditary spastic paraplegia. Wei Q, et al. Mol Genet Genomic Med, 2022 May. PMID 35347897, Free PMC Article
    2. Two novel truncating variants in UBAP1 are responsible for hereditary spastic paraplegia. Bian X, et al. PLoS One, 2021. PMID 34191852, Free PMC Article
    3. Identification of UBAP1 mutations in juvenile hereditary spastic paraplegia in the 100,000 Genomes Project. Bourinaris T, et al. Eur J Hum Genet, 2020 Dec. PMID 32934340, Free PMC Article
    4. Truncating variants in UBAP1 associated with childhood-onset nonsyndromic hereditary spastic paraplegia. Gu S, et al. Hum Mutat, 2020 Mar. PMID 31696996, Free PMC Article
    5. Truncating Mutations in UBAP1 Cause Hereditary Spastic Paraplegia. Farazi Fard MA, et al. Am J Hum Genet, 2019 Apr 4. PMID 30929741, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel UBAP1 truncated variant in a Chinese family with hereditary spastic paraplegia.
      Title: A novel UBAP1 truncated variant in a Chinese family with hereditary spastic paraplegia.
    2. Two novel truncating variants in UBAP1 are responsible for hereditary spastic paraplegia.
      Title: Two novel truncating variants in UBAP1 are responsible for hereditary spastic paraplegia.
    3. Truncating variants in UBAP1 associated with childhood-onset nonsyndromic hereditary spastic paraplegia.
      Title: Truncating variants in UBAP1 associated with childhood-onset nonsyndromic hereditary spastic paraplegia.
    4. Identification of UBAP1 mutations in juvenile hereditary spastic paraplegia in the 100,000 Genomes Project.
      Title: Identification of UBAP1 mutations in juvenile hereditary spastic paraplegia in the 100,000 Genomes Project.
    5. mRNA in the fibroblasts of individuals with pathological truncating variants in UBAP1 escapes nonsense-mediated decay and thus leads to the expression of truncated proteins. In addition, concentrations of the full-length protein are reduced in comparison to those in controls. This suggests either a dominant-negative effect or haploinsufficiency.
      Title: Truncating Mutations in UBAP1 Cause Hereditary Spastic Paraplegia.
    6. Our study provides genetic and biochemical evidence that mutations in UBAP1 can cause pure autosomal dominant spastic paraplegia.
      Title: Stop-gain mutations in UBAP1 cause pure autosomal-dominant spastic paraplegia.
    7. UBAP1 links endosomal trafficking to the ubiquitination machinery pathways that have been previously implicated in Hereditary Spastic Paraplegia
      Title: Truncating Mutations in UBAP1 Cause Hereditary Spastic Paraplegia.
    8. The full-length UBAP1 protein is involved in endosomal dynamics in neurons, while loss of UBAP1 function may perturb endosomal fusion and sorting of ubiquitinated cargos. These effects could be more prominent in neurons, thereby giving rise to the phenotype of a neurodegenerative disease such as hereditary spastic paraplegia.
      Title: UBAP1 mutations cause juvenile-onset hereditary spastic paraplegias (SPG80) and impair UBAP1 targeting to endosomes.
    9. Combined targeting of UBAP1 and toll-like receptor adaptors TIRAP and MyD88 by Pseudomonas aeruginosa PumA impedes both cytokine and toll-like receptor signalling, highlighting a novel strategy for innate immune evasion.
      Title: A Pseudomonas aeruginosa TIR effector mediates immune evasion by targeting UBAP1 and TLR adaptors.
    10. Results present crystal structures of the coiled-coil domain of the HD-PTP phosphatase and its complex with UBAP1. The coiled-coil domain adopts an unexpected open and rigid conformation. The HD-PTP:UBAP1 structure identifies the molecular determinants of the interaction and provides a molecular basis for the specific functional cooperation between HD-PTP and UBAP1.
      Title: Structural Basis for Selective Interaction between the ESCRT Regulator HD-PTP and UBAP1.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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
    Spastic paraplegia 80, autosomal dominant
    MedGen: C5193084 OMIM: 618418 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu Physiological levels of Vpu requires the core ESCRT pathway (TSG1010 and UBAP1) and HGA (HRS) for Vpu-mediated BST-2 (tetherin) degradation but does not require these proteins for counteraction of BST2 (tetherin's) physical antiviral activity PubMed
    vpu The ubiquitin associated protein 1 (UBAP1)-containing ESCRT-I is essential for degradation of antiviral cell-surface proteins such as tetherin (BST-2/CD317) by HIV-1 Vpu PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC8710, MGC119669

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in membrane fission NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in multivesicular body assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of ESCRT I complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ESCRT I complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ESCRT I complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin-associated protein 1
    Names
    nasopharyngeal carcinoma-associated gene 20 protein

    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.

    mRNA and Protein(s)

    1. NM_001171201.1 → NP_001164672.1  ubiquitin-associated protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an internal coding exon, which results in an in-frame upstream AUG start codon, as compared to variant 1. The resulting isoform (2) is longest and has a different N-terminus, as compared to isoform 1.
      Source sequence(s)
      AK303711, AL353662, BC020950
      Consensus CDS
      CCDS55303.1
      UniProtKB/TrEMBL
      A0A0D9SG79
      Related
      ENSP00000486574.1, ENST00000625521.2
      Conserved Domains (2) summary
      cd14315
      Location:452 → 494
      UBA1_UBAP1; UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1)
      cd14316
      Location:524 → 560
      UBA2_UBAP1_like; UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins

    2. NM_001171202.1 → NP_001164673.1  ubiquitin-associated protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an internal coding exon, which results in an in-frame upstream AUG start codon, as compared to variant 1. The resulting isoform (3) is longer and has a different N-terminus, as compared to isoform 1.
      Source sequence(s)
      AK074812, AK295482, AL353662, BC020950
      UniProtKB/TrEMBL
      A0A0D9SG79
      Related
      ENSP00000487222.1, ENST00000626262.2
      Conserved Domains (2) summary
      cd14315
      Location:424 → 466
      UBA1_UBAP1; UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1)
      cd14316
      Location:496 → 532
      UBA2_UBAP1_like; UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins

    3. NM_001171203.3 → NP_001164674.1  ubiquitin-associated protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001164674.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is the longest transcript; it has an additional exon in the 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform 1.
      Source sequence(s)
      AK303711, AL353662, BC100668, DA741347
      Consensus CDS
      CCDS6550.1
      UniProtKB/Swiss-Prot
      B7Z348, B7Z8N9, D3DRL7, F5GXE2, F5H0J8, Q4V759, Q53FP7, Q5T7B3, Q6FI75, Q8NC52, Q8NCG6, Q8NCH9, Q9NZ09
      UniProtKB/TrEMBL
      A0A0D9SG79, A0A6G6AA68
      Conserved Domains (2) summary
      cd14315
      Location:388 → 430
      UBA1_UBAP1; UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1)
      cd14316
      Location:460 → 496
      UBA2_UBAP1_like; UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins

    4. NM_001171204.3 → NP_001164675.1  ubiquitin-associated protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001164675.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an additional exon in the 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform 1.
      Source sequence(s)
      AK074969, AL353662, BC020950
      Consensus CDS
      CCDS6550.1
      UniProtKB/Swiss-Prot
      B7Z348, B7Z8N9, D3DRL7, F5GXE2, F5H0J8, Q4V759, Q53FP7, Q5T7B3, Q6FI75, Q8NC52, Q8NCG6, Q8NCH9, Q9NZ09
      UniProtKB/TrEMBL
      A0A0D9SG79, A0A6G6AA68
      Conserved Domains (2) summary
      cd14315
      Location:388 → 430
      UBA1_UBAP1; UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1)
      cd14316
      Location:460 → 496
      UBA2_UBAP1_like; UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins

    5. NM_016525.5 → NP_057609.2  ubiquitin-associated protein 1 isoform 1

      See identical proteins and their annotated locations for NP_057609.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the dominant transcript and encodes the dominant isoform (1).
      Source sequence(s)
      AK074812, AL353662
      Consensus CDS
      CCDS6550.1
      UniProtKB/Swiss-Prot
      B7Z348, B7Z8N9, D3DRL7, F5GXE2, F5H0J8, Q4V759, Q53FP7, Q5T7B3, Q6FI75, Q8NC52, Q8NCG6, Q8NCH9, Q9NZ09
      UniProtKB/TrEMBL
      A0A0D9SG79, A0A6G6AA68
      Related
      ENSP00000297661.4, ENST00000297661.9
      Conserved Domains (2) summary
      cd14315
      Location:388 → 430
      UBA1_UBAP1; UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1)
      cd14316
      Location:460 → 496
      UBA2_UBAP1_like; UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins

    RNA

    1. NR_033243.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) has an additional exon, as compared to variant 1. The transcript has two uORFs; the second uORF has a strong Kozak signal and overlaps the downstream ORF, so the transcript is a nonsense-mediated mRNA decay candidate.
      Source sequence(s)
      AL353662, BC100668, BP237024

    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

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      34179005..34252523
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011517898.2 → XP_011516200.1  ubiquitin-associated protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0D9SG79
      Conserved Domains (2) summary
      cd14315
      Location:395 → 437
      UBA1_UBAP1; UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1)
      cd14316
      Location:467 → 503
      UBA2_UBAP1_like; UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins

    2. XM_006716779.5 → XP_006716842.1  ubiquitin-associated protein 1 isoform X2

      See identical proteins and their annotated locations for XP_006716842.1

      UniProtKB/Swiss-Prot
      B7Z348, B7Z8N9, D3DRL7, F5GXE2, F5H0J8, Q4V759, Q53FP7, Q5T7B3, Q6FI75, Q8NC52, Q8NCG6, Q8NCH9, Q9NZ09
      UniProtKB/TrEMBL
      A0A0D9SG79, A0A6G6AA68
      Conserved Domains (2) summary
      cd14315
      Location:388 → 430
      UBA1_UBAP1; UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1)
      cd14316
      Location:460 → 496
      UBA2_UBAP1_like; UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins

    3. XM_047423458.1 → XP_047279414.1  ubiquitin-associated protein 1 isoform X2

      UniProtKB/Swiss-Prot
      B7Z348, B7Z8N9, D3DRL7, F5GXE2, F5H0J8, Q4V759, Q53FP7, Q5T7B3, Q6FI75, Q8NC52, Q8NCG6, Q8NCH9, Q9NZ09
      UniProtKB/TrEMBL
      A0A6G6AA68
      Related
      ENSP00000352541.2, ENST00000359544.2

    4. XM_047423457.1 → XP_047279413.1  ubiquitin-associated protein 1 isoform X2

      UniProtKB/Swiss-Prot
      B7Z348, B7Z8N9, D3DRL7, F5GXE2, F5H0J8, Q4V759, Q53FP7, Q5T7B3, Q6FI75, Q8NC52, Q8NCG6, Q8NCH9, Q9NZ09
      UniProtKB/TrEMBL
      A0A6G6AA68

    5. XM_017014802.2 → XP_016870291.1  ubiquitin-associated protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A0D9SG79

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      34197963..34271456
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363080.1 → XP_054219055.1  ubiquitin-associated protein 1 isoform X1

    2. XM_054363081.1 → XP_054219056.1  ubiquitin-associated protein 1 isoform X2

      UniProtKB/Swiss-Prot
      B7Z348, B7Z8N9, D3DRL7, F5GXE2, F5H0J8, Q4V759, Q53FP7, Q5T7B3, Q6FI75, Q8NC52, Q8NCG6, Q8NCH9, Q9NZ09
      UniProtKB/TrEMBL
      A0A6G6AA68

    3. XM_054363082.1 → XP_054219057.1  ubiquitin-associated protein 1 isoform X2

      UniProtKB/Swiss-Prot
      B7Z348, B7Z8N9, D3DRL7, F5GXE2, F5H0J8, Q4V759, Q53FP7, Q5T7B3, Q6FI75, Q8NC52, Q8NCG6, Q8NCH9, Q9NZ09
      UniProtKB/TrEMBL
      A0A6G6AA68

    4. XM_054363083.1 → XP_054219058.1  ubiquitin-associated protein 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZ09.1 GenPept UniProtKB/Swiss-Prot:Q9NZ09

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