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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
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Genomic context

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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
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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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