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    UBIAD1 UbiA prenyltransferase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 29914, updated on 3-Nov-2024

    Summary

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    Official Symbol
    UBIAD1provided by HGNC
    Official Full Name
    UbiA prenyltransferase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:30791
    See related
    Ensembl:ENSG00000120942 MIM:611632; AllianceGenome:HGNC:30791
    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
    SCCD; TERE1
    Summary
    This gene encodes a protein thought to be involved in cholesterol and phospholipid metabolism. Mutations in this gene are associated with Schnyder crystalline corneal dystrophy. [provided by RefSeq, Oct 2008]
    Expression
    Ubiquitous expression in testis (RPKM 2.8), ovary (RPKM 2.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See UBIAD1 in Genome Data Viewer
    Location:
    1p36.22
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (11273198..11299574)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (10814791..10841185)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11333255..11359631)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene mechanistic target of rapamycin kinase Neighboring gene RNA, U6 small nuclear 291, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:11301605-11302164 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:11308472-11309038 Neighboring gene ribosomal protein L39 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 167 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:11349216-11349398 Neighboring gene ubiquitin conjugating enzyme E2 V2 pseudogene 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:11365397-11366222 Neighboring gene uncharacterized LOC105376737 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11390449-11391426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11391427-11392404 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11393897-11394399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11403662-11404162 Neighboring gene uncharacterized LOC105376739

    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 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 Golgi retention signal RPWS for tumor suppressor UBIAD1. Wang X, et al. PLoS One, 2013. PMID 23977195, Free PMC Article
    2. Clinical and para-clinical description of a novel mutation for Schnyder dystrophy in a French family. Gonzalvez M, et al. J Fr Ophtalmol, 2018 Dec. PMID 30446344
    3. Schnyder corneal dystrophy and associated phenotypes caused by novel and recurrent mutations in the UBIAD1 gene. Evans CJ, et al. BMC Ophthalmol, 2018 Sep 17. PMID 30223810, Free PMC Article
    4. Identification of mutations in UBIAD1 following exclusion of coding mutations in the chromosome 1p36 locus for Schnyder crystalline corneal dystrophy. Yellore VS, et al. Mol Vis, 2007 Sep 24. PMID 17960116
    5. Depletion of ubiA prenyltransferase domain containing 1 expression promotes angiotensin II‑induced hypertrophic response in AC16 human myocardial cells via modulating the expression levels of coenzyme Q10 and endothelial nitric oxide synthase. Yan B, et al. Mol Med Rep, 2017 Nov. PMID 28901410

    See all (73) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. UBIAD1 and CoQ10 protect melanoma cells from lipid peroxidation-mediated cell death.
      Title: UBIAD1 and CoQ10 protect melanoma cells from lipid peroxidation-mediated cell death.
    2. Functional study of SCCD pathogenic gene UBIAD1 (Review).
      Title: Functional study of SCCD pathogenic gene UBIAD1 (Review).
    3. Schnyder corneal dystrophy-associated UBIAD1 is defective in MK-4 synthesis and resists autophagy-mediated degradation.
      Title: Schnyder corneal dystrophy-associated UBIAD1 is defective in MK-4 synthesis and resists autophagy-mediated degradation.
    4. Results demonstrate that schnyder corneal dystrophy (SCD)-associated mutations of UBIAD1 impair its ER-to-Golgi transportation and enhance its interaction with HMGCR. The stabilization of HMGCR by UBIAD1 increases cholesterol biosynthesis and eventually causes cholesterol accumulation in the cornea.
      Title: Schnyder corneal dystrophy-associated UBIAD1 mutations cause corneal cholesterol accumulation by stabilizing HMG-CoA reductase.
    5. UBIAD1 suppresses the proliferation of bladder carcinoma cells by regulating H-Ras intracellular trafficking via interaction with the C-terminal domain of H-Ras.
      Title: UBIAD1 suppresses the proliferation of bladder carcinoma cells by regulating H-Ras intracellular trafficking via interaction with the C-terminal domain of H-Ras.
    6. Genetic analysis of our family revealed a mutation of the UBIAD1 gene not described in the literature for Schnyder Dystrophy.
      Title: Clinical and para-clinical description of a novel mutation for Schnyder dystrophy in a French family.
    7. The novel p.Thr120Arg is the fourth Schnyder corneal dystrophy-causing variant lying within the FARM motif of the UBIAD1 protein, which underlines a high importance of this motif for SCD pathogenesis.
      Title: Clinical diversity in patients with Schnyder corneal dystrophy-a novel and known UBIAD1 pathogenic variants.
    8. Although de novo occurrence of mutations in UBIAD1 is extremely rare, SCD should be considered in the differential diagnosis of bilateral corneal haze and/or crystal deposition, especially in children
      Title: Schnyder corneal dystrophy and associated phenotypes caused by novel and recurrent mutations in the UBIAD1 gene.
    9. Silencing UBIAD1 further aggravates the deleterious effects rendered by Ang II, indicating that a normal or increased level of UBIAD1 may offer protection against the Ang IIinduced hypertrophic response and apoptosis.
      Title: Depletion of ubiA prenyltransferase domain containing 1 expression promotes angiotensin II‑induced hypertrophic response in AC16 human myocardial cells via modulating the expression levels of coenzyme Q10 and endothelial nitric oxide synthase.
    10. these findings disclose a novel sensing mechanism that allows for stringent metabolic control of intracellular trafficking of UBIAD1, which directly modulates reductase degradation and becomes disrupted in Schnyder corneal dystrophy (SCD).
      Title: Geranylgeranyl-regulated transport of the prenyltransferase UBIAD1 between membranes of the ER and Golgi.
    Submit: New GeneRIF Correction See all GeneRIFs (36)

    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
    Schnyder crystalline corneal dystrophy
    MedGen: C0271287 OMIM: 121800 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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables antioxidant activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables prenyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables prenyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables prenyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular oxidant detoxification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in menaquinone biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in menaquinone biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in menaquinone biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ubiquinone biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vitamin K biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vitamin K biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in vitamin K biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vitamin K metabolic process TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ubiA prenyltransferase domain-containing protein 1
    Names
    transitional epithelia response protein
    transitional epithelial response protein 1
    NP_001317278.1
    NP_001317279.1
    NP_037451.1
    XP_047274683.1
    XP_054192166.1

    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.

    Genomic

    1. NG_009443.2 RefSeqGene

      Range
      5001..20237
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001330349.2 → NP_001317278.1  ubiA prenyltransferase domain-containing protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL031291
      Conserved Domains (1) summary
      cd13962
      Location:50 → 209
      PT_UbiA_UBIAD1; 1,4-Dihydroxy-2-naphthoate octaprenyltransferase

    2. NM_001330350.2 → NP_001317279.1  ubiA prenyltransferase domain-containing protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL031291
      Consensus CDS
      CCDS81260.1
      UniProtKB/Swiss-Prot
      Q9Y5Z9
      Related
      ENSP00000366000.1, ENST00000376804.2
      Conserved Domains (1) summary
      cd13962
      Location:50 → 176
      PT_UbiA_UBIAD1; 1,4-Dihydroxy-2-naphthoate octaprenyltransferase

    3. NM_013319.3 → NP_037451.1  ubiA prenyltransferase domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_037451.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AA505091, AK074890, AK222808, BC004468, BX507524
      Consensus CDS
      CCDS129.1
      UniProtKB/Swiss-Prot
      B3KQG3, Q53GX3, Q5THD4, Q9Y5Z9
      Related
      ENSP00000366006.5, ENST00000376810.6
      Conserved Domains (1) summary
      cd13962
      Location:50 → 326
      PT_UbiA_UBIAD1; 1,4-Dihydroxy-2-naphthoate octaprenyltransferase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      11273198..11299574
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418727.1 → XP_047274683.1  ubiA prenyltransferase domain-containing protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      10814791..10841185
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336191.1 → XP_054192166.1  ubiA prenyltransferase domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5Z9.1 GenPept UniProtKB/Swiss-Prot:Q9Y5Z9

    Gene LinkOut

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