Atlas of Genetics and Cytogenetics in Oncology and Haematology

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USB1 (U6 snRNA biogenesis 1)

Written2014-02Elisa Adele Colombo
Genetica Medica, Dipartimento di Scienze della Salute, Universita degli Studi di Milano, Italy

Abstract C16orf57 alias USB1 is the gene which mutations underlie poikiloderma with neutropenia (PN) syndrome, a rare genodermatosis with autosomic recessive inheritance. PN patients have an increased risk to develop myelodysplasia and acute myeloid leukaemia in the second decade of life. In 2012, the protein encoded by USB1 has been recognised to be a 2H phosphodiesterase involved in the processing of U6 snRNA, but its action pathway and hence role in the pathogenesis of PN has not yet been elucidated.

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Alias (NCBI)C16orf57
EC 3.1.4.
HGNC (Hugo) USB1
HGNC Alias symbFLJ13154
HGNC Alias nameHVSL motif containing 1
 poikiloderma with neutropenia
 U six biogenesis 1
 mutated in poikiloderma with neutropenia protein 1
HGNC Previous nameC16orf57
HGNC Previous namechromosome 16 open reading frame 57
 U6 snRNA biogenesis 1
LocusID (NCBI) 79650
Atlas_Id 44608
Location 16q21  [Link to chromosome band 16q21]
Location_base_pair Starts at 58001407 and ends at 58021618 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping USB1.png]
  Figure 1. The region on chromosome 16q21 containing USB1 and its neighbouring genes ZNF139 (zinc finger protein 319) and MMP15 (matrix metalloproteinase 15) (UCSC database -GRCh37/hg19, Feb 2009).
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
USB1 (16q21)::DRC7 (16q21)


  Figure 2. Schematic representation of exon-intron structure of USB1 and the two major transcripts resulting from alternative splicing of the two mutually exclusive exons 4.
Description According to UCSC database (GRCh37/hg19, Feb.2009), USB1 gene maps in the region between 58035277 and 58055527 bp from pter of chromosome 16 with a centromeric-telomeric orientation.
It spans 20 kb and is composed of seven exons (GI:305855061; NM_024598.3) (Fig.2).
Transcription Two physiological isoforms, generated by alternative splicing (Fig. 2), have been detected in normal samples (leucocytes, keratinocytes, melanocytes and fibroblasts). The major transcript of 2282 nt (isoform 1, NM_024598.3) includes all the seven exons of the gene, while the shorter isoform of 1217 nt (NM_001204911.1) comprises the first three exons and an alternative terminal fourth exon located in IVS3 (Arnold et al., 2010).
Several additional transcripts, a few detected in cancer samples, are reported in the Ensembl database.
Pseudogene No pseudogene for USB1 is known.


  Figure 3. Ribbon model of the USB1 protein showing its globular symmetrical conformation with two lobes separated by a central groove that exposes the catalytic site containing the two HLSL motifs (encircled). The terminal lobe comprises both the N- and the C-termini. Both the terminal and transit lobe consist of antiparallel β-sheets and α-helices (modified from Colombo et al., 2012).
Description The crystal structure of the human USB1 protein, translated by isoform 1 mRNA has been recently resolved (Hilcenko et al., 2013).The main USB1 protein comprises 265 aa, while translation of isoform 4 mRNA predicts a 186 amino acid protein with a different C-terminus.
The USB1 protein is characterized by two tetrapeptide motifs (HLSL), containing histidine and serine residues (H120, S122, and H208, S210) which are essential for its catalytic activity. Recognition of these motifs by computational analysis of the protein sequence has predicted USB1 belongs to the 2H phosphodiesterase superfamily present in bacteria, archea and eukaryotes (Colombo et al., 2012). The protein has a globular architecture with two juxtaposed lobes with a pseudo two-fold symmetry separated by a central groove, which exposes the two HLSL motifs of the active site (Fig.3).
Expression USB1 is ubiquitously expressed in humans (Volpi et al., 2010).The high evolutionary conservation of the protein is consistent with the housekeeping function of the gene.
Localisation A nuclear localization of USB1 has been demonstrated in HeLa cells (Mroczek et al., 2012); both nuclear and mitochondrial localizations have been observed for the yeast orthologue (Glatigny et al., 2011).
Function Usb1 is a 3'-5' RNA exoribonuclease that trims the 3' end of the U6 snRNA leading to the formation of a terminal 2',3' cyclic phosphate. This post-transcriptionally modification influences U6 stability and recycling. Evidence has been obtained in yeast where Usb1 depletion leads to reduced levels of U6, generalized pre-mRNA splicing defects and shorter telomeres. In human use of PN cell lines confirmed that U6 is a substrate of USB1, but failed to reveal a splicing defect leaving unsolved how PN develops (Hilcenko et al., 2012; Mroczek et al., 2012; Shchepachev et al., 2012).


  Figure 4. Map across the USB1 gene of the currently known 19 mutations. Nonsense mutations are represented with a red hexagon, deletions with a yellow star and splicing mutations with a blue triangle. The Table lists for each mutation the intragenic position, the description (cDNA nomenclature) and the effect at the protein level.
Germinal Biallelic mutations in USB1 gene (OMIM*613276) cause poikiloderma with neutropenia syndrome (OMIM#604173).
To date, 19 different "loss-of-function" mutations have been identified in 38 molecularly tested PN patients: 7 non-sense mutations, 6 out-of-frame deletions and 6 canonical splice site mutations. The latter also include the only missense mutation so far reported which however leads to exon skipping (Volpi et al., 2010). Recurrent mutations can be identified in patients of Navajo, Turkish and Caucasian origin attesting a founder effect (Colombo et al., 2012).
Somatic No information is currently available on mutations of USB1 in sporadic cancers.

Implicated in

Entity (PN)
Note The disease is caused by mutations affecting the gene represented in this entry.
The clinical presentation of PN patients partially overlaps that of patients affected with Rothmund-Thomson syndrome (RTS; OMIM#268400) and dyskeratosis congenita (DC; OMIM#613987, #613988, #613989, #615190, #224230).
Disease Poikiloderma with neutropenia is a rare inherited genodermatosis characterized by skin alterations (poikiloderma, nail dystrophy, palmo-plantar hyperkeratosis), short stature and non cyclic neutropenia.
In infancy, neutropenia is responsible of the recurrent infections, mainly of the respiratory system, observed in PN patients and, later in life, may lead to myelodysplastic syndrome and acute myeloid leukaemia. Squamous cell carcinoma has also been reported in PN patients.
To date, 38 out of 66 PN patients described in literature have been molecularly tested and found to carry biallelic mutations of the USB1 gene. Most of the reported patients carry homozygous mutations, attesting inheritance by descent of the same ancestral mutation.
Prognosis The knowledge of USB1 3D structure with the essential amino acid motifs of the catalytic site might enhance the prediction of USB1 mutation effects.
All the mutations reported so far in PN patients (no. 19) interfere with USB1 function: 16 disrupt the catalytic activity due to the loss of one or both HLSL motifs, while the remaining 3 mutations, although not affecting the catalytically active tetrapeptide motifs destroy the internal symmetry of the protein. Owing to the restricted number of molecularly characterised PN patients no mutation-phenotype correlations have emerged suitable to stratify the patients according to life-long cancer risk (myelodysplasia and solid tumours).
Further studies focussing on the alternative transcript are necessary to establish the role of isoform 4 on PN pathogenesis and prognosis.


Poikiloderma with neutropenia: a novel C16orf57 mutation and clinical diagnostic criteria.
Arnold AW, Itin PH, Pigors M, Kohlhase J, Bruckner-Tuderman L, Has C.
Br J Dermatol. 2010 Oct;163(4):866-9. doi: 10.1111/j.1365-2133.2010.09929.x. Epub 2010 Sep 7.
PMID 20618321
Novel C16orf57 mutations in patients with Poikiloderma with Neutropenia: bioinformatic analysis of the protein and predicted effects of all reported mutations.
Colombo EA, Bazan JF, Negri G, Gervasini C, Elcioglu NH, Yucelten D, Altunay I, Cetincelik U, Teti A, Del Fattore A, Luciani M, Sullivan SK, Yan AC, Volpi L, Larizza L.
Orphanet J Rare Dis. 2012 Jan 23;7:7. doi: 10.1186/1750-1172-7-7.
PMID 22269211
An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae.
Glatigny A, Mathieu L, Herbert CJ, Dujardin G, Meunier B, Mucchielli-Giorgi MH.
BMC Syst Biol. 2011 Oct 25;5:173. doi: 10.1186/1752-0509-5-173.
PMID 22027258
Aberrant 3' oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia.
Hilcenko C, Simpson PJ, Finch AJ, Bowler FR, Churcher MJ, Jin L, Packman LC, Shlien A, Campbell P, Kirwan M, Dokal I, Warren AJ.
Blood. 2013 Feb 7;121(6):1028-38. doi: 10.1182/blood-2012-10-461491. Epub 2012 Nov 27.
PMID 23190533
C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification.
Mroczek S, Krwawicz J, Kutner J, Lazniewski M, Kucin'ski I, Ginalski K, Dziembowski A.
Genes Dev. 2012 Sep 1;26(17):1911-25. doi: 10.1101/gad.193169.112. Epub 2012 Aug 16.
PMID 22899009
Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA.
Shchepachev V, Wischnewski H, Missiaglia E, Soneson C, Azzalin CM.
Cell Rep. 2012 Oct 25;2(4):855-65. doi: 10.1016/j.celrep.2012.08.031. Epub 2012 Sep 27.
PMID 23022480
Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene.
Volpi L, Roversi G, Colombo EA, Leijsten N, Concolino D, Calabria A, Mencarelli MA, Fimiani M, Macciardi F, Pfundt R, Schoenmakers EF, Larizza L.
Am J Hum Genet. 2010 Jan;86(1):72-6. doi: 10.1016/j.ajhg.2009.11.014. Epub 2009 Dec 10.
PMID 20004881


This paper should be referenced as such :
EA Colombo
USB1 (U6 snRNA biogenesis 1)
Atlas Genet Cytogenet Oncol Haematol. 2014;18(9):678-681.
Free journal version : [ pdf ]   [ DOI ]

External links


HGNC (Hugo)USB1   25792
LRG (Locus Reference Genomic)LRG_352
Entrez_Gene (NCBI)USB1    U6 snRNA biogenesis phosphodiesterase 1
AliasesC16orf57; HVSL1; Mpn1; PN; 
GeneCards (Weizmann)USB1
Ensembl hg19 (Hinxton)ENSG00000103005 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000103005 [Gene_View]  ENSG00000103005 [Sequence]  chr16:58001407-58021618 [Contig_View]  USB1 [Vega]
ICGC DataPortalENSG00000103005
TCGA cBioPortalUSB1
AceView (NCBI)USB1
Genatlas (Paris)USB1
SOURCE (Princeton)USB1
Genetics Home Reference (NIH)USB1
Genomic and cartography
GoldenPath hg38 (UCSC)USB1  -     chr16:58001407-58021618 +  16q21   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)USB1  -     16q21   [Description]    (hg19-Feb_2009)
GoldenPathUSB1 - 16q21 [CytoView hg19]  USB1 - 16q21 [CytoView hg38]
Genome Data Viewer NCBIUSB1 [Mapview hg19]  
OMIM604173   613276   
Gene and transcription
Genbank (Entrez)AK023216 AK124443 AK126223 AK293220 AK298473
RefSeq transcript (Entrez)NM_001195302 NM_001204911 NM_001330568 NM_001330569 NM_024598
Consensus coding sequences : CCDS (NCBI)USB1
Gene ExpressionUSB1 [ NCBI-GEO ]   USB1 [ EBI - ARRAY_EXPRESS ]   USB1 [ SEEK ]   USB1 [ MEM ]
Gene Expression Viewer (FireBrowse)USB1 [ Firebrowse - Broad ]
GenevisibleExpression of USB1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)79650
GTEX Portal (Tissue expression)USB1
Human Protein AtlasENSG00000103005-USB1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BQ65   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9BQ65  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BQ65
Domains : Interpro (EBI)Usb1   
Domain families : Pfam (Sanger)HVSL (PF09749)   
Domain families : Pfam (NCBI)pfam09749   
Conserved Domain (NCBI)USB1
PDB (RSDB)4H7W    5V1M    6D2Z    6D30    6D31   
PDB Europe4H7W    5V1M    6D2Z    6D30    6D31   
PDB (PDBSum)4H7W    5V1M    6D2Z    6D30    6D31   
PDB (IMB)4H7W    5V1M    6D2Z    6D30    6D31   
Structural Biology KnowledgeBase4H7W    5V1M    6D2Z    6D30    6D31   
SCOP (Structural Classification of Proteins)4H7W    5V1M    6D2Z    6D30    6D31   
CATH (Classification of proteins structures)4H7W    5V1M    6D2Z    6D30    6D31   
AlphaFold pdb e-kbQ9BQ65   
Human Protein Atlas [tissue]ENSG00000103005-USB1 [tissue]
Protein Interaction databases
IntAct (EBI)Q9BQ65
Ontologies - Pathways
Ontology : AmiGO3'-5'-exoribonuclease activity  3'-5'-exoribonuclease activity  nucleus  nucleus  nucleoplasm  RNA splicing  U6 snRNA 3'-end processing  U6 snRNA 3'-end processing  intercellular bridge  RNA phosphodiester bond hydrolysis, exonucleolytic  poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends  
Ontology : EGO-EBI3'-5'-exoribonuclease activity  3'-5'-exoribonuclease activity  nucleus  nucleus  nucleoplasm  RNA splicing  U6 snRNA 3'-end processing  U6 snRNA 3'-end processing  intercellular bridge  RNA phosphodiester bond hydrolysis, exonucleolytic  poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends  
NDEx NetworkUSB1
Atlas of Cancer Signalling NetworkUSB1
Wikipedia pathwaysUSB1
Orthology - Evolution
GeneTree (enSembl)ENSG00000103005
Phylogenetic Trees/Animal Genes : TreeFamUSB1
Homologs : HomoloGeneUSB1
Homology/Alignments : Family Browser (UCSC)USB1
Gene fusions - Rearrangements
Fusion : FusionGDB3.1.4.-   
Fusion : QuiverUSB1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerUSB1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)USB1
Exome Variant ServerUSB1
GNOMAD BrowserENSG00000103005
Varsome BrowserUSB1
ACMGUSB1 variants
Genomic Variants (DGV)USB1 [DGVbeta]
DECIPHERUSB1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisUSB1 
ICGC Data PortalUSB1 
TCGA Data PortalUSB1 
Broad Tumor PortalUSB1
OASIS PortalUSB1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICUSB1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DUSB1
Mutations and Diseases : HGMDUSB1
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
DgiDB (Drug Gene Interaction Database)USB1
DoCM (Curated mutations)USB1
CIViC (Clinical Interpretations of Variants in Cancer)USB1
NCG (London)USB1
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
OMIM604173    613276   
Orphanet477    18933   
Genetic Testing Registry USB1
NextProtQ9BQ65 [Medical]
Target ValidationUSB1
Huge Navigator USB1 [HugePedia]
Clinical trials, drugs, therapy
Protein Interactions : CTDUSB1
Pharm GKB GenePA143485394
Clinical trialUSB1
DataMed IndexUSB1
PubMed34 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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