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    SNURF SNRPN upstream open reading frame [ Homo sapiens (human) ]

    Gene ID: 8926, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SNURFprovided by HGNC
    Official Full Name
    SNRPN upstream open reading frameprovided by HGNC
    Primary source
    HGNC:HGNC:11171
    See related
    Ensembl:ENSG00000273173 AllianceGenome:HGNC:11171
    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
    Summary
    This gene is located within the Prader-Willi Syndrome critical region on chromosome 15. Transcripts produced from this gene initiate at an imprinting center and are paternally-imprinted. These transcripts may be bicistronic and also encode SNRPN (small nuclear ribonucleoprotein polypeptide N) from a downstream open reading frame. The small protein represented by this gene is encoded by an evolutionarily-conserved upstream open reading frame and is localized to the nucleus. Extensive alternative splicing and promoter usage occurs in this region and the full-length nature of some of these transcripts has not been determined. Alterations in the imprinting center are associated with parental imprint switch failure, which may cause Angelman syndrome or Prader-Willi syndrome. [provided by RefSeq, Mar 2017]
    Orthologs
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    Genomic context

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    See SNURF in Genome Data Viewer
    Location:
    15q11.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (24954987..24978723)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (22691653..22715388)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (25200134..25223870)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA host gene 14 Neighboring gene small nuclear ribonucleoprotein polypeptide N Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:25196020-25196660 Neighboring gene ribosomal protein S27 pseudogene 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:25200549-25201114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:25201115-25201680 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:25201681-25202246 Neighboring gene ribosomal protein L5 pseudogene 1 Neighboring gene small nucleolar RNA, C/D box 107 Neighboring gene small nucleolar RNA, C/D box 64 Neighboring gene Prader Willi/Angelman region RNA, SNRPN neighbor Neighboring gene Prader Willi/Angelman region RNA 5

    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 deletion of SNURF/SNRPN exon 1 in a patient with Prader-Willi-like phenotype. Cao Y, et al. Eur J Med Genet, 2017 Aug. PMID 28554868
    2. Small mosaic deletion encompassing the snoRNAs and SNURF-SNRPN results in an atypical Prader-Willi syndrome phenotype. Anderlid BM, et al. Am J Med Genet A, 2014 Feb. PMID 24311433
    3. Novel Tandem Duplication in Exon 1 of the SNURF/SNRPN Gene in a Child with Transient Excessive Eating Behaviour and Weight Gain. Naik S, et al. Mol Syndromol, 2012 Jan. PMID 22511895, Free PMC Article
    4. Prader-Willi syndrome and atypical submicroscopic 15q11-q13 deletions with or without imprinting defects. Hassan M, et al. Eur J Med Genet, 2016 Nov. PMID 27659713, Free PMC Article
    5. Primary structure of a human small nuclear ribonucleoprotein polypeptide as deduced by cDNA analysis. Rokeach LA, et al. J Biol Chem, 1989 Mar 25. PMID 2522449

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A de novo 6.4 kb deletion at 15q11.2, containing exon 1 of the SNURF gene and exon 1 of the shortest isoform of the SNRPN gene was identified in a patient with Prader-Willi-like phenotype. DNA methylation analysis confirmed the paternal origin of the deletion.
      Title: A novel deletion of SNURF/SNRPN exon 1 in a patient with Prader-Willi-like phenotype.
    2. significant IGF2 hypermethylation (20 +/- 10 vs. 14 +/- 7%; p<0.05) and SNURF hypomethylation (23 +/- 6 vs. 32 6%; p<0.001) was found in Albright's hereditary osteodystrophy patients vs. controls.
      Title: Methylation defect in imprinted genes detected in patients with an Albright's hereditary osteodystrophy like phenotype and platelet Gs hypofunction.
    3. Differences between genetic subtypes were also statistically significant in Prader Willi syndrome
      Title: Behavioral phenotype in adults with Prader-Willi syndrome.
    4. Identification of cis- and trans-acting regulatory elements within the endogenous SNURF-SNRPN locus.
      Title: Characterization of cis- and trans-acting elements in the imprinted human SNURF-SNRPN locus.
    5. The SNURF-SNRPN sense/UBE3A antisense transcription unit spans more than 460 kb.
      Title: The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A.
    Submit: New GeneRIF Correction

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2023-03-28)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2023-03-28)

    ClinGen Genome Curation PagePubMed

    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

    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 ATPase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nuclear speck IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SNRPN upstream reading frame 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.

    Genomic

    1. NG_012958.1 RefSeqGene

      Range
      136247..160077
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001394334.1 → NP_001381263.1  SNRPN upstream reading frame protein

      Status: REVIEWED

      Source sequence(s)
      AC090602, AC124312
      Consensus CDS
      CCDS10016.1
      UniProtKB/Swiss-Prot
      A6NCW2, Q9Y675
      Related
      ENSP00000463201.1, ENST00000577949.6
      Conserved Domains (1) summary
      pfam07192
      Location:4 → 68
      SNURF; SNURF/RPN4 protein

    2. NM_005678.5 → NP_005669.2  SNRPN upstream reading frame protein

      See identical proteins and their annotated locations for NP_005669.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the predominant splice variant and represents a bicistronic transcript that can also encode the SNRPN protein.
      Source sequence(s)
      AC124312, DA369087, DB554158, U41303
      Consensus CDS
      CCDS10016.1
      UniProtKB/Swiss-Prot
      A6NCW2, Q9Y675
      Related
      ENSP00000463396.1, ENST00000580062.5
      Conserved Domains (1) summary
      pfam07192
      Location:4 → 68
      SNURF; SNURF/RPN4 protein

    3. NM_022804.3 → NP_073715.1  SNRPN upstream reading frame protein

      See identical proteins and their annotated locations for NP_073715.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks multiple 3' exons and contains an alternate 3' UTR compared to variant 1. This variant is monocistronic and cannot encode the SNRPN protein.
      Source sequence(s)
      AW451120, DA134019
      Consensus CDS
      CCDS10016.1
      UniProtKB/Swiss-Prot
      A6NCW2, Q9Y675
      Related
      ENSP00000342152.4, ENST00000338327.4
      Conserved Domains (1) summary
      pfam07192
      Location:4 → 68
      SNURF; SNURF/RPN4 protein

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      24954987..24978723
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      22691653..22715388
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y675.1 GenPept UniProtKB/Swiss-Prot:Q9Y675

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