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

Gene ID: 8926, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (24954987..24978723)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (22691653..22715388)
105.20220307 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
  • 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. Behavioral phenotype in adults with Prader-Willi syndrome. Sinnema M, et al. Res Dev Disabil, 2011 Mar-Apr. PMID 21227640

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_2023_10

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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