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    SON SON DNA and RNA binding protein [ Homo sapiens (human) ]

    Gene ID: 6651, updated on 7-Apr-2024

    Summary

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    Official Symbol
    SONprovided by HGNC
    Official Full Name
    SON DNA and RNA binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:11183
    See related
    Ensembl:ENSG00000159140 MIM:182465; AllianceGenome:HGNC:11183
    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
    SON3; BASS1; DBP-5; NREBP; TOKIMS; C21orf50
    Summary
    This gene encodes a protein that contains multiple simple repeats. The encoded protein binds RNA and promotes pre-mRNA splicing, particularly of transcripts with poor splice sites. The protein also recognizes a specific DNA sequence found in the human hepatitis B virus (HBV) and represses HBV core promoter activity. There is a pseudogene for this gene on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in bone marrow (RPKM 43.7), lymph node (RPKM 33.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    21q22.11
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (33543038..33577481)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (31924877..31959322)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (34915344..34949787)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene DnaJ heat shock protein family (Hsp40) member C28 Neighboring gene phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:34903402-34904601 Neighboring gene basic transcription factor 3 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13260 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:34914753-34915484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13261 Neighboring gene microRNA 6501 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:34960679-34961178 Neighboring gene DNA replication fork stabilization factor DONSON Neighboring gene crystallin zeta like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18383

    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. Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON. Dingemans AJM, et al. Eur J Hum Genet, 2022 Mar. PMID 34521999, Free PMC Article
    2. The SON RNA splicing factor is required for intracellular trafficking structures that promote centriole assembly and ciliogenesis. Stemm-Wolf AJ, et al. Mol Biol Cell, 2021 Oct 1. PMID 34406792, Free PMC Article
    3. ZTTK syndrome: Clinical and molecular findings of 15 cases and a review of the literature. Kushary ST, et al. Am J Med Genet A, 2021 Dec. PMID 34331327, Free PMC Article
    4. Establishing SON in 21q22.11 as a cause a new syndromic form of intellectual disability: Possible contribution to Braddock-Carey syndrome phenotype. Takenouchi T, et al. Am J Med Genet A, 2016 Oct. PMID 27256762
    5. Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. Zhu X, et al. Genet Med, 2015 Oct. PMID 25590979, Free PMC Article

    See all (148) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SON is an essential m[6]A target for hematopoietic stem cell fate.
      Title: SON is an essential m(6)A target for hematopoietic stem cell fate.
    2. Expanding the mutational spectrum of ZTTK syndrome: A de novo variant with global developmental delay and malnutrition in a Chinese patient.
      Title: Expanding the mutational spectrum of ZTTK syndrome: A de novo variant with global developmental delay and malnutrition in a Chinese patient.
    3. Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON.
      Title: Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON.
    4. ZTTK syndrome: Clinical and molecular findings of 15 cases and a review of the literature.
      Title: ZTTK syndrome: Clinical and molecular findings of 15 cases and a review of the literature.
    5. SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia.
      Title: SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia.
    6. The SON RNA splicing factor is required for intracellular trafficking structures that promote centriole assembly and ciliogenesis.
      Title: The SON RNA splicing factor is required for intracellular trafficking structures that promote centriole assembly and ciliogenesis.
    7. SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity.
      Title: SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity.
    8. Phenotypic expansion in Zhu-Tokita-Takenouchi-Kim syndrome caused by de novo variants in the SON gene.
      Title: Phenotypic expansion in Zhu-Tokita-Takenouchi-Kim syndrome caused by de novo variants in the SON gene.
    9. SON DNA-binding protein mediates macrophage autophagy and responses to intracellular infection.
      Title: SON DNA-binding protein mediates macrophage autophagy and responses to intracellular infection.
    10. SON and SRRM2 are essential for nuclear speckle formation.
      Title: SON and SRRM2 are essential for nuclear speckle formation.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    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
    ZTTK syndrome
    MedGen: C4310696 OMIM: 617140 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2019-04-24)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2019-04-24)

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag HIV-1 Gag interacts with SON as demonstrated by proximity dependent biotinylation proteomics 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

    • FLJ21099, FLJ33914, KIAA1019

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding 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 RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of microtubule cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of mitotic cytokinesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein SON
    Names
    Bax antagonist selected in Saccharomyces 1
    NRE-binding protein
    SON DNA binding protein
    negative regulatory element-binding 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_052981.2 RefSeqGene

      Range
      5002..39445
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001291411.2 → NP_001278340.2  protein SON isoform E

      Status: REVIEWED

      Description
      Transcript Variant: This variant (e) lacks multiple 3' coding exons and contains an alternate 3' exon, resulting in a distinct 3' coding region and 3' UTR, compared to variant f. It encodes isoform E which is shorter and has a distinct C-terminus, compared to isoform F.
      Source sequence(s)
      AP000303
      Consensus CDS
      CCDS74784.1
      Related
      ENSP00000371095.4, ENST00000381679.8
      Conserved Domains (4) summary
      PHA03247
      Location:170 → 460
      PHA03247; large tegument protein UL36; Provisional
      PHA03379
      Location:340 → 673
      PHA03379; EBNA-3A; Provisional
      PRK10811
      Location:1289 → 1481
      rne; ribonuclease E; Reviewed
      NF000535
      Location:730 → 903
      MSCRAMM_SdrC; MSCRAMM family adhesin SdrC

    2. NM_001291412.3 → NP_001278341.1  protein SON isoform H

      Status: REVIEWED

      Description
      Transcript Variant: This variant (h) represents the allele encoded by the GRCh38 reference genome and encodes isoform (H).
      Source sequence(s)
      AP000303, AP000304
      Consensus CDS
      CCDS77624.1
      UniProtKB/TrEMBL
      A0A994J4Y9, J3QSZ5
      Related
      ENSP00000371111.2, ENST00000381692.6
      Conserved Domains (2) summary
      pfam01585
      Location:333 → 376
      G-patch; G-patch domain
      cl00054
      Location:398 → 441
      DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...

    3. NM_001412132.1 → NP_001399061.1  protein SON isoform I

      Status: REVIEWED

      Description
      Transcript Variant: This variant (i) uses the same exon combination as variant h but represents the allele encoded by the T2T genome assembly. The encoded isoform (I) has a slightly different sequence in the C-terminal region compared to isoform H.
      Source sequence(s)
      CP068257
      UniProtKB/TrEMBL
      Q6ZRV7

    4. NM_001412133.1 → NP_001399062.1  protein SON isoform J

      Status: REVIEWED

      Description
      Transcript Variant: This variant (j) uses the same exon combination as variant f but represents the allele encoded by the T2T genome assembly. The encoded isoform (J) has a slightly different sequence in the C-terminal region compared to isoform F.
      Source sequence(s)
      CP068257

    5. NM_032195.3 → NP_115571.3  protein SON isoform B

      Status: REVIEWED

      Description
      Transcript Variant: This variant (b) lacks multiple 3' coding exons and contains an alternate 3' exon, resulting in a distinct 3' coding region and 3' UTR, compared to variant f. The encoded isoform (B) is shorter and has a distinct C-terminus, compared to isoform F.
      Source sequence(s)
      AP000303, AP000304
      Consensus CDS
      CCDS13631.1
      Related
      ENSP00000300278.2, ENST00000300278.8
      Conserved Domains (4) summary
      PHA03247
      Location:170 → 460
      PHA03247; large tegument protein UL36; Provisional
      PHA03379
      Location:340 → 673
      PHA03379; EBNA-3A; Provisional
      PRK10811
      Location:1289 → 1481
      rne; ribonuclease E; Reviewed
      NF000535
      Location:730 → 903
      MSCRAMM_SdrC; MSCRAMM family adhesin SdrC

    6. NM_138927.4 → NP_620305.3  protein SON isoform F

      Status: REVIEWED

      Description
      Transcript Variant: This variant (f) represents the allele encoded by the GRCh38 reference genome and encodes isoform (F).
      Source sequence(s)
      AF380184, AK307612, AP000303
      Consensus CDS
      CCDS13629.1
      UniProtKB/Swiss-Prot
      D3DSF5, D3DSF6, E7ETE8, E7EU67, E7EVW3, E9PFQ2, O14487, O95981, P18583, Q14120, Q6PKE0, Q9H7B1, Q9P070, Q9P072, Q9UKP9, Q9UPY0
      Related
      ENSP00000348984.4, ENST00000356577.10
      Conserved Domains (6) summary
      PHA03247
      Location:170 → 460
      PHA03247; large tegument protein UL36; Provisional
      PHA03379
      Location:340 → 673
      PHA03379; EBNA-3A; Provisional
      PRK10811
      Location:1289 → 1481
      rne; ribonuclease E; Reviewed
      NF000535
      Location:730 → 903
      MSCRAMM_SdrC; MSCRAMM family adhesin SdrC
      pfam01585
      Location:2305 → 2349
      G-patch; G-patch domain
      cl00054
      Location:2369 → 2419
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    RNA

    1. NR_103797.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (c) contains an alternate internal exon and uses an alternate splice site at the 3' exon, compared to variant f. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant f, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AP000303, AP000304
      Related
      ENST00000455528.5

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      33543038..33577481
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      31924877..31959322
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_003103.5: Suppressed sequence

      Description
      NM_003103.5: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_138925.1: Suppressed sequence

      Description
      NM_138925.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    3. NR_103796.1: Suppressed sequence

      Description
      NR_103796.1: This RefSeq was permanently suppressed because it is now thought that this transcript variant does encode a protein.

    4. NR_103798.1: Suppressed sequence

      Description
      NR_103798.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P18583.4 GenPept UniProtKB/Swiss-Prot:P18583

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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