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. Alternati... See more...

Aliases for SON Gene

Aliases for SON Gene

  • SON DNA And RNA Binding Protein 2 3 5
  • Negative Regulatory Element-Binding Protein 2 3 4
  • Bax Antagonist Selected In Saccharomyces 1 2 3 4
  • NRE-Binding Protein 2 3 4
  • BASS1 2 3 4
  • NREBP 2 3 4
  • SON DNA Binding Protein 2 3
  • Protein SON 3 4
  • C21orf50 3 4
  • KIAA1019 2 4
  • DBP-5 2 3
  • SON3 3 4
  • Protein DBP-5 4
  • FLJ21099 2
  • FLJ33914 2
  • TOKIMS 3
  • DBP5 4
  • SON 5

External Ids for SON Gene

Previous HGNC Symbols for SON Gene

  • C21orf50

Previous GeneCards Identifiers for SON Gene

  • GC21P031492
  • GC21P031575
  • GC21P033835
  • GC21P033837
  • GC21P034914
  • GC21P020393

Summaries for SON Gene

Entrez Gene Summary for SON Gene

  • 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]

GeneCards Summary for SON Gene

SON (SON DNA And RNA Binding Protein) is a Protein Coding gene. Diseases associated with SON include Zttk Syndrome and Agenesis Of Corpus Callosum, Cardiac, Ocular, And Genital Syndrome. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding.

UniProtKB/Swiss-Prot Summary for SON Gene

  • RNA-binding protein that acts as a mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. Specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Probably acts by facilitating the interaction between Serine/arginine-rich proteins such as SRSF2 and the RNA polymerase II. Also binds to DNA; binds to the consensus DNA sequence: 5'-GA[GT]AN[CG][AG]CC-3'. May indirectly repress hepatitis B virus (HBV) core promoter activity and transcription of HBV genes and production of HBV virions. Essential for correct RNA splicing of multiple genes critical for brain development, neuronal migration and metabolism, including TUBG1, FLNA, PNKP, WDR62, PSMD3, PCK2, PFKL, IDH2, and ACY1 (PubMed:27545680).

Gene Wiki entry for SON Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SON Gene

Genomics for SON Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SON Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SON on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SON

Top Transcription factor binding sites by QIAGEN in the SON gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-5
  • Sp1

Genomic Locations for SON Gene

Latest Assembly
chr21:33,543,038-33,577,481
(GRCh38/hg38)
Size:
34,444 bases
Orientation:
Plus strand

Previous Assembly
chr21:34,915,344-34,949,787
(GRCh37/hg19 by Entrez Gene)
Size:
34,444 bases
Orientation:
Plus strand

chr21:34,914,924-34,949,812
(GRCh37/hg19 by Ensembl)
Size:
34,889 bases
Orientation:
Plus strand

Genomic View for SON Gene

Genes around SON on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SON Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SON Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SON Gene

Proteins for SON Gene

  • Protein details for SON Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P18583-SON_HUMAN
    Recommended name:
    Protein SON
    Protein Accession:
    P18583
    Secondary Accessions:
    • D3DSF5
    • D3DSF6
    • E7ETE8
    • E7EU67
    • E7EVW3
    • E9PFQ2
    • O14487
    • O95981
    • Q14120
    • Q6PKE0
    • Q9H7B1
    • Q9P070
    • Q9P072
    • Q9UKP9
    • Q9UPY0

    Protein attributes for SON Gene

    Size:
    2426 amino acids
    Molecular mass:
    263830 Da
    Quaternary structure:
    • Interacts with SRSF2. Associates with the spliceosome. Interacts with the AML1-MTG8 (AML1-ETO) fusion protein, possibly leading to trigger signals inhibiting leukemogenesis.
    SequenceCaution:
    • Sequence=AAH02422.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA82971.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=CAA44793.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=CAC69885.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part.; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform C]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform E]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for SON Gene

neXtProt entry for SON Gene

Post-translational modifications for SON Gene

  • Glycosylation at Thr252 and Thr253
  • Ubiquitination at Lys16, Lys2173, and Lys2382
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Antibodies for research

  • Abcam antibodies for SON
  • Santa Cruz Biotechnology (SCBT) Antibodies for SON

No data available for DME Specific Peptides for SON Gene

Domains & Families for SON Gene

Gene Families for SON Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins
  • Transporters

Protein Domains for SON Gene

InterPro:
Blocks:
  • D111/G-patch domain
  • Double-stranded RNA binding (DsRBD) domain

Suggested Antigen Peptide Sequences for SON Gene

GenScript: Design optimal peptide antigens:
  • SON protein (A0JLP4_HUMAN)
  • SON DNA binding protein, isoform CRA_b (D3DSF7_HUMAN)
  • SON protein (Q3SWV4_HUMAN)
  • SON protein SON3 (Q3YL85_HUMAN)
  • SON3 (SON_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P18583

UniProtKB/Swiss-Prot:

SON_HUMAN :
  • Contains 8 types of repeats which are distributed in 3 regions.
Domain:
  • Contains 8 types of repeats which are distributed in 3 regions.
genes like me logo Genes that share domains with SON: view

Function for SON Gene

Molecular function for SON Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein that acts as a mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. Specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Probably acts by facilitating the interaction between Serine/arginine-rich proteins such as SRSF2 and the RNA polymerase II. Also binds to DNA; binds to the consensus DNA sequence: 5'-GA[GT]AN[CG][AG]CC-3'. May indirectly repress hepatitis B virus (HBV) core promoter activity and transcription of HBV genes and production of HBV virions. Essential for correct RNA splicing of multiple genes critical for brain development, neuronal migration and metabolism, including TUBG1, FLNA, PNKP, WDR62, PSMD3, PCK2, PFKL, IDH2, and ACY1 (PubMed:27545680).
GENATLAS Biochemistry:
DNA binding protein with some homology to c-mos,ubiquitously expressed,involved in chromatin remodeling

Phenotypes From GWAS Catalog for SON Gene

Gene Ontology (GO) - Molecular Function for SON Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA,IDA 21504830
GO:0005515 protein binding IPI 21504830
genes like me logo Genes that share ontologies with SON: view
genes like me logo Genes that share phenotypes with SON: view

Human Phenotype Ontology for SON Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for SON Gene

miRTarBase miRNAs that target SON

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SON

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SON Gene

Localization for SON Gene

Subcellular locations from UniProtKB/Swiss-Prot for SON Gene

Nucleus speckle. Note=Colocalizes with the pre-mRNA splicing factor SRSF2.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SON gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SON Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0016607 nuclear speck IDA 21504830
genes like me logo Genes that share ontologies with SON: view

Pathways & Interactions for SON Gene

PathCards logo

SuperPathways for SON Gene

No Data Available

SIGNOR curated interactions for SON Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SON Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000226 microtubule cytoskeleton organization IMP 21504830
GO:0000281 mitotic cytokinesis IMP 21504830
GO:0006397 mRNA processing IEA,IDA 21504830
GO:0007049 cell cycle IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SON: view

No data available for Pathways by source for SON Gene

Drugs & Compounds for SON Gene

No Compound Related Data Available

Transcripts for SON Gene

mRNA/cDNA for SON Gene

6 REFSEQ mRNAs :
38 NCBI additional mRNA sequence :
20 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SON

Alternative Splicing Database (ASD) splice patterns (SP) for SON Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b · 13c ^ 14a · 14b ^ 15a · 15b ^ 16 ^ 17a · 17b · 17c ^ 18a ·
SP1: - - - -
SP2: - - - -
SP3: - - -
SP4: -
SP5: -
SP6:
SP7:
SP8:
SP9: -
SP10: -
SP11:
SP12: -
SP13:
SP14:
SP15:

ExUns: 18b · 18c ^ 19 ^ 20 ^ 21a · 21b · 21c · 21d · 21e · 21f · 21g
SP1: - -
SP2: -
SP3: -
SP4: - -
SP5: -
SP6:
SP7:
SP8: -
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for SON Gene

GeneLoc Exon Structure for
SON

Expression for SON Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SON Gene

Protein differential expression in normal tissues from HIPED for SON Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.4), Heart (7.3), and Testis (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SON Gene



Protein tissue co-expression partners for SON Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SON

SOURCE GeneReport for Unigene cluster for SON Gene:

Hs.517262

mRNA Expression by UniProt/SwissProt for SON Gene:

P18583-SON_HUMAN
Tissue specificity: Widely expressed, with the higher expression seen in leukocyte and heart.

Evidence on tissue expression from TISSUES for SON Gene

  • Nervous system(4.9)
  • Liver(4.9)
  • Blood(4.6)
  • Muscle(4.4)
  • Eye(2.7)
  • Skin(2.4)
  • Intestine(2.4)
  • Lung(2.4)
  • Kidney(2.3)
  • Spleen(2)
genes like me logo Genes that share expression patterns with SON: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SON Gene

Orthologs for SON Gene

This gene was present in the common ancestor of animals.

Orthologs for SON Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SON 29 30
  • 99.52 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Son 29
  • 93.53 (n)
Dog
(Canis familiaris)
Mammalia LOC100856585 29
  • 91.61 (n)
-- 30
  • 90 (a)
OneToMany
-- 30
  • 90 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia SON 29 30
  • 89.41 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Son 29 16 30
  • 87.54 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SON 30
  • 73 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SON 30
  • 72 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SON 30
  • 36 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SON 30
  • 62 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.21268 29
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.16651 29
Zebrafish
(Danio rerio)
Actinopterygii SON 30
  • 52 (a)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10141 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG8273 30 31
  • 29 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea D1037.1 30 31
  • 28 (a)
OneToOne
Species where no ortholog for SON was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SON Gene

ENSEMBL:
Gene Tree for SON (if available)
TreeFam:
Gene Tree for SON (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SON: view image
Alliance of Genome Resources:
Additional Orthologs for SON

Paralogs for SON Gene

Pseudogenes.org Pseudogenes for SON Gene

genes like me logo Genes that share paralogs with SON: view

No data available for Paralogs for SON Gene

Variants for SON Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SON Gene

SNP ID Clinical significance and condition Chr 21 pos Variation AA Info Type
1011631 Uncertain Significance: not provided 33,550,481(+) C/T
NM_138927.4(SON):c.1250C>T (p.Pro417Leu)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON
1013462 Pathogenic: not provided 33,551,954(+) C/CA
NM_138927.4(SON):c.2727dup (p.Ser910fs)
FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON
1028929 Uncertain Significance: ZTTK syndrome 33,550,322(+) T/C
NM_138927.4(SON):c.1091T>C (p.Leu364Pro)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON
1028930 Uncertain Significance: ZTTK syndrome 33,550,799(+) A/G
NM_138927.4(SON):c.1568A>G (p.Glu523Gly)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON
1028931 Uncertain Significance: ZTTK syndrome 33,551,946(+) G/A
NM_138927.4(SON):c.2715G>A (p.Met905Ile)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SON Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SON Gene

Variant ID Type Subtype PubMed ID
esv2723354 CNV deletion 23290073
esv2723355 CNV deletion 23290073
esv2723356 CNV deletion 23290073
nsv1078502 CNV duplication 25765185
nsv1115615 CNV duplication 24896259

Variation tolerance for SON Gene

Residual Variation Intolerance Score: 0.699% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.07; 80.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SON Gene

Human Gene Mutation Database (HGMD)
SON
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SON
Leiden Open Variation Database (LOVD)
SON

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SON Gene

Disorders for SON Gene

MalaCards: The human disease database

(11) MalaCards diseases for SON Gene - From: OMI, CVR, GTR, ORP, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search SON in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SON_HUMAN
  • ZTTK syndrome (ZTTKS) [MIM:617140]: An autosomal dominant syndrome characterized by intellectual disability, developmental delay, malformations of the cerebral cortex, epilepsy, vision problems, musculo-skeletal abnormalities, and congenital malformations. {ECO:0000269 PubMed:25590979, ECO:0000269 PubMed:27256762, ECO:0000269 PubMed:27545676, ECO:0000269 PubMed:27545680}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for SON

genes like me logo Genes that share disorders with SON: view

No data available for Genatlas for SON Gene

Publications for SON Gene

  1. De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive. (PMID: 27545676) Tokita MJ … Walkiewicz MA (American journal of human genetics 2016) 3 4 72
  2. De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome. (PMID: 27545680) Kim JH … Ahn EYE (American journal of human genetics 2016) 3 4 72
  3. Establishing SON in 21q22.11 as a cause a new syndromic form of intellectual disability: Possible contribution to Braddock-Carey syndrome phenotype. (PMID: 27256762) Takenouchi T … Kosaki K (American journal of medical genetics. Part A 2016) 3 4 72
  4. Transcription repression of human hepatitis B virus genes by negative regulatory element-binding protein/SON. (PMID: 11306577) Sun CT … Ting LP (The Journal of biological chemistry 2001) 3 4 22
  5. Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. (PMID: 25590979) Zhu X … Goldstein DB (Genetics in medicine : official journal of the American College of Medical Genetics 2015) 3 4

Products for SON Gene

Sources for SON Gene