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SMN2 Gene

protein-coding   GIFtS: 63
GCID: GC05P069345

Survival Of Motor Neuron 2, Centromeric

  See SMN2-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 9.2

Aliases
Survival Of Motor Neuron 2, Centromeric1 2     TDRD16B2
Tudor Domain Containing 16B1 2     gemin-12
Component Of Gems 12 3     Survival Motor Neuron Protein2
SMNC2 3     Gemin-13
BCD5412     SMN3
C-BCD5412     SMNT3
GEMIN12     

External Ids:    HGNC: 111181   Entrez Gene: 66072   Ensembl: ENSG000002055717   OMIM: 6016275   UniProtKB: Q166373   
ORGUL members:    fRNAdb10:FR161108 FR261454 FR161649 FR230846 FR261454      
H-InvDB12:HIT000327947_01 HIT000327947_02 HIT000327947_03 HIT000327947_04 HIT000327947_05 see all 48    
NCBI13:Z70696 Z70715 Z70715 BC033526 Z70715 see all 13    
NONCODE14:n384662 n387347 n337408 n334486 n387352    
RNAdb15:EVF19212 EVF9215 EVF9472 EVF18113 EVF38759 see all 16    

Export aliases for SMN2 gene to outside databases

Previous GC identifers: GC05U990054 GC05M034821 GC05P069880 GC05P069382


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SMN2 Gene:
This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least
four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and
complexity of the sequence have also caused difficulty in determining the organization of this genomic region.
The telomeric and centromeric copies of this gene are nearly identical and encode the same protein. While
mutations in the telomeric copy are associated with spinal muscular atrophy, mutations in this gene, the
centromeric copy, do not lead to disease. This gene may be a modifier of disease caused by mutation in the
telomeric copy. The critical sequence difference between the two genes is a single nucleotide in exon 7, which is
thought to be an exon splice enhancer. Note that the nine exons of both the telomeric and centromeric copies are
designated historically as exon 1, 2a, 2b, and 3-8. It is thought that gene conversion events may involve the two
genes, leading to varying copy numbers of each gene. The full length protein encoded by this gene localizes to
both the cytoplasm and the nucleus. Within the nucleus, the protein localizes to subnuclear bodies called gems
which are found near coiled bodies containing high concentrations of small ribonucleoproteins (snRNPs). This
protein forms heteromeric complexes with proteins such as SIP1 and GEMIN4, and also interacts with several
proteins known to be involved in the biogenesis of snRNPs, such as hnRNP U protein and the small nucleolar RNA
binding protein. Four transcript variants encoding distinct isoforms have been described. (provided by RefSeq,
Sep 2008)

GeneCards Summary for SMN2 Gene:
SMN2 (survival of motor neuron 2, centromeric) is a protein-coding gene. Diseases associated with SMN2 include spinal muscular atrophy, and spinal muscular atrophy, type iii, modifier of. GO annotations related to this gene include RNA binding and identical protein binding. An important paralog of this gene is SMN1.

UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637
Function: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the
building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most
spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG
that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the
cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by
the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from
the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their
transport to the nucleus. Ensures the correct splicing of U12 intron-containing genes that may be important for
normal motor and proprioceptive neurons development. May also play a role in the metabolism of small nucleolar
ribonucleoprotein (snoRNPs)

Gene Wiki entry for SMN2 Gene

fRNAdb sequence ontologies for SMN2 - the ORGUL cluster for this gene includes several descriptions:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for SMN2

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000005.9  NC_018916.2  NT_034772.7  NT_187651.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMN2 gene promoter:
         POU2F1   POU2F1a   STAT5A   XBP-1   Evi-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMN2 promoter sequence
   Search Chromatin IP Primers for SMN2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMN2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q13.2   Ensembl cytogenetic band:  5q13.2   HGNC cytogenetic band: 5q13.2

SMN2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMN2 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P069345:  view genomic region     (about GC identifiers)

Start:
69,345,350 bp from pter      End:
69,374,349 bp from pter
Size:
29,000 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637 (See protein sequence)
Recommended Name: Survival motor neuron protein  
Size: 294 amino acids; 31849 Da
Subunit: Homodimer. Part of the core SMN complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5,
GEMIN6, GEMIN7, GEMIN8 and STRAP/UNRIP. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3,
GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE,
SNRPF and SNRPG. Component of an import snRNP complex composed of KPNB1, RNUT1, SMN1 and ZNF259. Interacts with
DDX20, FBL, NOLA1, RNUT1, SYNCRIP and with several spliceosomal snRNP core Sm proteins, including SNRPB, SNRPD1,
SNRPD2, SNRPD3, SNRPE and ILF3. Interacts with OSTF1, LSM10, LSM11 and RPP20/POP7
Miscellaneous: The SMN gene is present in two highly homologous and functional copies (TelSMN/SMN1 and
CenSMN/SMN2). The telomeric copy of SMN gene (TelSMN/SMN1) seems to be the SMA-determining gene while the
centromeric copy seems unaffected
Selected PDB 3D structures from and Proteopedia for SMN2 (see all 7):
1G5V (3D)        1MHN (3D)        2LEH (3D)        3S6N (3D)        4A4E (3D)        4A4G (3D)    
Secondary accessions: A8K0V4 Q13119 Q549U5 Q96J51
Alternative splicing: 4 isoforms:  Q16637-1   Q16637-2   Q16637-3   Q16637-4   (Thought to be a non-functional protein that lacks the capacity to oligomerize and thus cannot interact with Sm proteins. Primarily derived from SMN2 gene)

Explore the universe of human proteins at neXtProt for SMN2: NX_Q16637

Explore proteomics data for SMN2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SMN2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_059107.1  NP_075013.1  NP_075014.1  NP_075015.1  

    ENSEMBL proteins: 
     ENSP00000370119   ENSP00000424282   ENSP00000424799   ENSP00000370118   ENSP00000475824  
     ENSP00000475331   ENSP00000370117  
    Reactome Protein details: Q16637

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    TDRD: Tudor domain containing

    2 InterPro protein domains:
     IPR010304 Survival_motor_neuron
     IPR002999 Tudor

    Graphical View of Domain Structure for InterPro Entry Q16637

    ProtoNet protein and cluster: Q16637

    2 Blocks protein domains:
    IPB002999 Tudor domain
    IPB010304 Survival motor neuron


    UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637
    Domain: The Tudor domain mediates association with dimethylarginines, which are common in snRNP proteins
    Similarity: Belongs to the SMN family
    Similarity: Contains 1 Tudor domain


    Find genes that share domains with SMN2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SMN_HUMAN, Q16637
    Function: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the
    building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most
    spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG
    that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the
    cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by
    the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from
    the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their
    transport to the nucleus. Ensures the correct splicing of U12 intron-containing genes that may be important for
    normal motor and proprioceptive neurons development. May also play a role in the metabolism of small nucleolar
    ribonucleoprotein (snoRNPs)

         Genatlas biochemistry entry for SMN2:
    survival motor neuron,centromeric copy,highly homologous to SMNT,involved in the expression of SMA with a single
    nucleotide change in exon 7 resulting in the splicing out of this exon from most of the transcripts from SMN2

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding IEA--
    GO:0005515protein binding IPI11714716
    GO:0042802identical protein binding IPI16189514
         
    Find genes that share ontologies with SMN2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SMN2:
     Decreased G3BP1 protein expres 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMN2
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    hsa-mir-193a-3p (MIRT044885), hsa-mir-26b-5p (MIRT029070), hsa-mir-30a-5p (MIRT028415), hsa-mir-186-5p (MIRT045172)

    Block miRNA regulation of human, mouse, rat SMN2 using miScript Target Protectors
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SMN_HUMAN, Q16637: Cytoplasm. Nucleus, gem. Cytoplasmic granule. Cytoplasm, myofibril, sarcomere, Z line (By
    similarity). Note=Colocalizes with Actn at the Z-line of skeletal muscle (By similarity). Under stress conditions
    colocalizes with RPP20/POP7 in punctuated cytoplasmic granules
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol4
    extracellular1
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005654nucleoplasm TAS--
    GO:0005681spliceosomal complex ----
    GO:0005737cytoplasm IDA9845364
    GO:0005829cytosol TAS--

    Find genes that share ontologies with SMN2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SMN2 About    
    See pathways by source

    SuperPathContained pathways About
    1Regulation of Glucokinase by Glucokinase Regulatory Protein
    Metabolism of non-coding RNA0.54
    snRNP Assembly0.54
    2Gene Expression
    Gene Expression0.40
    3RNA transport
    RNA transport


    Find genes that share SuperPaths with SMN2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    1 Reactome Pathway for SMN2
        snRNP Assembly


    1 Kegg Pathway  (Kegg details for SMN2):
        RNA transport

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SMN2
    Interactions:

        GeneGlobe Interaction Network for SMN2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SMN2 (Q166371, 2, 3 ENSP000003701194) via UniProtKB, MINT, STRING, and/or I2D (see all 989)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000245spliceosomal complex assembly NAS9323129
    GO:0000387spliceosomal snRNP assembly TAS--
    GO:0006397mRNA processing ----
    GO:0007399nervous system development IEA--
    GO:0008219cell death IEA--

    Find genes that share ontologies with SMN2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SMN2 (SMN)

    8 Novoseek inferred chemical compound relationships for SMN2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    phenylbutyrate 76.2 9 18345520 (3), 14560316 (3), 16508748 (1), 17076267 (1)
    nsc34 69.6 3 11734549 (1), 17220171 (1)
    valproic acid 51.5 6 12915451 (3), 16805808 (1), 16508748 (1), 17076267 (1)
    aclarubicin 45.3 4 11734549 (2), 17220171 (1)
    sodium orthovanadate 32.3 5 17220171 (2), 11704813 (1)
    oligonucleotide 22.2 6 16449646 (3), 17647030 (1), 19535574 (1)
    ribonucleic acid 6.92 10 17761657 (4), 17761653 (1)
    butyrate 5.05 2 11504946 (1), 17076267 (1)



    Find genes that share compounds with SMN2           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    5/17 fRNAdb Secondary structures (see all 17):


    REFSEQ mRNAs for SMN2 gene (4 alternative transcripts): 
    NM_017411.3  NM_022875.2  NM_022876.2  NM_022877.2  

    Unigene Cluster for SMN2:

    Survival of motor neuron 2, centromeric
    Hs.202179  [show with all ESTs]
    Unigene Representative Sequence: NM_017411
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000380743 ENST00000511812(uc011crm.2) ENST00000506734 ENST00000380742
    ENST00000503678 ENST00000511873 ENST00000509805 ENST00000505346 ENST00000514914
    ENST00000508258 ENST00000507458 ENST00000380741(uc003jyd.3 uc003jyf.3 uc003jye.3 uc003jyg.3)

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    Additional mRNA sequence: 

    AK289669.1 BC000908.2 BC015308.1 BC070242.1 DQ185039.1 JQ690861.1 JQ690862.1 JQ690863.1 
    JQ690864.1 JQ690865.1 JQ690866.1 U21914.1 

    21 DOTS entries:

    DT.91752366  DT.100810925  DT.99958452  DT.100810924  DT.95367672  DT.100708213  DT.91693694  DT.91752362 
    DT.100018657  DT.100810927  DT.86835738  DT.95367668  DT.100810920  DT.100810926  DT.100799306  DT.91748418 
    DT.100765329  DT.100810917  DT.120845147  DT.428244  DT.91941076 

    Selected AceView cDNA sequences (see all 485):

    BU633623 CR626737 BU728019 AI921459 BI962625 BM142213 AI687994 BM054868 
    BM311283 AF073520 BX642318 AI762053 AA916956 NM_022978 CR623997 BM461719 
    BU622712 BM711678 BI496007 AI921471 AI367511 AA732879 AI690649 AW467123 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SMN2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SMN2 Expression
    About this image

    SMN2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMN2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.202179

    UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637
    Tissue specificity: Expressed in a wide variety of tissues. Expressed at high levels in brain, kidney and liver,
    moderate levels in skeletal and cardiac muscle, and low levels in fibroblasts and lymphocytes. Also seen at high
    levels in spinal cord. Present in osteoclasts and mononuclear cells (at protein level)

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SMN2 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smn11 survival motor neuron 1 83.67(n)
    82.86(a)
      20595  NM_011420.2  NP_035550.1 
    chicken
    (Gallus gallus)
    Aves SMN1 survival of motor neuron 65.35(n)
    62.56(a)
      374025  NM_204199.1  NP_989530.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    62(a)
    1 → many
    2(16889501-16899457)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia smn21 survival of motor neuron 2, centromeric 63.51(n)
    58.85(a)
      100101724  NM_001100240.1  NP_001093710.1 
    zebrafish
    (Danio rerio)
    Actinopterygii smn11 survival motor neuron 1 58.65(n)
    55.27(a)
      30432  NM_131191.1  NP_571266.1 
    worm
    (Caenorhabditis elegans)
    Secernentea smn-16
    Protein SMN-1, isoform a (smn-1) mRNA, complete cd...
    31(a)
    1 → many
    I(9511190-9512139) WBGene00004887


    ENSEMBL Gene Tree for SMN2 (if available)
    TreeFam Gene Tree for SMN2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SMN2 gene
    SMN11 2  
    1 SIMAP similar gene for SMN2 using alignment to 8 protein entries:     SMN_HUMAN (see all proteins):
    SMN1

    Find genes that share paralogs with SMN2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SMN2 (see all 36)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1219091921,2
    C,Fpathogenic169372372(+) AAGAAG/CGAAGG 6 /R /G int1 mis12Minor allele frequency- C:0.00NA EU 4695
    rs716242221,2
    C,F--69371499(+) TTTTAC/AATTTA 4 -- int11Minor allele frequency- A:0.50NA 2
    rs789306451,2
    C--70196182(-) CAAGCG/AGTTCT 4 -- ds50011Minor allele frequency- A:0.00NA 2
    rs1395916661,2
    C--70196771(-) AAAGAC/GTGAGG 4 -- ut310--------
    rs1459996181,2
    --70197236(-) GGTTGA/GTTGTG 4 -- int10--------
    rs2006535281,2
    C--70197467(-) GTGCTC/GACATT 6 S * int1 stg10--------
    rs2015785191,2
    C--70197868(-) CTAGCA/CTGAGC 4 -- int10--------
    rs1888041681,2
    --70198393(-) CATTAC/TAGGCA 4 -- int10--------
    rs1840756651,2
    --70198432(-) TGATCC/TGCCCG 4 -- int10--------
    rs1821939241,2
    --70198486(-) TAGAGA/TCGGGA 4 -- int10--------

    HapMap Linkage Disequilibrium report for SMN2 (69345350 - 69374349 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SMN2 (see all 103):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv19n31CNV Duplication19718026
    nsv471547CNV Duplication19718026
    nsv471433CNV Duplication19718026
    nsv507261CNV Insertion20534489
    dgv6149n71CNV Loss21882294
    nsv881768CNV Loss21882294
    dgv6144n71CNV Loss21882294
    nsv821643CNV Loss15273396
    nsv882115CNV Loss21882294
    dgv6101n71CNV Loss21882294

    Human Gene Mutation Database (HGMD): SMN2
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing SMN2
    DNA2.0 Custom Variant and Variant Library Synthesis for SMN2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601627OMIM information: 612344 601888 610119 600354 600380 600562 609185    
    OMIM disorders: 253400  
    UniProtKB/Swiss-Prot: SMN_HUMAN, Q16637
  • Spinal muscular atrophy 1 (SMA1) [MIM:253300]: A form of spinal muscular atrophy, a group of
    neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to
    symmetrical muscle weakness and atrophy. Autosomal recessive forms are classified according to the age of onset,
    the maximum muscular activity achieved, and survivorship. The severity of the disease is mainly determined by the
    copy number of SMN2, a copy gene which predominantly produces exon 7-skipped transcripts and only low amount of
    full-length transcripts that encode for a protein identical to SMN1. Only about 4% of SMA patients bear one SMN1
    copy with an intragenic mutation. SMA1 is a severe form, with onset before 6 months of age. SMA1 patients never
    achieve the ability to sit. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Spinal muscular atrophy 2 (SMA2) [MIM:253550]: An autosomal recessive form of spinal muscular atrophy, a
    neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to
    symmetrical muscle weakness and atrophy. It has intermediate severity, with onset between 6 and 18 months.
    Patients do not reach the motor milestone of standing, and survive into adulthood. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Spinal muscular atrophy 3 (SMA3) [MIM:253400]: An autosomal recessive form of spinal muscular atrophy, a
    neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to
    symmetrical muscle weakness and atrophy. Onset is after 18 months. Patients develop ability to stand and walk and
    survive into adulthood. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Spinal muscular atrophy 4 (SMA4) [MIM:271150]: An autosomal recessive form of spinal muscular atrophy, a
    neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to
    symmetrical muscle weakness and atrophy. Onset is in adulthood, disease progression is slow, and patients can
    stand and walk. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 14 diseases for SMN2:    
    About MalaCards
    spinal muscular atrophy    spinal muscular atrophy, type iii, modifier of    adult spinal muscular atrophy    muscular atrophy
    spinal muscular atrophy 1    motor neuron disease    juvenile spinal muscular atrophy    spinal muscular atrophy type 2
    cerebellar ataxia and hypogonadotropic hypogonadism    proximal spinal muscular atrophy    werdnig-hoffmann disease    progressive muscular atrophy
    multifocal motor neuropathy    amyotrophic lateral sclerosis

    4 diseases from the University of Copenhagen DISEASES database for SMN2:
    Muscular atrophy     Motor neuron disease     Neuropathy     Autosomal recessive disease

    Find genes that share disorders with SMN2           About GenesLikeMe

    9 Novoseek inferred disease relationships for SMN2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    muscular atrophy spinal 98.3 72 16554261 (3), 17761649 (2), 18546169 (2), 20194437 (2) (see all 58)
    werdnig-hoffmann disease 83.5 2 19207472 (1)
    neuromuscular diseases 81.9 4 17761649 (1), 18546169 (1), 16439605 (1), 18971205 (1)
    motor neuron disease 79.5 3 19207472 (1), 17850955 (1)
    sma ii 75.9 2 17407069 (1), 17433677 (1)
    sma iii 75.6 9 17407069 (4), 18842367 (1), 15305106 (1), 19953646 (1)
    motor neuron disease lower 71.9 6 11993528 (3), 16931506 (1), 11835381 (1)
    spinal disorder 59.8 1 15944201 (1)
    amyotrophic lateral sclerosis 33 4 9585359 (1), 19922137 (1), 16931506 (1), 11835381 (1)

    GeneTests: SMN2
    GeneReviews: SMN2
    Genetic Association Database (GAD): SMN2
    Human Genome Epidemiology (HuGE) Navigator: SMN2 (19 documents)

    Export disorders for SMN2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SMN2 gene, integrated from 10 sources (see all 286):
    (articles sorted by number of sources associating them with SMN2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of a spinal muscular atrophy- determining gene. (PubMed id 7813012)1, 2, 3 Lefebvre S....Melki J. (Cell 1995)
    2. Combination of SMN2 copy number and NAIP deletion predicts disease severity in spinal muscular atrophy. (PubMed id 18842367)1, 4, 9 Watihayati M.S....Zilfalil B.A. (amp 2009)
    3. SMN1 gene, but not SMN2, is a risk factor for sporadic ALS. (PubMed id 16931506)1, 4, 9 Corcia P....Andres C.R. (Neurology 2006)
    4. Determination of SMN1 and SMN2 copy numbers in a Korean population using multiplex ligation-dependent probe amplification. (PubMed id 20197730)1, 4, 9 Yoon S....Lee K.A. (Korean J Lab Med 2010)
    5. C117T variant in the SMN1 gene found in the Japanese population. (PubMed id 17250497)1, 4, 9 Sadewa A.H....Nishio H. (Pediatr Int 2007)
    6. The survival motor neuron protein in spinal muscular atrophy. (PubMed id 9259265)1, 2, 9 Coovert D.D.... Burghes A.H.M. (Hum. Mol. Genet. 1997)
    7. Quantification of SMN1 and SMN2 genes by capillary electrophoresis for diagnosis of spinal muscular atrophy. (PubMed id 18546169)1, 4, 9 Wang C.C....Yeh C.H. (Electrophoresis 2008)
    8. SMN genotypes producing less SMN protein increase susceptibility to and severity of sporadic ALS. (PubMed id 16093455)1, 4, 9 Veldink J.H....Van den Berg L.H. (Neurology 2005)
    9. Determination of SMN1/SMN2 gene dosage by a quantitative genotyping platform combining capillary electrophoresis and MALDI-TOF mass spectrometry. (PubMed id 16439605)1, 4, 9 Kao H.Y....Chen Y.J. (Clin. Chem. 2006)
    10. An extended inhibitory context causes skipping of exon 7 of SMN2 in spinal muscular atrophy. (PubMed id 14766219)1, 4, 9 Singh N.N....Singh R.N. (Biochem. Biophys. Res. Commun. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6607 HGNC: 11118 AceView: SMN1 Ensembl:ENSG00000205571 euGenes: HUgn6607
    ECgene: SMN2 Kegg: 6607 H-InvDB: SMN2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SMN2 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SMN1[genesymbol]
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SMN2[genesymbol]
    SHMPDhttp://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=SMN1

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SMN2 gene:
    Search GeneIP for patents involving SMN2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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