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    SMN2 survival of motor neuron 2, centromeric [ Homo sapiens (human) ]

    Gene ID: 6607, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SMN2provided by HGNC
    Official Full Name
    survival of motor neuron 2, centromericprovided by HGNC
    Primary source
    HGNC:HGNC:11118
    See related
    Ensembl:ENSG00000205571 MIM:601627; AllianceGenome:HGNC:11118
    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
    SMNC; BCD541; GEMIN1; TDRD16B; C-BCD541
    Summary
    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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 24.2), testis (RPKM 21.9) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SMN2 in Genome Data Viewer
    Location:
    5q13.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (70049523..70090528)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (70791126..70837821, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (69345350..69373422)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene cadherin 12 pseudogene 2 Neighboring gene mitochondrial import receptor subunit TOM5 homolog Neighboring gene small EDRK-rich factor 1B Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:69351921-69352560 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:69352561-69353200 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:69384675-69385378 Neighboring gene NAIP pseudogene 2 Neighboring gene GUSB pseudogene 14 Neighboring gene cadherin 12 pseudogene 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Congenital heart disease is a feature of severe infantile spinal muscular atrophy. Rudnik-Schöneborn S, et al. J Med Genet, 2008 Oct. PMID 18662980
    2. A rare SMN2 variant in a previously unrecognized composite splicing regulatory element induces exon 7 inclusion and reduces the clinical severity of spinal muscular atrophy. Vezain M, et al. Hum Mutat, 2010 Jan. PMID 19953646
    3. A-44G transition in SMN2 intron 6 protects patients with spinal muscular atrophy. Wu X, et al. Hum Mol Genet, 2017 Jul 15. PMID 28460014, Free PMC Article
    4. An analysis of disease severity based on SMN2 copy number in adults with spinal muscular atrophy. Elsheikh B, et al. Muscle Nerve, 2009 Oct. PMID 19760790
    5. A positive modifier of spinal muscular atrophy in the SMN2 gene. Prior TW, et al. Am J Hum Genet, 2009 Sep. PMID 19716110, Free PMC Article

    See all (297) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical Phenotype of Pediatric and Adult Patients With Spinal Muscular Atrophy With Four SMN2 Copies: Are They Really All Stable?
      Title: Clinical Phenotype of Pediatric and Adult Patients With Spinal Muscular Atrophy With Four SMN2 Copies: Are They Really All Stable?
    2. The Carrier Frequency of Two SMN1 Genes in Parents of Symptomatic Children with SMA and the Significance of SMN1 Exon 8 in Carriers.
      Title: The Carrier Frequency of Two SMN1 Genes in Parents of Symptomatic Children with SMA and the Significance of SMN1 Exon 8 in Carriers.
    3. Newborn screening for spinal muscular atrophy in Osaka -challenges in a Japanese pilot study.
      Title: Newborn screening for spinal muscular atrophy in Osaka -challenges in a Japanese pilot study.
    4. A splicing silencer in SMN2 intron 6 is critical in spinal muscular atrophy.
      Title: A splicing silencer in SMN2 intron 6 is critical in spinal muscular atrophy.
    5. Effects of Inhibitors of SLC9A-Type Sodium-Proton Exchangers on Survival Motor Neuron 2 (SMN2) mRNA Splicing and Expression.
      Title: Effects of Inhibitors of SLC9A-Type Sodium-Proton Exchangers on Survival Motor Neuron 2 (SMN2) mRNA Splicing and Expression.
    6. Revealing diverse alternative splicing variants of the highly homologous SMN1 and SMN2 genes by targeted long-read sequencing.
      Title: Revealing diverse alternative splicing variants of the highly homologous SMN1 and SMN2 genes by targeted long-read sequencing.
    7. Spinal Muscular Atrophy - Is Newborn Screening Too Late for Children with Two SMN2 Copies?
      Title: Spinal Muscular Atrophy - Is Newborn Screening Too Late for Children with Two SMN2 Copies?
    8. High Concentration or Combined Treatment of Antisense Oligonucleotides for Spinal Muscular Atrophy Perturbed SMN2 Splicing in Patient Fibroblasts.
      Title: High Concentration or Combined Treatment of Antisense Oligonucleotides for Spinal Muscular Atrophy Perturbed SMN2 Splicing in Patient Fibroblasts.
    9. SMN protein is required throughout life to prevent spinal muscular atrophy disease progression.
      Title: SMN protein is required throughout life to prevent spinal muscular atrophy disease progression.
    10. Identification of SRSF10 as a regulator of SMN2 ISS-N1.
      Title: Identification of SRSF10 as a regulator of SMN2 ISS-N1.
    Submit: New GeneRIF Correction See all GeneRIFs (154)

    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
    Kugelberg-Welander disease
    MedGen: C0152109 OMIM: 253400 GeneReviews: Spinal Muscular Atrophy
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Clone Names

    • MGC5208, FLJ76644, MGC20996

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA-templated transcription termination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spliceosomal complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in spliceosomal complex assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in spliceosomal snRNP assembly EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in spliceosomal snRNP assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spliceosomal snRNP assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Cajal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Cajal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in Gemini of coiled bodies IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Gemini of coiled bodies IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SMN complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SMN complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SMN complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of SMN-Sm protein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Z disc IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in neuron projection IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perikaryon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    survival motor neuron protein
    Names
    component of gems 1
    gemin-1
    tudor domain containing 16B

    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_008728.1 RefSeqGene

      Range
      5147..33073
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_677

    mRNA and Protein(s)

    1. NM_017411.4 → NP_059107.1  survival motor neuron protein isoform d

      See identical proteins and their annotated locations for NP_059107.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d).
      Source sequence(s)
      AI312583, BC015308, CN272420
      Consensus CDS
      CCDS4007.1
      UniProtKB/Swiss-Prot
      A8K0V4, Q13119, Q16637, Q549U5, Q96J51
      Related
      ENSP00000370119.4, ENST00000380743.9
      Conserved Domains (1) summary
      pfam06003
      Location:27 → 291
      SMN; Survival motor neuron protein (SMN)

    2. NM_022875.3 → NP_075013.1  survival motor neuron protein isoform a

      See identical proteins and their annotated locations for NP_075013.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (a) lacks an alternate exon in the 3' CDS compared to variant d. The resulting protein (isoform a) is shorter and has a distinct C-terminus compared to isoform d. This variant is thought to be the predominant transcript produced by this copy of the gene.
      Source sequence(s)
      AA029652, AI312583, BC000908
      Consensus CDS
      CCDS54867.1
      Related
      ENSP00000486152.1, ENST00000626847.2
      Conserved Domains (1) summary
      pfam06003
      Location:27 → 278
      SMN; Survival motor neuron protein (SMN)

    3. NM_022876.2 → NP_075014.1  survival motor neuron protein isoform b

      See identical proteins and their annotated locations for NP_075014.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (b) lacks an alternate in-frame exon in the 3' CDS compared to variant d. The resulting protein (isoform b) is shorter but has the same N- and C- termini compared to isoform d.
      Source sequence(s)
      AC140134, AI312583, BC015308, CN272420
      Consensus CDS
      CCDS4008.1
      Related
      ENSP00000370118.4, ENST00000380742.8
      Conserved Domains (1) summary
      pfam06003
      Location:27 → 259
      SMN; Survival motor neuron protein (SMN)

    4. NM_022877.2 → NP_075015.1  survival motor neuron protein isoform c

      See identical proteins and their annotated locations for NP_075015.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (c) lacks two alternate exons in the 3' CDS compared to variant d. The resulting protein (isoform c) is shorter and has a distinct C-terminus compared to isoform d.
      Source sequence(s)
      AA029652, AC140134, AI312583, BC000908
      Conserved Domains (2) summary
      smart00333
      Location:90 → 147
      TUDOR; Tudor domain
      pfam06003
      Location:27 → 246
      SMN; Survival motor neuron protein (SMN)

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      70049523..70090528
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417619.1 → XP_047273575.1  survival motor neuron protein isoform X3

    2. XM_047417620.1 → XP_047273576.1  survival motor neuron protein isoform X5

    3. XM_047417621.1 → XP_047273577.1  survival motor neuron protein isoform X6

    4. XM_047417622.1 → XP_047273578.1  survival motor neuron protein isoform X9

    5. XM_011543600.3 → XP_011541902.1  survival motor neuron protein isoform X7

      See identical proteins and their annotated locations for XP_011541902.1

      UniProtKB/TrEMBL
      B4DP61
      Related
      ENSP00000424282.1, ENST00000511812.5
      Conserved Domains (1) summary
      pfam06003
      Location:27 → 224
      SMN; Survival motor neuron protein (SMN)

    6. XM_011543601.2 → XP_011541903.1  survival motor neuron protein isoform X8

      See identical proteins and their annotated locations for XP_011541903.1

      Conserved Domains (1) summary
      pfam06003
      Location:27 → 211
      SMN; Survival motor neuron protein (SMN)

    7. XM_011543602.4 → XP_011541904.1  survival motor neuron protein isoform X10

      See identical proteins and their annotated locations for XP_011541904.1

      Conserved Domains (1) summary
      pfam06003
      Location:27 → 192
      SMN; Survival motor neuron protein (SMN)

    8. XM_011543603.4 → XP_011541905.1  survival motor neuron protein isoform X2

      See identical proteins and their annotated locations for XP_011541905.1

      Conserved Domains (1) summary
      pfam06003
      Location:27 → 179
      SMN; Survival motor neuron protein (SMN)

    9. XM_011543599.2 → XP_011541901.1  survival motor neuron protein isoform X4

      See identical proteins and their annotated locations for XP_011541901.1

      UniProtKB/TrEMBL
      E7EQZ4
      Related
      ENSP00000486268.1, ENST00000628696.2
      Conserved Domains (2) summary
      smart00333
      Location:90 → 147
      TUDOR; Tudor domain
      pfam06003
      Location:27 → 278
      SMN; Survival motor neuron protein (SMN)

    10. XM_017009787.2 → XP_016865276.1  survival motor neuron protein isoform X1

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791777.1 Reference GRCh38.p14 PATCHES

      Range
      809289..850685 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333028.1 → XP_054189003.1  survival motor neuron protein isoform X3

    2. XM_054333034.1 → XP_054189009.1  survival motor neuron protein isoform X9

    3. XM_054333031.1 → XP_054189006.1  survival motor neuron protein isoform X6

    4. XM_054333030.1 → XP_054189005.1  survival motor neuron protein isoform X5

    5. XM_054333035.1 → XP_054189010.1  survival motor neuron protein isoform X10

    6. XM_054333033.1 → XP_054189008.1  survival motor neuron protein isoform X8

    7. XM_054333032.1 → XP_054189007.1  survival motor neuron protein isoform X7

      UniProtKB/TrEMBL
      B4DP61

    8. XM_054333029.1 → XP_054189004.1  survival motor neuron protein isoform X4

      UniProtKB/TrEMBL
      E7EQZ4

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_187651.1 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      274862..321547
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329970.1 → XP_054185945.1  survival motor neuron protein isoform X3

    2. XM_054329973.1 → XP_054185948.1  survival motor neuron protein isoform X5

    3. XM_054329974.1 → XP_054185949.1  survival motor neuron protein isoform X6

    4. XM_054329977.1 → XP_054185952.1  survival motor neuron protein isoform X9

    5. XM_054329975.1 → XP_054185950.1  survival motor neuron protein isoform X7

      UniProtKB/TrEMBL
      B4DP61

    6. XM_054329976.1 → XP_054185951.1  survival motor neuron protein isoform X8

    7. XM_054329978.1 → XP_054185953.1  survival motor neuron protein isoform X10

    8. XM_054329979.1 → XP_054185954.1  survival motor neuron protein isoform X2

    9. XM_054329971.1 → XP_054185946.1  survival motor neuron protein isoform X4

      UniProtKB/TrEMBL
      E7EQZ4

    10. XM_054329972.1 → XP_054185947.1  survival motor neuron protein isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      70791126..70837821 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353292.1 → XP_054209267.1  survival motor neuron protein isoform X3

    2. XM_054353299.1 → XP_054209274.1  survival motor neuron protein isoform X9

    3. XM_054353296.1 → XP_054209271.1  survival motor neuron protein isoform X6

    4. XM_054353294.1 → XP_054209269.1  survival motor neuron protein isoform X5

    5. XM_054353301.1 → XP_054209276.1  survival motor neuron protein isoform X2

    6. XM_054353300.1 → XP_054209275.1  survival motor neuron protein isoform X10

    7. XM_054353298.1 → XP_054209273.1  survival motor neuron protein isoform X8

    8. XM_054353297.1 → XP_054209272.1  survival motor neuron protein isoform X7

      UniProtKB/TrEMBL
      B4DP61

    9. XM_054353295.1 → XP_054209270.1  survival motor neuron protein isoform X11

    10. XM_054353293.1 → XP_054209268.1  survival motor neuron protein isoform X4

      UniProtKB/TrEMBL
      E7EQZ4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q16637.1 GenPept UniProtKB/Swiss-Prot:Q16637

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