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Scnm1 sodium channel modifier 1 [ Mus musculus (house mouse) ]

Gene ID: 69269, updated on 25-Apr-2024

Summary

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Official Symbol
Scnm1provided by MGI
Official Full Name
sodium channel modifier 1provided by MGI
Primary source
MGI:MGI:1341284
See related
AllianceGenome:MGI:1341284
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Scnm1-ps; 3110001I17Rik
Summary
Mutations in the voltage-gated sodium channel gene Scn8a lead to neurological problems in mice. For one particular mutation, Scn8amedJ, mice live to adulthood but have tremors and muscle weakness, among other problems, in all strains except those derived from C57BL6 mice. In these strains, the product of the Scnm1 gene (229 aa) partially overcomes the effects of the Scn8amedJ mutation. However, in C57BL6-derived mice, a one nt change in the penultimate exon creates a premature stop codon, truncating the Scnm1 protein at 186 aa. This truncated protein lacks the ability to overcome the effects of the Scn8amedJ mutation, and these mice suffer paralysis and juvenile death. [provided by RefSeq, Jul 2009]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 24.1), CNS E14 (RPKM 23.1) and 28 other tissues See more
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Genomic context

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Location:
3 F2.1; 3 40.74 cM
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (95037030..95041285, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (95129719..95134050, complement)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4-phosphate 5-kinase, type 1 alpha Neighboring gene predicted gene, 22301 Neighboring gene STARR-seq mESC enhancer starr_08367 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94914795-94915038 Neighboring gene vacuolar protein sorting 72 Neighboring gene tropomodulin 4 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94937828-94938011 Neighboring gene LysM, putative peptidoglycan-binding, domain containing 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94945477-94945712 Neighboring gene microRNA 8099-1 Neighboring gene tumor necrosis factor, alpha-induced protein 8-like 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Molecular and pathological effects of a modifier gene on deficiency of the sodium channel Scn8a (Na(v)1.6). Kearney JA, et al. Hum Mol Genet, 2002 Oct 15. PMID 12374766
  2. High-resolution mapping of the sodium channel modifier Scnm1 on mouse chromosome 3 and identification of a 1.3-kb recombination hot spot. Buchner DA, et al. Genomics, 2003 Oct. PMID 13679025
  3. A targeted deleterious allele of the splicing factor SCNM1 in the mouse. Howell VM, et al. Genetics, 2008 Nov. PMID 18791226, Free PMC Article
  4. SCNM1, a putative RNA splicing factor that modifies disease severity in mice. Buchner DA, et al. Science, 2003 Aug 15. PMID 12920299
  5. Behavioral audiograms of homozygous med(J) mutant mice with sodium channel deficiency and unaffected controls. Koay G, et al. Hear Res, 2002 Sep. PMID 12204355

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RNA splicing IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within RNA splicing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in alternative mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
sodium channel modifier 1
Names
sodium channel modifier 1, pseudogene

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.

mRNA and Protein(s)

  1. NM_001409852.1 → NP_001396781.1  sodium channel modifier 1

    Status: VALIDATED

    Source sequence(s)
    BC028867
    UniProtKB/Swiss-Prot
    Q8K136, Q9CXV5

RNA

  1. NR_176904.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC131769

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    95037030..95041285 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001163573.1: Suppressed sequence

    Description
    NM_001163573.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

  2. NM_001406472.1: Suppressed sequence

    Description
    NM_001406472.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

  3. NM_001406473.1: Suppressed sequence

    Description
    NM_001406473.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

  4. NM_001406474.1: Suppressed sequence

    Description
    NM_001406474.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

  5. NM_001406475.1: Suppressed sequence

    Description
    NM_001406475.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

  6. NM_001406476.1: Suppressed sequence

    Description
    NM_001406476.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

  7. NM_001406486.1: Suppressed sequence

    Description
    NM_001406486.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

  8. NM_027013.3: Suppressed sequence

    Description
    NM_027013.3: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8K136.1 GenPept UniProtKB/Swiss-Prot:Q8K136

Gene LinkOut

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