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Aliases for SCNM1 Gene

Aliases for SCNM1 Gene

  • Sodium Channel Modifier 1 2 3 5

External Ids for SCNM1 Gene

Previous GeneCards Identifiers for SCNM1 Gene

  • GC01P147913
  • GC01P148355
  • GC01P147951
  • GC01P149405

Summaries for SCNM1 Gene

Entrez Gene Summary for SCNM1 Gene

  • SCNM1 is a zinc finger protein and putative splicing factor. In mice, Scnm1 modifies phenotypic expression of Scn8a (MIM 600702) mutations (Buchner et al., 2003 [PubMed 12920299]).[supplied by OMIM, Oct 2009]

GeneCards Summary for SCNM1 Gene

SCNM1 (Sodium Channel Modifier 1) is a Protein Coding gene. Diseases associated with SCNM1 include Lennox-Gastaut Syndrome. Gene Ontology (GO) annotations related to this gene include enzyme binding.

UniProtKB/Swiss-Prot for SCNM1 Gene

  • Plays a role in RNA splicing, possibly contributing to the recognition of non-consensus donor sites.

Additional gene information for SCNM1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCNM1 Gene

Genomics for SCNM1 Gene

GeneHancer (GH) Regulatory Elements for SCNM1 Gene

Promoters and enhancers for SCNM1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I151164 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.4 +9.4 9385 3.1 CLOCK DMAP1 IRF4 YY1 E2F8 ZNF143 SP3 NFYC MEF2D ZNF610 LYSMD1 SCNM1 PRPF3 SETDB1 PI4KB ARNT UBE2D3P3 ZNF687 PIP5K1A CTSK
GH01I151156 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +1.9 1918 4.9 HDGF ARID4B RAD21 ZBTB40 RFX5 ZNF366 ZNF143 ZNF207 ETV6 IKZF2 SCNM1 TNFAIP8L2 TNFAIP8L2-SCNM1 SEMA6C BNIPL LYSMD1
GH01I150998 Enhancer 1.3 Ensembl ENCODE dbSUPER 9.7 -157.3 -157287 1.2 PKNOX1 ATF1 ARNT TCF12 ZNF766 E2F8 ATF7 NCOA1 ZNF592 MEF2D RNU6-884P CERS2 ENSG00000231073 BNIPL C1orf56 SCNM1 LYSMD1 TMOD4 MINDY1 ANXA9
GH01I151000 Enhancer 1 ENCODE dbSUPER 9.7 -155.4 -155369 0.7 PKNOX1 TAF9B ZNF366 ATF7 CREM ZBTB2 CEBPB USF2 REST ZNF398 RNU6-884P ENSG00000231073 CERS2 SEMA6C BNIPL C1orf56 SCNM1 LYSMD1 TMOD4 MINDY1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCNM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCNM1 gene promoter:

Genomic Locations for SCNM1 Gene

Genomic Locations for SCNM1 Gene
13,634 bases
Plus strand

Genomic View for SCNM1 Gene

Genes around SCNM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCNM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCNM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCNM1 Gene

Proteins for SCNM1 Gene

  • Protein details for SCNM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium channel modifier 1
    Protein Accession:
    Secondary Accessions:
    • B4DWR1
    • Q5JR74

    Protein attributes for SCNM1 Gene

    230 amino acids
    Molecular mass:
    25949 Da
    Quaternary structure:
    • Interacts with LUC7L2 and SNRNP70, which suggests a role as a spliceosome component.

    Alternative splice isoforms for SCNM1 Gene


neXtProt entry for SCNM1 Gene

Post-translational modifications for SCNM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SCNM1 Gene

No data available for DME Specific Peptides for SCNM1 Gene

Domains & Families for SCNM1 Gene

Gene Families for SCNM1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SCNM1 Gene

Suggested Antigen Peptide Sequences for SCNM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCNM1: view

No data available for UniProtKB/Swiss-Prot for SCNM1 Gene

Function for SCNM1 Gene

Molecular function for SCNM1 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in RNA splicing, possibly contributing to the recognition of non-consensus donor sites.

Gene Ontology (GO) - Molecular Function for SCNM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0019899 enzyme binding IPI 23382074
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SCNM1: view
genes like me logo Genes that share phenotypes with SCNM1: view

Animal Models for SCNM1 Gene

MGI Knock Outs for SCNM1:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCNM1 Gene

Localization for SCNM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCNM1 Gene

Nucleus. Nucleus speckle. Note=Colocalizes with LUC7L2 and SNRNP70 in nuclear speckles. {ECO:0000250}.

Subcellular locations from

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 SCNM1 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SCNM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0016607 nuclear speck IEA --
genes like me logo Genes that share ontologies with SCNM1: view

Pathways & Interactions for SCNM1 Gene

SuperPathways for SCNM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCNM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SCNM1: view

No data available for Pathways by source and SIGNOR curated interactions for SCNM1 Gene

Drugs & Compounds for SCNM1 Gene

No Compound Related Data Available

Transcripts for SCNM1 Gene

Unigene Clusters for SCNM1 Gene

Sodium channel modifier 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCNM1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b · 7c
SP1: - - - - -
SP2: - - - - -
SP3: - - - -
SP4: - - -
SP5: - -
SP6: - -
SP7: -

Relevant External Links for SCNM1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCNM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCNM1 Gene

mRNA differential expression in normal tissues according to GTEx for SCNM1 Gene

This gene is overexpressed in Whole Blood (x4.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SCNM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCNM1 Gene:


SOURCE GeneReport for Unigene cluster for SCNM1 Gene:


Evidence on tissue expression from TISSUES for SCNM1 Gene

  • Eye(4.3)
  • Liver(4.2)
  • Nervous system(3.3)
genes like me logo Genes that share expression patterns with SCNM1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCNM1 Gene

Orthologs for SCNM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCNM1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCNM1 33 34
  • 99.57 (n)
(Bos Taurus)
Mammalia SCNM1 33 34
  • 90.87 (n)
(Canis familiaris)
Mammalia SCNM1 33 34
  • 88.41 (n)
(Mus musculus)
Mammalia Scnm1 33 16 34
  • 84.59 (n)
(Rattus norvegicus)
Mammalia Scnm1 33
  • 84.43 (n)
(Monodelphis domestica)
Mammalia SCNM1 34
  • 72 (a)
(Gallus gallus)
Aves LOC425744 33
  • 55.31 (n)
SCNM1 34
  • 44 (a)
(Anolis carolinensis)
Reptilia SCNM1 34
  • 47 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia scnm1 33
  • 57.74 (n)
(Danio rerio)
Actinopterygii scnm1 33 34
  • 51.77 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 29 (a)
Species where no ortholog for SCNM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SCNM1 Gene

Gene Tree for SCNM1 (if available)
Gene Tree for SCNM1 (if available)

Paralogs for SCNM1 Gene

No data available for Paralogs for SCNM1 Gene

Variants for SCNM1 Gene

Sequence variations from dbSNP and Humsavar for SCNM1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000901120 -- 151,164,922(+) T/G upstream_transcript_variant
rs1001309604 -- 151,164,080(+) G/C upstream_transcript_variant
rs1001354526 -- 151,168,461(+) T/G intron_variant
rs1001465731 -- 151,170,622(+) G/A/T downstream_transcript_variant
rs1002178677 -- 151,165,932(+) C/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SCNM1 Gene

Variant ID Type Subtype PubMed ID
dgv2n68 CNV loss 17160897
esv3587520 CNV loss 21293372
nsv522840 CNV gain 19592680

Variation tolerance for SCNM1 Gene

Residual Variation Intolerance Score: 61.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.86; 48.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCNM1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCNM1 Gene

Disorders for SCNM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCNM1 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
lennox-gastaut syndrome
  • lgs
- elite association - COSMIC cancer census association via MalaCards
Search SCNM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SCNM1

genes like me logo Genes that share disorders with SCNM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCNM1 Gene

Publications for SCNM1 Gene

  1. SCNM1, a putative RNA splicing factor that modifies disease severity in mice. (PMID: 12920299) Buchner DA … Meisler MH (Science (New York, N.Y.) 2003) 2 3 22 58
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for SCNM1 Gene

Sources for SCNM1 Gene

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