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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. 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

Regulatory Elements for SCNM1 Gene

Enhancers for SCNM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H151193 2 FANTOM5 Ensembl ENCODE dbSUPER 22.5 +41.0 40983 7 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF207 ZNF143 ZNF687 PIP5K1A SETDB1 ARNT PI4KB PRPF3 GOLPH3L UBE2D3P3 PRUNE1 SCNM1
GH01H151508 2 FANTOM5 Ensembl ENCODE dbSUPER 11.6 +356.5 356455 8 HDGF PKNOX1 FOXA2 ARID4B SIN3A ZNF2 ZBTB7B YY1 FOS SP3 ARNT SETDB1 PIP5K1A PI4KB CGN PRUNE1 GOLPH3L UBE2D3P3 C1orf56 CTSK
GH01H152045 2 FANTOM5 Ensembl ENCODE dbSUPER 11.6 +891.9 891941 6 HDGF PKNOX1 ARNT ARID4B SIN3A YBX1 FEZF1 DMAP1 ZNF2 ZBTB7B PI4KB ZNF687 ENSG00000229021 FLG-AS1 PIP5K1A MRPL9 RPS10P6 SCNM1 S100A11 S100A10
GH01H151971 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.6 +816.3 816292 2 PKNOX1 ATF1 FEZF1 ZNF2 GLIS2 FOS TSHZ1 MAFF ZNF610 SMARCA4 ENSG00000229021 THEM4 S100A10 SCNM1 S100A11 PI4KB THEM5 ENSG00000252840 CGN LINGO4
GH01H152032 1.7 FANTOM5 ENCODE dbSUPER 11.6 +879.3 879340 6 PKNOX1 ARNT ARID4B SIN3A FEZF1 ZNF2 ZNF766 ZNF143 DEK SP3 PI4KB GABPB2 MRPL9 PIP5K1A S100A11 RPS10P6 THEM4 SCNM1 ZNF687 POGZ
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SCNM1 on UCSC Golden Path with GeneCards custom track

Promoters for SCNM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000013586 536 1201 CTCF ETV1 SIN3A MAX POLR2A ZNF366 EED ZNF207 ETV6 RUNX3

Genomic Location for SCNM1 Gene

Chromosome:
1
Start:
151,156,664 bp from pter
End:
151,170,297 bp from pter
Size:
13,634 bases
Orientation:
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:
    Q9BWG6-SCNM1_HUMAN
    Recommended name:
    Sodium channel modifier 1
    Protein Accession:
    Q9BWG6
    Secondary Accessions:
    • B4DWR1
    • Q5JR74

    Protein attributes for SCNM1 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

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.

Phenotypes From GWAS Catalog for SCNM1 Gene

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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SCNM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , 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

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 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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SCNM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
SCNM1
ECgene alternative splicing isoforms for
SCNM1

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:

SCNM1

SOURCE GeneReport for Unigene cluster for SCNM1 Gene:

Hs.732060

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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia SCNM1 33 34
  • 99.57 (n)
cow
(Bos Taurus)
Mammalia SCNM1 33 34
  • 90.87 (n)
dog
(Canis familiaris)
Mammalia SCNM1 33 34
  • 88.41 (n)
mouse
(Mus musculus)
Mammalia Scnm1 33 16 34
  • 84.59 (n)
rat
(Rattus norvegicus)
Mammalia Scnm1 33
  • 84.43 (n)
oppossum
(Monodelphis domestica)
Mammalia SCNM1 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCNM1 33 34
  • 55.31 (n)
lizard
(Anolis carolinensis)
Reptilia SCNM1 34
  • 47 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scnm1 33
  • 57.74 (n)
zebrafish
(Danio rerio)
Actinopterygii scnm1 33 34
  • 51.77 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 29 (a)
OneToOne
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

ENSEMBL:
Gene Tree for SCNM1 (if available)
TreeFam:
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 Sequence Context AA Info Type
rs1000901120 -- 151,164,922(+) AGGAC(G/T)TGTGC intron-variant, upstream-variant-2KB
rs1001309604 -- 151,164,080(+) GTAGA(C/G)ACAGG intron-variant, upstream-variant-2KB
rs1001354526 -- 151,168,461(+) TGGAG(G/T)GCAAT intron-variant
rs1001465731 -- 151,170,622(+) AGCAC(A/G)GTGGC downstream-variant-500B, reference, synonymous-codon
rs1002178677 -- 151,165,932(+) GTCTG(C/T)GGAGT intron-variant, upstream-variant-2KB, utr-variant-5-prime

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)

Relevant External Links for SCNM1 Gene

Human Gene Mutation Database (HGMD)
SCNM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCNM1

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
  • lennox syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SCNM1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SCNM1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  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 60
  5. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. (PMID: 28112733) Hendriks IA … Nielsen ML (Nature structural & molecular biology 2017) 4 60

Products for SCNM1 Gene

Sources for SCNM1 Gene

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