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SCNM1 sodium channel modifier 1 [ Homo sapiens (human) ]

Gene ID: 79005, updated on 18-Nov-2020

Summary

Official Symbol
SCNM1provided by HGNC
Official Full Name
sodium channel modifier 1provided by HGNC
Primary source
HGNC:HGNC:23136
See related
Ensembl:ENSG00000163156 MIM:608095
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Ubiquitous expression in spleen (RPKM 7.6), lymph node (RPKM 7.6) and 25 other tissues See more
Orthologs

Genomic context

See SCNM1 in Genome Data Viewer
Location:
1q21.3
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (151166144..151170296)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151138482..151142773)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene semaphorin 6C Neighboring gene TNFAIP8L2-SCNM1 readthrough Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene tropomodulin 4 Neighboring gene vacuolar protein sorting 72 homolog Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 alpha

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough TNFAIP8L2-SCNM1

Readthrough gene: TNFAIP8L2-SCNM1, Included gene: TNFAIP8L2

Homology

Clone Names

  • MGC3180

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
alternative mRNA splicing, via spliceosome ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
nuclear speck ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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_001204856.2NP_001191785.1  sodium channel modifier 1 isoform 2

    See identical proteins and their annotated locations for NP_001191785.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. These differences causes translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK056322, AL592424, AV718162
    Consensus CDS
    CCDS55636.1
    UniProtKB/Swiss-Prot
    Q9BWG6
    Related
    ENSP00000357898.1, ENST00000368902.1
    Conserved Domains (2) summary
    pfam15803
    Location:935
    zf-SCNM1; Zinc-finger of sodium channel modifier 1
    pfam15805
    Location:148193
    SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1
  2. NM_024041.4NP_076946.1  sodium channel modifier 1 isoform 1

    See identical proteins and their annotated locations for NP_076946.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL592424
    Consensus CDS
    CCDS987.1
    UniProtKB/Swiss-Prot
    Q9BWG6
    Related
    ENSP00000357901.4, ENST00000368905.9
    Conserved Domains (2) summary
    pfam15803
    Location:4470
    zf-SCNM1; Zinc-finger of sodium channel modifier 1
    pfam15805
    Location:183228
    SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1

RNA

  1. NR_037937.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK056322, AL592424, BU540926, CD103880

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    151166144..151170296
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001002234.1: Suppressed sequence

    Description
    NM_001002234.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript.
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