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

Gene ID: 79005, updated on 2-Nov-2024

Summary

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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; AllianceGenome:HGNC:23136
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
Also known as
OFD19
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
all
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Genomic context

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See SCNM1 in Genome Data Viewer
Location:
1q21.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151166144..151170296)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150289872..150294025)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151138620..151142772)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151104130-151104914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1313 Neighboring gene semaphorin 6C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1315 Neighboring gene TNFAIP8L2-SCNM1 readthrough Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:151137860-151138565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151138566-151139272 Neighboring gene tropomodulin 4 Neighboring gene vacuolar protein sorting 72 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1711 Neighboring gene uncharacterized LOC124904419 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 alpha

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

Bibliography

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Related articles in PubMed

  1. Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia. Iturrate A, et al. Am J Hum Genet, 2022 Oct 6. PMID 36084634, Free PMC Article
  2. SCNM1, a putative RNA splicing factor that modifies disease severity in mice. Buchner DA, et al. Science, 2003 Aug 15. PMID 12920299
  3. Evidence for a direct role of the disease modifier SCNM1 in splicing. Howell VM, et al. Hum Mol Genet, 2007 Oct 15. PMID 17656373
  4. Protein microarray analysis identifies human cellular prion protein interactors. Satoh J, et al. Neuropathol Appl Neurobiol, 2009 Feb. PMID 18482256
  5. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Armour SM, et al. Mol Cell Biol, 2013 Apr. PMID 23382074, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia.
    Title: Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia.
Submit: New GeneRIF Correction

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
Orofaciodigital syndrome 19
MedGen: C5774248 OMIM: 620107 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough TNFAIP8L2-SCNM1

Readthrough gene: TNFAIP8L2-SCNM1, Included gene: TNFAIP8L2

Homology

Clone Names

  • MGC3180

Gene Ontology Provided by GOA

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

General protein information

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Preferred Names
sodium channel modifier 1

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_001204856.2 → NP_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
    UniProtKB/Swiss-Prot
    Q9BWG6
    Related
    ENSP00000357898.1, ENST00000368902.1
    Conserved Domains (2) summary
    pfam15803
    Location:9 → 35
    zf-SCNM1; Zinc-finger of sodium channel modifier 1
    pfam15805
    Location:148 → 193
    SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1

  2. NM_024041.4 → NP_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
    B4DWR1, Q5JR74, Q9BWG6
    Related
    ENSP00000357901.4, ENST00000368905.9
    Conserved Domains (2) summary
    pfam15803
    Location:44 → 70
    zf-SCNM1; Zinc-finger of sodium channel modifier 1
    pfam15805
    Location:183 → 228
    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: 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_000001.11 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    150289872..150294025
    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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BWG6.1 GenPept UniProtKB/Swiss-Prot:Q9BWG6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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