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

Summary

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]
Annotation information: Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
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

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_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Scnm1 is the first example of a modifier gene which influences disease severity through a trans-effect on splicing of the disease gene transcript.
Title: Evidence for a direct role of the disease modifier SCNM1 in splicing.
Variation between inbred strains of mice can be used to identify modifier genes affecting the susceptibility to inherited disease. The severity of the neurological disorder is determined by the modifier locus Scnm1.
Title: High-resolution mapping of the sodium channel modifier Scnm1 on mouse chromosome 3 and identification of a 1.3-kb recombination hot spot.

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Variation

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Alleles

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

Chemically induced (ENU) (2) 1 citation
Spontaneous (2) 1 citation
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3Umi10 (e-PCR), detects polymorphism
- UniSTS:281088

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

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)

NM_001409852.1 → NP_001396781.1 sodium channel modifier 1

Status: VALIDATED

Source sequence(s)

BC028867

UniProtKB/Swiss-Prot

Q8K136, Q9CXV5

RNA

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

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

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.
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.
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.
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.
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.
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.
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.
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.