SELENON selenoprotein N [Homo sapiens (human)] - Gene

Summary

Official Symbol: SELENONprovided by HGNC
Official Full Name: selenoprotein Nprovided by HGNC
Primary source: HGNC:HGNC:15999
See related: Ensembl:ENSG00000162430 MIM:606210; AllianceGenome:HGNC:15999
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RSS; CFTD; SELN; CMYO3; CMYP3; MDRS1; RSMD1; SEPN1
Summary: This gene encodes a glycoprotein that is localized in the endoplasmic reticulum. It plays an important role in cell protection against oxidative stress, and in the regulation of redox-related calcium homeostasis. Mutations in this gene are associated with early onset muscle disorders, referred to as SEPN1-related myopathy. SEPN1-related myopathy consists of 4 autosomal recessive disorders, originally thought to be separate entities: rigid spine muscular dystrophy (RSMD1), the classical form of multiminicore disease, desmin related myopathy with Mallory-body like inclusions, and congenital fiber-type disproportion (CFTD). This protein is a selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. A second stop-codon redefinition element (SRE) adjacent to the UGA codon has been identified in this gene (PMID:15791204). SRE is a phylogenetically conserved stem-loop structure that stimulates readthrough at the UGA codon, and augments the Sec insertion efficiency by SECIS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2016]
Expression: Ubiquitous expression in prostate (RPKM 28.6), lung (RPKM 27.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.11

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (25800193..25818221)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (25637681..25655660)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (26126684..26144712)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Cardiac Involvement in LAMA2-Related Muscular Dystrophy and SELENON-Related Congenital Myopathy: A Case Series.
Title: Cardiac Involvement in LAMA2-Related Muscular Dystrophy and SELENON-Related Congenital Myopathy: A Case Series.
Defective endoplasmic reticulum-mitochondria contacts and bioenergetics in SEPN1-related myopathy.
Title: Defective endoplasmic reticulum-mitochondria contacts and bioenergetics in SEPN1-related myopathy.
Selenoprotein N-related myopathy: a retrospective natural history study to guide clinical trials.
Title: Selenoprotein N-related myopathy: a retrospective natural history study to guide clinical trials.
[Selenoprotein-related myopathy in a patient with old-age-onset type 2 respiratory failure: a case report].
Title: [Selenoprotein-related myopathy in a patient with old-age-onset type 2 respiratory failure: a case report].
The first report of two homozygous sequence variants in FKRP and SELENON genes associated with syndromic congenital muscular dystrophy in Iran: Further expansion of the clinical phenotypes.
Title: The first report of two homozygous sequence variants in FKRP and SELENON genes associated with syndromic congenital muscular dystrophy in Iran: Further expansion of the clinical phenotypes.
The clinical, histologic, and genotypic spectrum of SEPN1-related myopathy: A case series.
Title: The clinical, histologic, and genotypic spectrum of SEPN1-related myopathy: A case series.
Selenoprotein N is an endoplasmic reticulum calcium sensor that links luminal calcium levels to a redox activity.
Title: Selenoprotein N is an endoplasmic reticulum calcium sensor that links luminal calcium levels to a redox activity.
significantly down-regulated in mesangial cells exposed to high glucose or TGF-beta1
Title: High glucose and TGF-β1 reduce expression of endoplasmic reticulum-resident selenoprotein S and selenoprotein N in human mesangial cells.
Case Report: rigid spine muscular dystrophy 1 in a compound heterozygote with two novel mutations in SEPN1 gene; a novel missense mutation (c.1384T>C; p.Sec462Arg) and a novel nonsense mutation (c.1525C>T; p.Gln509Ter), inherited from his father and mother respectively.
Title: Targeted next generation sequencing identifies two novel mutations in SEPN1 in rigid spine muscular dystrophy 1.
We report two previously undescribed mutations in SEPN1. Our study adds two novel homozygous mutations to the number of reported pathogenic SEPN1 variants.
Title: SEPN1-related myopathy in three patients: novel mutations and diagnostic clues.

Submit: New GeneRIF Correction See all GeneRIFs (26)

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
Congenital myopathy with fiber type disproportion MedGen: C0546264 GeneReviews: Not available	Compare labs
Eichsfeld type congenital muscular dystrophy MedGen: C0410180 OMIM: 602771 GeneReviews: Not available	Compare labs
Multiminicore myopathy MedGen: C0270962 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

L18426 (e-PCR)
- UniSTS:34648

SHGC-74434 (e-PCR)
- UniSTS:23641

A010A48 (e-PCR)
- UniSTS:46464

G33062 (e-PCR)
- UniSTS:117638

D1S2885 (e-PCR), detects polymorphism
- UniSTS:43203

D5S1597E (e-PCR)
- UniSTS:151019

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in ATP metabolic process	IEA Inferred from Electronic Annotation more info
involved_in L-ascorbic acid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in L-ascorbic acid transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to caffeine	IEA Inferred from Electronic Annotation more info
involved_in cellular response to oxidative stress	IEA Inferred from Electronic Annotation more info
involved_in collagen fibril organization	IEA Inferred from Electronic Annotation more info
involved_in energy reserve metabolic process	IEA Inferred from Electronic Annotation more info
involved_in lung alveolus development	IEA Inferred from Electronic Annotation more info
involved_in membrane biogenesis	IEA Inferred from Electronic Annotation more info
involved_in membrane organization	IEA Inferred from Electronic Annotation more info
involved_in membrane to membrane docking	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in mitochondrion organization	IEA Inferred from Electronic Annotation more info
involved_in mitochondrion-endoplasmic reticulum membrane tethering	IEA Inferred from Electronic Annotation more info
involved_in multicellular organismal response to stress	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of skeletal muscle cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in regulation of ryanodine-sensitive calcium-release channel activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in respiratory system process	IEA Inferred from Electronic Annotation more info
involved_in response to muscle activity involved in regulation of muscle adaptation	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle fiber development	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal muscle satellite cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration	IEA Inferred from Electronic Annotation more info
involved_in transforming growth factor beta receptor signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondria-associated endoplasmic reticulum membrane contact site	IEA Inferred from Electronic Annotation more info
located_in mitochondrial membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: selenoprotein N

Names: selenoprotein N, 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.

Genomic

NG_009930.1 RefSeqGene

Range

5018..23046

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_857

mRNA and Protein(s)

NM_020451.3 → NP_065184.2 selenoprotein N isoform 2

See identical proteins and their annotated locations for NP_065184.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an additional in-frame, Alu-derived coding exon in the 5' region compared to variant 1. The encoded isoform (2) is longer than isoform 1, containing two potential selenocysteine (Sec) residues. The first Sec found in the novel exon is not conserved, while the second Sec is highly conserved. Expression of isoform 2 was not detected in vivo or in transfection studies, leaving open the possibility that the UGA codon in the novel exon may be recognized as a stop codon, and not as a Sec codon (PMID:12700173).

Source sequence(s)

AA613025, AJ306399, BC021028, BQ217758

Consensus CDS

CCDS41282.1

UniProtKB/Swiss-Prot

A6NJG8, A8MQ64, Q6PI70, Q969F6, Q9NUI6, Q9NZV5

UniProtKB/TrEMBL

H9KV50

Related

ENSP00000355141.2, ENST00000361547.7
NM_206926.2 → NP_996809.1 selenoprotein N isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes the canonical isoform (1).

Source sequence(s)

AA613025, AJ306399, BC021028, BQ217758

Consensus CDS

CCDS41283.1

UniProtKB/TrEMBL

H9KV50

Related

ENSP00000363434.1, ENST00000374315.1