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    SEPHS1 selenophosphate synthetase 1 [ Homo sapiens (human) ]

    Gene ID: 22929, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SEPHS1provided by HGNC
    Official Full Name
    selenophosphate synthetase 1provided by HGNC
    Primary source
    HGNC:HGNC:19685
    See related
    Ensembl:ENSG00000086475 MIM:600902; AllianceGenome:HGNC:19685
    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
    SPS; SELD; SPS1
    Summary
    This gene encodes an enzyme that synthesizes selenophosphate from selenide and ATP. Selenophosphate is the selenium donor used to synthesize selenocysteine, which is co-translationally incorporated into selenoproteins at in-frame UGA codons. [provided by RefSeq, Sep 2010]
    Expression
    Ubiquitous expression in thyroid (RPKM 16.5), kidney (RPKM 11.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SEPHS1 in Genome Data Viewer
    Location:
    10p13
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (13317428..13348293, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (13330509..13361341, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (13359428..13390293, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3051 Neighboring gene uncharacterized LOC124902377 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13343766-13344266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3053 Neighboring gene RBIS pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13371420-13371920 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13371921-13372421 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13376783-13377284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13377285-13377784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:13383617-13384469 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2154 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13390478-13391268 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13391269-13392060 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:13397412-13397565 Neighboring gene uncharacterized LOC105376419 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:13437106-13438069 Neighboring gene Sharpr-MPRA regulatory region 1825 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13452136-13452642 Neighboring gene uncharacterized LOC105376420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3054

    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. De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features. Mullegama SV, et al. Am J Hum Genet, 2024 Apr 4. PMID 38531365, Free PMC Article
    2. Cloning and functional characterization of human selenophosphate synthetase, an essential component of selenoprotein synthesis. Low SC, et al. J Biol Chem, 1995 Sep 15. PMID 7665581
    3. The role of selenium-mediated redox signaling by selenophosphate synthetase 1 (SEPHS1) in hESCs. Lee MO, et al. Biochem Biophys Res Commun, 2019 Dec 3. PMID 31607477
    4. Human selenophosphate synthetase 1 has five splice variants with unique interactions, subcellular localizations and expression patterns. Kim JY, et al. Biochem Biophys Res Commun, 2010 Jun 18. PMID 20471958, Free PMC Article
    5. Selenium, selenoprotein genes and Crohn's disease in a case-control population from Auckland, New Zealand. Gentschew L, et al. Nutrients, 2012 Sep. PMID 23112913, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features.
      Title: De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features.
    2. Selenophosphate synthetase 1 deficiency exacerbates osteoarthritis by dysregulating redox homeostasis.
      Title: Selenophosphate synthetase 1 deficiency exacerbates osteoarthritis by dysregulating redox homeostasis.
    3. SEPHS1 expression is high in undifferentiated embryonic stem cells.SEPHS1 expression is required to obtain pluripotency.SEPHS1 plays a role in the embryonic stem cell survival via reactive oxygen species signaling and apoptosis.
      Title: The role of selenium-mediated redox signaling by selenophosphate synthetase 1 (SEPHS1) in hESCs.
    4. Data confirm interactions among components of the early steps of the selenocysteine biosynthesis pathway (SEPSECS, SECP43, SEPHS1, and SEPHS2); SECP43, which interacts with SEPSECS and SEPHS1, is a globular protein that forms oligomers in vivo.
      Title: Analysis of Novel Interactions between Components of the Selenocysteine Biosynthesis Pathway, SEPHS1, SEPHS2, SEPSECS, and SECp43.
    5. Three SNPs in SEPSECS and SEPHS1 were found to significantly interact with serum selenium level and Crohn's Disease.
      Title: Selenium, selenoprotein genes and Crohn's disease in a case-control population from Auckland, New Zealand.
    6. Five alternative splice variants of human SPS1 (major type, DeltaE2, DeltaE8, +E9, +E9a) were identified wherein +E9 and +E9a make the same protein.
      Title: Human selenophosphate synthetase 1 has five splice variants with unique interactions, subcellular localizations and expression patterns.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
    8. the Sps1-encoded enzyme depends on a selenium salvage system that recycles l-selenocysteine, whereas the Sps2 enzyme can function with a selenite assimilation system
      Title: Selenophosphate synthetase genes from lung adenocarcinoma cells: Sps1 for recycling L-selenocysteine and Sps2 for selenite assimilation.
    9. Sps1 affect cell viability upon ionizing radiation via modulation of p53 activity. Sps1 and its product selenophosphate might be involved in cancer prevention in a p53-dependent manner and could be applied to development of a novel cancer therapy.
      Title: p53-Mediated enhancement of radiosensitivity by selenophosphate synthetase 1 overexpression.
    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

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC4980

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTP binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables identical protein 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 
    enables protein heterodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables selenide, water dikinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in phosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein modification process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in selenocysteine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    selenide, water dikinase 1
    Names
    selenium donor protein 1
    selenophosphate synthase 1
    selenophosphate synthetase 1 +E9
    selenophosphate synthetase 1 +E9a
    selenophosphate synthetase 1 delta E2
    selenophosphate synthetase 1 delta E8
    selenophosphate synthetase 1 major
    NP_001182531.1
    NP_001182533.1
    NP_001362698.1
    NP_036379.2
    XP_047280795.1
    XP_047280796.1
    XP_047280797.1
    XP_054221208.1
    XP_054221209.1
    XP_054221210.1

    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_001195602.2 → NP_001182531.1  selenide, water dikinase 1 isoform 2

      See identical proteins and their annotated locations for NP_001182531.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' region and uses a downstream start codon, compared to variant 1. Isoform 2 (also called Delta E2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK301568, AL138764, BC064610, CT000832, GU954546
      Consensus CDS
      CCDS55702.1
      UniProtKB/TrEMBL
      B4DLS1
      Related
      ENSP00000441119.2, ENST00000545675.5
      Conserved Domains (1) summary
      cd02195
      Location:1 → 290
      SelD; Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The ...

    2. NM_001195604.2 → NP_001182533.1  selenide, water dikinase 1 isoform 3

      See identical proteins and their annotated locations for NP_001182533.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region, compared to variant 1. Isoform 3 (also called Delta E8) is shorter, compared to isoform 1.
      Source sequence(s)
      AK301568, AL138764, BC064610, CT000832, GU954547
      Consensus CDS
      CCDS55703.1
      UniProtKB/Swiss-Prot
      P49903
      Related
      ENSP00000367877.3, ENST00000378614.8
      Conserved Domains (1) summary
      cd02195
      Location:20 → 286
      SelD; Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The ...

    3. NM_001375769.1 → NP_001362698.1  selenide, water dikinase 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL138764, AL355870
      UniProtKB/TrEMBL
      B4DLS1
      Conserved Domains (1) summary
      TIGR00476
      Location:19 → 331
      selD; selenium donor protein

    4. NM_012247.5 → NP_036379.2  selenide, water dikinase 1 isoform 1

      See identical proteins and their annotated locations for NP_036379.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK301568, AL138764, BC064610, CT000832, GU954545
      Consensus CDS
      CCDS7098.1
      UniProtKB/Swiss-Prot
      B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4
      UniProtKB/TrEMBL
      B4DLS1
      Related
      ENSP00000367893.3, ENST00000327347.10
      Conserved Domains (1) summary
      TIGR00476
      Location:19 → 333
      selD; selenium donor protein

    RNA

    1. NR_164738.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL138764, AL355870

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      13317428..13348293 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424841.1 → XP_047280797.1  selenide, water dikinase 1 isoform X3

    2. XM_047424840.1 → XP_047280796.1  selenide, water dikinase 1 isoform X2

    3. XM_047424839.1 → XP_047280795.1  selenide, water dikinase 1 isoform X1

      UniProtKB/Swiss-Prot
      B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      13330509..13361341 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365235.1 → XP_054221210.1  selenide, water dikinase 1 isoform X3

    2. XM_054365233.1 → XP_054221208.1  selenide, water dikinase 1 isoform X1

      UniProtKB/Swiss-Prot
      B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4

    3. XM_054365234.1 → XP_054221209.1  selenide, water dikinase 1 isoform X2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001375770.1: Suppressed sequence

      Description
      NM_001375770.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P49903.2 GenPept UniProtKB/Swiss-Prot:P49903

    Gene LinkOut

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

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