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    SMDT1 single-pass membrane protein with aspartate rich tail 1 [ Homo sapiens (human) ]

    Gene ID: 91689, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SMDT1provided by HGNC
    Official Full Name
    single-pass membrane protein with aspartate rich tail 1provided by HGNC
    Primary source
    HGNC:HGNC:25055
    See related
    Ensembl:ENSG00000183172 MIM:615588; AllianceGenome:HGNC:25055
    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
    DDDD; EMRE; C22orf32
    Summary
    This gene encodes a core regulatory component of a calcium channel in the mitochondrial inner membrane. [provided by RefSeq, Apr 2017]
    Expression
    Ubiquitous expression in ovary (RPKM 28.8), prostate (RPKM 18.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMDT1 in Genome Data Viewer
    Location:
    22q13.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42079700..42084284)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42559289..42563873)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42475704..42480288)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985551 Neighboring gene alpha-N-acetylgalactosaminidase Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:42462918-42464117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19153 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42469572-42470304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42470305-42471035 Neighboring gene Sharpr-MPRA regulatory region 6008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42473646-42474208 Neighboring gene small nucleolar RNA, C/D box 13 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 7943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42475449-42476221 Neighboring gene PH domain containing endocytic trafficking adaptor 2 Neighboring gene NADH:ubiquinone oxidoreductase subunit A6 Neighboring gene NDUFA6 divergent transcript Neighboring gene OLA1 pseudogene 1

    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. SMDT1 variants impair EMRE-mediated mitochondrial calcium uptake in patients with muscle involvement. Bulthuis EP, et al. Biochim Biophys Acta Mol Basis Dis, 2023 Dec. PMID 37454773
    2. EMRE Is a Matrix Ca(2+) Sensor that Governs Gatekeeping of the Mitochondrial Ca(2+) Uniporter. Vais H, et al. Cell Rep, 2016 Jan 26. PMID 26774479, Free PMC Article
    3. SMDT1-driven change in mitochondrial dynamics mediate cell apoptosis in PDAC. Xie KF, et al. Biochem Biophys Res Commun, 2019 Apr 2. PMID 30782485
    4. Structural Mechanism of EMRE-Dependent Gating of the Human Mitochondrial Calcium Uniporter. Wang Y, et al. Cell, 2019 May 16. PMID 31080062, Free PMC Article
    5. Variable Assembly of EMRE and MCU Creates Functional Channels with Distinct Gatekeeping Profiles. Payne R, et al. iScience, 2020 Apr 24. PMID 32315830, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMDT1 variants impair EMRE-mediated mitochondrial calcium uptake in patients with muscle involvement.
      Title: SMDT1 variants impair EMRE-mediated mitochondrial calcium uptake in patients with muscle involvement.
    2. Mechanisms of EMRE-Dependent MCU Opening in the Mitochondrial Calcium Uniporter Complex.
      Title: Mechanisms of EMRE-Dependent MCU Opening in the Mitochondrial Calcium Uniporter Complex.
    3. the human MCU-EMRE complex, which constitutes the minimal channel components among metazoans, provides a framework for future mechanistic studies on MCU.
      Title: Structural Mechanism of EMRE-Dependent Gating of the Human Mitochondrial Calcium Uniporter.
    4. SMDT1 overexpression induced mitochondrial mediated apoptosis.
      Title: SMDT1-driven change in mitochondrial dynamics mediate cell apoptosis in PDAC.
    5. Here, the authors determine the transmembrane orientation of EMRE, and show that its known MCU-activating function is mediated by the interaction of transmembrane helices from both proteins.
      Title: Dual functions of a small regulatory subunit in the mitochondrial calcium uniporter complex.
    6. Our experiments provide novel details about how MCU/EMRE is regulated by MICU1 and an original approach to investigate MCU/EMRE activation in intact cells.
      Title: Rearrangement of MICU1 multimers for activation of MCU is solely controlled by cytosolic Ca(2.).
    7. EMRE is essential for in vivo uniporter current and additionally bridges the calcium-sensing role of MICU1 and MICU2 with the calcium-conducting role of MCU.
      Title: EMRE is an essential component of the mitochondrial calcium uniporter complex.
    8. EMRE (C22orf32) is an integral mitochondrial inner membrane protein and component of the mitochondrial uniporter complex (uniplex). It is essential for uniporter channel activity. In its absence, the pore does not interact with its regulators MICU1/2.
      Title: EMRE is an essential component of the mitochondrial calcium uniporter complex.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    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
    Biological insights from 108 schizophrenia-associated genetic loci.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables channel activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-macromolecule adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in calcium import into the mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in calcium import into the mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in calcium import into the mitochondrion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in calcium import into the mitochondrion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cellular response to calcium ion starvation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial calcium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial calcium ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial calcium ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrial calcium ion homeostasis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in mitochondrial calcium ion transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial inner membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    part_of uniplex complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of uniplex complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of uniplex complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of uniplex complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of uniplex complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    essential MCU regulator, mitochondrial
    Names
    UPF0466 protein C22orf32, mitochondrial
    single-pass membrane protein with aspartate-rich tail 1, mitochondrial

    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_033318.5 → NP_201575.3  essential MCU regulator, mitochondrial precursor

      See identical proteins and their annotated locations for NP_201575.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the protein.
      Source sequence(s)
      AL021878, BC024237, BI754670, Z82192
      Consensus CDS
      CCDS14031.1
      UniProtKB/Swiss-Prot
      B2R5D1, Q8TAB9, Q9H4I9
      Related
      ENSP00000327467.3, ENST00000331479.4
      Conserved Domains (1) summary
      pfam10161
      Location:36 → 101
      DDDD; Putative mitochondrial precursor protein

    RNA

    1. NR_146715.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' region and is represented as non-coding because use of the expected translational start codon would render the transcript a candidate for nonsense-mediated decay (NMD).
      Source sequence(s)
      AL021878, BC024237, BI754670

    2. NR_146717.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL021878, Z82192

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      42079700..42084284
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011530509.3 → XP_011528811.1  essential MCU regulator, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_011528811.1

      UniProtKB/Swiss-Prot
      B2R5D1, Q8TAB9, Q9H4I9
      Conserved Domains (1) summary
      pfam10161
      Location:36 → 101
      DDDD; Putative mitochondrial precursor protein

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315971.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      2045..6629
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329612.1 → XP_054185587.1  essential MCU regulator, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      B2R5D1, Q8TAB9, Q9H4I9

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NW_004504305.1 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      2045..6629
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330208.1 → XP_054186183.1  essential MCU regulator, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      B2R5D1, Q8TAB9, Q9H4I9

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_187682.1 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      2045..6629
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330450.1 → XP_054186425.1  essential MCU regulator, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      B2R5D1, Q8TAB9, Q9H4I9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      42559289..42563873
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326132.1 → XP_054182107.1  essential MCU regulator, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      B2R5D1, Q8TAB9, Q9H4I9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H4I9.1 GenPept UniProtKB/Swiss-Prot:Q9H4I9

    Gene LinkOut

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

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