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    PYROXD1 pyridine nucleotide-disulphide oxidoreductase domain 1 [ Homo sapiens (human) ]

    Gene ID: 79912, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PYROXD1provided by HGNC
    Official Full Name
    pyridine nucleotide-disulphide oxidoreductase domain 1provided by HGNC
    Primary source
    HGNC:HGNC:26162
    See related
    Ensembl:ENSG00000121350 MIM:617220; AllianceGenome:HGNC:26162
    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
    MFM8
    Summary
    This gene encodes a nuclear-cytoplasmic pyridine nucleotide-disulphide reductase (PNDR). PNDRs are flavoproteins that catalyze the pyridine nucleotide-dependent reduction of thiol residues in other proteins. The encoded protein belongs to the class I pyridine nucleotide-disulphide oxidoreductase family but lacks the C-terminal dimerization domain found in other family members and instead has a C-terminal nitrile reductase domain. It localizes to the nucleus and to striated sarcomeric compartments. Naturally occurring mutations in this gene cause early-onset myopathy with internalized nuclei and myofibrillar disorganization. A pseudogene of this gene has been defined on chromosome 11. [provided by RefSeq, Apr 2017]
    Expression
    Ubiquitous expression in thyroid (RPKM 12.4), lymph node (RPKM 11.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12p12.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (21437655..21471250)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (21316354..21349929)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (21590589..21624184)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene solute carrier organic anion transporter family member 1B1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:21386467-21387666 Neighboring gene uncharacterized LOC124902895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:21402494-21402994 Neighboring gene solute carrier organic anion transporter family member 1A2 Neighboring gene NANOG hESC enhancer GRCh37_chr12:21477387-21477904 Neighboring gene NANOG hESC enhancer GRCh37_chr12:21491840-21492346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:21546997-21547930 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:21547931-21548862 Neighboring gene islet amyloid polypeptide Neighboring gene NANOG hESC enhancer GRCh37_chr12:21569666-21570167 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:21572391-21572952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6086 Neighboring gene elongin C pseudogene 31 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6090 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:21654373-21655080 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:21655081-21655788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6092 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:21663989-21664186 Neighboring gene RecQ like helicase Neighboring gene golgi transport 1B Neighboring gene spexin hormone Neighboring gene glycogen synthase 2

    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
    • 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. Connective tissue presentation in two families expands the phenotypic spectrum of PYROXD1 disorders. Evesson FJ, et al. Hum Mol Genet, 2023 Jun 5. PMID 36920481, Free PMC Article
    2. Clinical and genetic characterization of PYROXD1-related myopathy patients from Turkey. Daimagüler HS, et al. Am J Med Genet A, 2021 Jun. PMID 33694278
    3. Myopathy associated with homozygous PYROXD1 pathogenic variants detected by genome sequencing. Woods JD, et al. Neuropathology, 2020 Jun. PMID 32037607, Free PMC Article
    4. A siRNA-based method for efficient silencing of PYROXD1 gene expression in the colon cancer cell line HCT116. Shabani S, et al. J Cell Biochem, 2019 Dec. PMID 31502705
    5. Recessive PYROXD1 mutations cause adult-onset limb-girdle-type muscular dystrophy. Sainio MT, et al. J Neurol, 2019 Feb. PMID 30515627, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Connective tissue presentation in two families expands the phenotypic spectrum of PYROXD1 disorders.
      Title: Connective tissue presentation in two families expands the phenotypic spectrum of PYROXD1 disorders.
    2. Clinical and genetic characterization of PYROXD1-related myopathy patients from Turkey.
      Title: Clinical and genetic characterization of PYROXD1-related myopathy patients from Turkey.
    3. The oxidoreductase PYROXD1 uses NAD(P)(+) as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response.
      Title: The oxidoreductase PYROXD1 uses NAD(P)(+) as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response.
    4. Myopathy associated with homozygous PYROXD1 pathogenic variants detected by genome sequencing.
      Title: Myopathy associated with homozygous PYROXD1 pathogenic variants detected by genome sequencing.
    5. A siRNA-based method for efficient silencing of PYROXD1 gene expression in the colon cancer cell line HCT116.
      Title: A siRNA-based method for efficient silencing of PYROXD1 gene expression in the colon cancer cell line HCT116.
    6. Pyroxd1 pathogenic mutations in the limb-girdle muscular dystrophy patients from Saudi Arabia and Sudan.
      Title: Impact of PYROXD1 deficiency on cellular respiration and correlations with genetic analyses of limb-girdle muscular dystrophy in Saudi Arabia and Sudan.
    7. PYROXD1 variants can cause an adult-onset slowly progressive limb-girdle muscular dystrophy-type phenotype.
      Title: Recessive PYROXD1 mutations cause adult-onset limb-girdle-type muscular dystrophy.
    8. We characterize variants in the oxidoreductase PYROXD1 as a cause of early-onset myopathy with distinctive histopathology and introduce altered redox regulation as a primary cause of congenital muscle disease.
      Title: Variants in the Oxidoreductase PYROXD1 Cause Early-Onset Myopathy with Internalized Nuclei and Myofibrillar Disorganization.
    9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    Myofibrillar myopathy 8
    MedGen: C4310645 OMIM: 617258 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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22028

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables flavin adenine dinucleotide 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 cellular response to oxidative stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in sarcomere IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1
    NP_001337841.1
    NP_001337842.1
    NP_079130.2
    XP_006719216.1
    XP_016875465.1
    XP_047285510.1
    XP_054229225.1
    XP_054229226.1

    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

    1. NG_053196.1 RefSeqGene

      Range
      5052..38647
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350912.2 → NP_001337841.1  pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC006559, AK125461
      Consensus CDS
      CCDS86287.1
      Related
      ENSP00000438505.1, ENST00000538582.5
      Conserved Domains (2) summary
      cl26176
      Location:229 → 423
      NirB; NAD(P)H-nitrite reductase, large subunit [Energy production and conversion]
      cl26177
      Location:12 → 312
      Pyr_redox_2; Pyridine nucleotide-disulphide oxidoreductase

    2. NM_001350913.2 → NP_001337842.1  pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC006559
      Conserved Domains (1) summary
      cl26176
      Location:51 → 235
      NirB; NAD(P)H-nitrite reductase, large subunit [Energy production and conversion]

    3. NM_024854.5 → NP_079130.2  pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_079130.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC006559, AL832441, BM980368, DB041552
      Consensus CDS
      CCDS31755.1
      UniProtKB/Swiss-Prot
      A6NKI6, B3KWN8, Q8WU10, Q9H6P1
      Related
      ENSP00000240651.9, ENST00000240651.14
      Conserved Domains (2) summary
      cl26176
      Location:300 → 494
      NirB; NAD(P)H-nitrite reductase, large subunit [Energy production and conversion]
      cl26177
      Location:24 → 383
      Pyr_redox_2; Pyridine nucleotide-disulphide oxidoreductase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      21437655..21471250
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429554.1 → XP_047285510.1  pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 isoform X1

    2. XM_006719153.4 → XP_006719216.1  pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 isoform X2

      Conserved Domains (1) summary
      cl21454
      Location:95 → 166
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    3. XM_017019976.3 → XP_016875465.1  pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      21316354..21349929
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373250.1 → XP_054229225.1  pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 isoform X1

    2. XM_054373251.1 → XP_054229226.1  pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WU10.1 GenPept UniProtKB/Swiss-Prot:Q8WU10

    Gene LinkOut

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

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