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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
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Genomic context

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See PYROXD1 in Genome Data Viewer
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
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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

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