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Aliases for PYROXD1 Gene

Aliases for PYROXD1 Gene

  • Pyridine Nucleotide-Disulphide Oxidoreductase Domain 1 2 3 5
  • Pyridine Nucleotide-Disulfide Oxidoreductase Domain-Containing Protein 1 3
  • EC 1.8.1.- 4
  • MFM8 3

External Ids for PYROXD1 Gene

Previous GeneCards Identifiers for PYROXD1 Gene

  • GC12P021482
  • GC12P021590

Summaries for PYROXD1 Gene

Entrez Gene Summary for PYROXD1 Gene

  • 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]

GeneCards Summary for PYROXD1 Gene

PYROXD1 (Pyridine Nucleotide-Disulphide Oxidoreductase Domain 1) is a Protein Coding gene. Diseases associated with PYROXD1 include Myopathy, Myofibrillar, 8 and Myofibrillar Myopathy. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity.

UniProtKB/Swiss-Prot for PYROXD1 Gene

  • Involved in cellular response to oxidative stress.

Additional gene information for PYROXD1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PYROXD1 Gene

Genomics for PYROXD1 Gene

GeneHancer (GH) Regulatory Elements for PYROXD1 Gene

Promoters and enhancers for PYROXD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J021436 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 715.4 +0.5 546 2.4 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 CBX5 E2F8 PYROXD1 ELOCP31
GH12J021452 Enhancer 0.5 ENCODE 55.6 +15.7 15706 1.6 IKZF1 ATF7 IKZF2 EZH2 PYROXD1 PIR48184 RECQL
GH12J021500 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.2 +64.1 64100 2.7 PKNOX1 SMAD1 ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B E2F8 ZNF207 RECQL GOLT1B PYROXD1
GH12J021455 Enhancer 0.4 ENCODE 55.2 +19.6 19616 3 JUND FOS PYROXD1 SPX RECQL PIR48184
GH12J021773 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 9.8 +337.5 337455 3.7 PKNOX1 FOXA2 ZNF2 RAD21 YY1 ZNF335 GLIS2 SCRT2 ZNF202 ZNF362 KCNJ8 PYROXD1 GC12M021765 LOC105369689
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PYROXD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PYROXD1 gene promoter:
  • Zic3
  • FOXJ2 (long isoform)
  • FOXJ2
  • Arnt
  • Pax-2a
  • Pax-2
  • NRF-2
  • Max
  • c-Myc
  • Pax-4a

Genomic Locations for PYROXD1 Gene

Genomic Locations for PYROXD1 Gene
chr12:21,437,604-21,471,252
(GRCh38/hg38)
Size:
33,649 bases
Orientation:
Plus strand
chr12:21,590,538-21,624,184
(GRCh37/hg19)
Size:
33,647 bases
Orientation:
Plus strand

Genomic View for PYROXD1 Gene

Genes around PYROXD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PYROXD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PYROXD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PYROXD1 Gene

Proteins for PYROXD1 Gene

  • Protein details for PYROXD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WU10-PYRD1_HUMAN
    Recommended name:
    Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1
    Protein Accession:
    Q8WU10
    Secondary Accessions:
    • A6NKI6
    • B3KWN8
    • Q9H6P1

    Protein attributes for PYROXD1 Gene

    Size:
    500 amino acids
    Molecular mass:
    55793 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB15214.1; Type=Frameshift; Positions=445; Evidence={ECO:0000305};

    Alternative splice isoforms for PYROXD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PYROXD1 Gene

Post-translational modifications for PYROXD1 Gene

  • Ubiquitination at posLast=142142
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PYROXD1 Gene

Domains & Families for PYROXD1 Gene

Gene Families for PYROXD1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for PYROXD1 Gene

Graphical View of Domain Structure for InterPro Entry

Q8WU10

UniProtKB/Swiss-Prot:

PYRD1_HUMAN :
  • Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. PYROXD1 subfamily.
Family:
  • Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. PYROXD1 subfamily.
genes like me logo Genes that share domains with PYROXD1: view

Function for PYROXD1 Gene

Molecular function for PYROXD1 Gene

UniProtKB/Swiss-Prot Function:
Involved in cellular response to oxidative stress.

Enzyme Numbers (IUBMB) for PYROXD1 Gene

Gene Ontology (GO) - Molecular Function for PYROXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with PYROXD1: view
genes like me logo Genes that share phenotypes with PYROXD1: view

Human Phenotype Ontology for PYROXD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PYROXD1 Gene

MGI Knock Outs for PYROXD1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PYROXD1

No data available for Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for PYROXD1 Gene

Localization for PYROXD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PYROXD1 Gene

Nucleus. Cytoplasm, myofibril, sarcomere.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PYROXD1 gene
Compartment Confidence
nucleus 5
cytosol 3
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PYROXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 27745833
GO:0005737 cytoplasm IEA --
GO:0030017 sarcomere IEA,IDA 27745833
genes like me logo Genes that share ontologies with PYROXD1: view

Pathways & Interactions for PYROXD1 Gene

SuperPathways for PYROXD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PYROXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034599 cellular response to oxidative stress IMP 27745833
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with PYROXD1: view

No data available for Pathways by source and SIGNOR curated interactions for PYROXD1 Gene

Drugs & Compounds for PYROXD1 Gene

(1) Drugs for PYROXD1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma 0

(1) Additional Compounds for PYROXD1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid
  • 2-KDN
  • 2-keto-3-Deoxy-D-glycero-D-galacto-NONONate
  • 2-keto-3-Deoxy-D-glycero-D-galacto-NONONic acid
  • 2-oxo-3-Deoxy-D-glycero-galactononulosonate
  • 2-oxo-3-Deoxy-D-glycero-galactononulosonic acid
22594-61-2
genes like me logo Genes that share compounds with PYROXD1: view

Transcripts for PYROXD1 Gene

Unigene Clusters for PYROXD1 Gene

Pyridine nucleotide-disulphide oxidoreductase domain 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PYROXD1

Alternative Splicing Database (ASD) splice patterns (SP) for PYROXD1 Gene

No ASD Table

Relevant External Links for PYROXD1 Gene

GeneLoc Exon Structure for
PYROXD1
ECgene alternative splicing isoforms for
PYROXD1

Expression for PYROXD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PYROXD1 Gene

Protein differential expression in normal tissues from HIPED for PYROXD1 Gene

This gene is overexpressed in Retina (23.3), Testis (7.6), and Islet of Langerhans (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PYROXD1 Gene



NURSA nuclear receptor signaling pathways regulating expression of PYROXD1 Gene:

PYROXD1

SOURCE GeneReport for Unigene cluster for PYROXD1 Gene:

Hs.709545

Evidence on tissue expression from TISSUES for PYROXD1 Gene

  • Kidney(4.3)
  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with PYROXD1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PYROXD1 Gene

Orthologs for PYROXD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PYROXD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PYROXD1 34 33
  • 99.4 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PYROXD1 34 33
  • 89.53 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PYROXD1 34 33
  • 89.41 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pyroxd1 33
  • 83.43 (n)
mouse
(Mus musculus)
Mammalia Pyroxd1 16 34 33
  • 83.17 (n)
oppossum
(Monodelphis domestica)
Mammalia PYROXD1 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 77 (a)
OneToMany
-- 34
  • 72 (a)
OneToMany
-- 34
  • 58 (a)
OneToMany
chicken
(Gallus gallus)
Aves PYROXD1 34 33
  • 75.96 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PYROXD1 34
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pyroxd1 33
  • 63.08 (n)
Str.19896 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.16405 33
zebrafish
(Danio rerio)
Actinopterygii ryroxd1 34 33
  • 65.2 (n)
OneToOne
zgc73254 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008042 33
  • 54.26 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG10721 34 33
  • 52.96 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C26D10.3 34 33
  • 45.33 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea Cin.6258 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6258 33
Species where no ortholog for PYROXD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PYROXD1 Gene

ENSEMBL:
Gene Tree for PYROXD1 (if available)
TreeFam:
Gene Tree for PYROXD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PYROXD1: view image

Paralogs for PYROXD1 Gene

Pseudogenes.org Pseudogenes for PYROXD1 Gene

genes like me logo Genes that share paralogs with PYROXD1: view

No data available for Paralogs for PYROXD1 Gene

Variants for PYROXD1 Gene

Sequence variations from dbSNP and Humsavar for PYROXD1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1057518754 pathogenic, Myopathy, myofibrillar, 8 21,449,692(+) G/A genic_upstream_transcript_variant, splice_donor_variant
rs1057518755 pathogenic, Myopathy, myofibrillar, 8 21,467,524(+) CAAA/CAAACAAA coding_sequence_variant, frameshift, genic_downstream_transcript_variant, non_coding_transcript_variant
rs369083786 pathogenic, Myopathy, myofibrillar, 8 21,445,467(+) G/A genic_upstream_transcript_variant, splice_donor_variant
rs755208949 pathogenic, Myopathy, myofibrillar, 8, Myopathy, myofibrillar, 8 (MFM8) [MIM:617258] 21,462,862(+) G/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs781565158 pathogenic, Myopathy, myofibrillar, 8, Myopathy, myofibrillar, 8 (MFM8) [MIM:617258] 21,452,130(+) A/G coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PYROXD1 Gene

Variant ID Type Subtype PubMed ID
esv3628807 CNV gain 21293372
nsv1054220 CNV gain 25217958
nsv469163 CNV loss 19166990
nsv526789 CNV loss 19592680
nsv557741 CNV gain 21841781
nsv557742 CNV loss 21841781
nsv975459 CNV duplication 23825009
nsv976585 CNV duplication 23825009

Variation tolerance for PYROXD1 Gene

Residual Variation Intolerance Score: 50% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.19; 23.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PYROXD1 Gene

Human Gene Mutation Database (HGMD)
PYROXD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PYROXD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PYROXD1 Gene

Disorders for PYROXD1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PYROXD1 Gene - From: HGMD, OMIM, ClinVar, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
myopathy, myofibrillar, 8
  • mfm8
myofibrillar myopathy
  • myopathy, myofibrillar, desmin-related
myopathy
  • muscular diseases
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PYRD1_HUMAN
  • Myopathy, myofibrillar, 8 (MFM8) [MIM:617258]: A form of myofibrillar myopathy, a group of chronic neuromuscular disorders characterized at ultrastructural level by disintegration of the sarcomeric Z disk and myofibrils, and replacement of the normal myofibrillar markings by small dense granules, or larger hyaline masses, or amorphous material. MFM8 is an autosomal recessive form, clinically characterized by slowly progressive symmetrical weakness affecting both proximal and distal muscles, with normal to moderately elevated creatine kinase. Mild facial weakness, a high palate, nasal speech, and swallowing difficulties are typical features, mild restrictive lung disease is common, and late-onset cardiac involvement may be present. {ECO:0000269 PubMed:27745833}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PYROXD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PYROXD1: view

No data available for Genatlas for PYROXD1 Gene

Publications for PYROXD1 Gene

  1. Variants in the Oxidoreductase PYROXD1 Cause Early-Onset Myopathy with Internalized Nuclei and Myofibrillar Disorganization. (PMID: 27745833) O'Grady GL … Cooper ST (American journal of human genetics 2016) 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  5. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C … Emili A (Nature 2015) 3 58

Products for PYROXD1 Gene

Sources for PYROXD1 Gene

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