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    PNKD PNKD metallo-beta-lactamase domain containing [ Homo sapiens (human) ]

    Gene ID: 25953, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PNKDprovided by HGNC
    Official Full Name
    PNKD metallo-beta-lactamase domain containingprovided by HGNC
    Primary source
    HGNC:HGNC:9153
    See related
    Ensembl:ENSG00000127838 MIM:609023; AllianceGenome:HGNC:9153
    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
    R1; MR1; PDC; DYT8; FPD1; MR-1; BRP17; MR-1S; PKND1; PNKD1; FKSG19; TAHCCP2; KIPP1184
    Summary
    This gene is thought to play a role in the regulation of myofibrillogenesis. Mutations in this gene have been associated with the movement disorder paroxysmal non-kinesigenic dyskinesia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
    Expression
    Ubiquitous expression in prostate (RPKM 19.3), kidney (RPKM 16.6) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See PNKD in Genome Data Viewer
    Location:
    2q35
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218270519..218346793)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (218756220..218832888)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219135242..219211516)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219126185-219126990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17115 Neighboring gene G protein-coupled bile acid receptor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219133153-219134038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17118 Neighboring gene angio associated migratory cell protein Neighboring gene transmembrane BAX inhibitor motif containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219150593-219151401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17119 Neighboring gene microRNA 6513 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:219154375-219154874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219155794-219156758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219156759-219157721 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:219157904-219158750 Neighboring gene uncharacterized LOC105373881 Neighboring gene uncharacterized LOC105373880 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:219187601-219188196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219191232-219191976 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219194397-219195223 Neighboring gene CATIP antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219208241-219208740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219213637-219214187 Neighboring gene microRNA 6810 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219221475-219221986 Neighboring gene ribosomal protein L19 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12315 Neighboring gene ciliogenesis associated TTC17 interacting protein Neighboring gene CATIP antisense RNA 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Myofibrillogenesis regulator 1 gene (MR-1) mutation in an Omani family with paroxysmal nonkinesigenic dyskinesia. Hempelmann A, et al. Neurosci Lett, 2006 Jul 10. PMID 16632198
    2. The PNKD gene is associated with Tourette Disorder or Tic disorder in a multiplex family. Sun N, et al. Mol Psychiatry, 2018 Jun. PMID 28894297, Free PMC Article
    3. [Expression of a novel biomarker, MR-1S, in ovarian carcinoma and its biological significance]. Lu RQ, et al. Zhonghua Zhong Liu Za Zhi, 2012 Mar. PMID 22780969
    4. Familial paroxysmal nonkinesigenic dyskinesia: clinical and genetic analysis of a Taiwanese family. Yeh TH, et al. J Neurol Sci, 2012 Dec 15. PMID 22967746
    5. Paroxysmal non-kinesigenic dyskinesia due to a PNKD recurrent mutation: report of two Southern European families. Pons R, et al. Eur J Paediatr Neurol, 2012 Jan. PMID 21962874

    See all (79) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Myofibrillogenesis Regulator-1 Regulates the Ubiquitin Lysosomal Pathway of Notch3 Intracellular Domain Through E3 Ubiquitin-Protein Ligase Itchy Homolog in the Metastasis of Non-Small Cell Lung Cancer.
      Title: Myofibrillogenesis Regulator-1 Regulates the Ubiquitin Lysosomal Pathway of Notch3 Intracellular Domain Through E3 Ubiquitin-Protein Ligase Itchy Homolog in the Metastasis of Non-Small Cell Lung Cancer.
    2. A rare heterozygous nonsense mutation (C to T transition) was identified in a Tourette Disorder multiplex family by whole exome sequencing. Tourette or Tic Disorder-affected family members shared a heterozygous nonsense mutation (chr2: 219204814 C/T), which is not present in the unaffected individuals and absent in the background sample
      Title: The PNKD gene is associated with Tourette Disorder or Tic disorder in a multiplex family.
    3. The short isoform of the myofibrillogenesis regulator 1 (MR-1S) as a new COX assembly factor, which works with the highly conserved PET100 and PET117 chaperones to assist COX biogenesis in higher eukaryotes.
      Title: MR-1S Interacts with PET100 and PET117 in Module-Based Assembly of Human Cytochrome c Oxidase.
    4. The combined analysis identified a new risk association for colorectal cancer (CRC) at 2q35 marked by rs992157 which is intronic to PNKD and TMBIM1.Intriguingly this susceptibility single-nucleotide polymorphism (SNP) is in strong linkage disequilibrium (r(2) = 0.90, D' = 0.96) with the previously discovered GWAS SNP rs2382817 for inflammatory bowel disease (IBD).
      Title: Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease.
    5. study highlights the frequency, novel mutations and clinical and molecular spectrum of PRRT2, SLC2A1 and PNKD mutations as well as the phenotype-genotype overlap among these paroxysmal movement disorders.
      Title: The clinical and genetic heterogeneity of paroxysmal dyskinesias.
    6. This study present the pedigree is the first PNKD family from Chinese Mainland, which is also the largest PNKD family among those reported across the globe. It included 5 generations and 26 patients.
      Title: A case of familial paroxysmal nonkinesigenic dyskinesia due to mutation of the PNKD gene in Chinese Mainland.
    7. MR-1 functions as a tumor promoter in MCF7 cells by activating the MEK/ERK signaling
      Title: Phosphorylation of myofibrillogenesis regulator-1 activates the MAPK signaling pathway and induces proliferation and migration in human breast cancer MCF7 cells.
    8. MR-1 overexpression was tightly associated with more aggressive tumor behavior and a poor prognosis in pancreatic ductal adenocarcinoma.
      Title: Clinicopathological and prognostic significance of myofibrillogenesis regulator-1 protein expression in pancreatic ductal adenocarcinoma.
    9. MR-1 was up-regulated in gastric cancer tissues. High expression of MR-1 in gastric cancer was significantly correlated with clinical stage. Postoperative survival of the MR-1 positive group tended to be poorer than that of the MR-1 negative group.
      Title: Myofibrillogenesis regulator-1 overexpression is associated with poor prognosis of gastric cancer patients.
    10. A Taiwanese family with paroxysmal nonkinesigenic dyskinesia has a heterozygous c.20 C>T (p.Ala7Val) mutation which was clearly segregated in the five affected patients.
      Title: Familial paroxysmal nonkinesigenic dyskinesia: clinical and genetic analysis of a Taiwanese family.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    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)

    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

    • KIAA1184, MGC31943, DKFZp564N1362

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables hydroxyacylglutathione hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of neurotransmitter secretion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neuromuscular process controlling posture IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of dopamine metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of synaptic transmission, dopaminergic IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynaptic cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    probable hydrolase PNKD
    Names
    PNKD, MBL domain containing
    brain protein 17
    myofibrillogenesis regulator 1
    trans-activated by hepatitis C virus core protein 2
    NP_001070867.1
    NP_056303.3
    NP_072094.1
    XP_016859260.1
    XP_016859261.1
    XP_054197290.1
    XP_054197291.1

    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_017060.1 RefSeqGene

      Range
      5128..81402
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001077399.3 → NP_001070867.1  probable hydrolase PNKD isoform 3 precursor

      See identical proteins and their annotated locations for NP_001070867.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3), alternately referred to as the short form (MR-1S), differs in the 3' UTR and has multiple coding region differences, compared to variant 1. This results in a frameshift in isoform 3, which has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AF318057, BQ028777
      Consensus CDS
      CCDS42816.1
      UniProtKB/Swiss-Prot
      Q8N490
      Related
      ENSP00000248451.3, ENST00000248451.7
      Conserved Domains (1) summary
      pfam15932
      Location:71 → 121
      DUF4748; Domain of unknown function (DUF4748)

    2. NM_015488.5 → NP_056303.3  probable hydrolase PNKD isoform 1 precursor

      See identical proteins and their annotated locations for NP_056303.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), alternately referred to as the long form (MR-1L), represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB033010, AF318057, BC002937, BC036457
      Consensus CDS
      CCDS2411.1
      UniProtKB/Swiss-Prot
      A8K1F2, Q8N490, Q96A48, Q9BU26, Q9NSX4, Q9ULN6, Q9Y4T1
      UniProtKB/TrEMBL
      A0A8J8ZTU4
      Related
      ENSP00000273077.4, ENST00000273077.9
      Conserved Domains (1) summary
      TIGR03413
      Location:121 → 380
      GSH_gloB; hydroxyacylglutathione hydrolase

    3. NM_022572.4 → NP_072094.1  probable hydrolase PNKD isoform 2

      See identical proteins and their annotated locations for NP_072094.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), alternately referred to as the medium form (MR-1M), differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC021016, BC002937, BC036457, BU553179
      Consensus CDS
      CCDS2413.1
      UniProtKB/Swiss-Prot
      Q8N490
      Related
      ENSP00000258362.3, ENST00000258362.7
      Conserved Domains (1) summary
      TIGR03413
      Location:97 → 356
      GSH_gloB; hydroxyacylglutathione hydrolase

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      218270519..218346793
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017003771.2 → XP_016859260.1  probable hydrolase PNKD isoform X1

      UniProtKB/TrEMBL
      A0A8I5QKK6
      Related
      ENSP00000508635.1, ENST00000688179.1

    2. XM_017003772.2 → XP_016859261.1  probable hydrolase PNKD isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      218756220..218832888
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341315.1 → XP_054197290.1  probable hydrolase PNKD isoform X1

      UniProtKB/TrEMBL
      A0A8I5QKK6

    2. XM_054341316.1 → XP_054197291.1  probable hydrolase PNKD isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N490.2 GenPept UniProtKB/Swiss-Prot:Q8N490

    Gene LinkOut

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

    Chemical Information
    Medical
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