Human Gene PNKD (ENST00000273077.9_6) from GENCODE V47lift37
  Description: PNKD metallo-beta-lactamase domain containing, transcript variant 1 (from RefSeq NM_015488.5)
Gencode Transcript: ENST00000273077.9_6
Gencode Gene: ENSG00000127838.15_9
Transcript (Including UTRs)
   Position: hg19 chr2:219,135,242-219,211,516 Size: 76,275 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr2:219,135,259-219,209,704 Size: 74,446 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:219,135,242-219,211,516)mRNA (may differ from genome)Protein (385 aa)
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PNKD_HUMAN
DESCRIPTION: RecName: Full=Probable hydrolase PNKD; EC=3.-.-.-; AltName: Full=Myofibrillogenesis regulator 1; Short=MR-1; AltName: Full=Paroxysmal nonkinesiogenic dyskinesia protein; AltName: Full=Trans-activated by hepatitis C virus core protein 2;
FUNCTION: Probable hydrolase that plays an aggravative role in the development of cardiac hypertrophy via activation of the NF-kappa- B signaling pathway (By similarity).
SUBUNIT: Isoform 2 interacts with the sarcomeric proteins, MRLC2, MYOM1 and ENO3.
SUBCELLULAR LOCATION: Isoform 1: Membrane; Peripheral membrane protein.
SUBCELLULAR LOCATION: Isoform 2: Cytoplasm. Nucleus.
SUBCELLULAR LOCATION: Isoform 3: Mitochondrion.
TISSUE SPECIFICITY: Isoform 1 is only expressed in the brain. Isoform 2 is ubiquitously detected with highest expression in skeletal muscle and detected in myocardial myofibrils. Variant Val-7 and Val-9 are detected in the brain only.
INDUCTION: By Hepatitis C virus core protein.
PTM: Isoform 2 is phosphorylated at Ser-121 upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in PNKD are the cause of dystonia type 8 (DYT8) [MIM:118800]. DYT8 is a paroxysmal non-kinesigenic dystonia/dyskinesia. Dystonia is defined by the presence of sustained involuntary muscle contractions, often leading to abnormal postures. DYT8 is characterized by attacks of involuntary movements brought on by stress, alcohol, fatigue or caffeine. The attacks generally last between a few seconds and four hours or longer. The attacks may begin in one limb and spread throughout the body, including the face.
SIMILARITY: Belongs to the metallo-beta-lactamase superfamily. Glyoxalase II family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PNKD";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PNKD
Diseases sorted by gene-association score: familial paroxysmal nonkinesigenic dyskinesia* (869), paroxysmal nonkinesigenic dyskinesia 1* (700), paroxysmal choreoathetosis* (400), multiple congenital anomalies-hypotonia-seizures syndrome 1 (12), hepatitis c virus (11), episodic kinesigenic dyskinesia 2 (10), dystonia, dopa-responsive, with or without hyperphenylalaninemia (9), hemidystonia (9), dyskinetic cerebral palsy (8), choreatic disease (8), dystonia-parkinsonism, x-linked (7), dystonia (4), benign epilepsy with centrotemporal spikes (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 44.53 RPKM in Liver
Total median expression: 717.00 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00170.000 Picture PostScript Text
3' UTR -636.501812-0.351 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001279 - Beta-lactamas-like
IPR017782 - Hydroxyacylglutathione_Hdrlase

Pfam Domains:
PF00753 - Metallo-beta-lactamase superfamily
PF16123 - Hydroxyacylglutathione hydrolase C-terminus

SCOP Domains:
56281 - Metallo-hydrolase/oxidoreductase

ModBase Predicted Comparative 3D Structure on Q8N490
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004416 hydroxyacylglutathione hydrolase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0019243 methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione
GO:0032225 regulation of synaptic transmission, dopaminergic
GO:0042053 regulation of dopamine metabolic process
GO:0046929 negative regulation of neurotransmitter secretion
GO:0050884 neuromuscular process controlling posture

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK289867 - Homo sapiens cDNA FLJ75909 complete cds, highly similar to Homo sapiens myofibrillogenesis regulator 1 (MR-1), transcript variant 1, mRNA.
BC036457 - Homo sapiens paroxysmal nonkinesigenic dyskinesia, mRNA (cDNA clone MGC:33461 IMAGE:4797574), complete cds.
AB384130 - Synthetic construct DNA, clone: pF1KSDA1184, Homo sapiens PNKD gene for myofibrillogenesis regulator 1 isoform 1, complete cds, without stop codon, in Flexi system.
KJ898577 - Synthetic construct Homo sapiens clone ccsbBroadEn_07971 PNKD gene, encodes complete protein.
KR709506 - Synthetic construct Homo sapiens clone CCSBHm_00002858 PNKD (PNKD) mRNA, encodes complete protein.
KR709507 - Synthetic construct Homo sapiens clone CCSBHm_00002859 PNKD (PNKD) mRNA, encodes complete protein.
AB033010 - Homo sapiens mRNA for KIAA1184 protein, partial cds.
AF318057 - Homo sapiens FKSG19 (FKSG19) mRNA, complete cds.
AF417001 - Homo sapiens myofibrillogenesis regulator MR-1 mRNA, complete cds.
LF383619 - JP 2014500723-A/191122: Polycomb-Associated Non-Coding RNAs.
AY039043 - Homo sapiens trans-activated by hepatitis C virus core protein 2 (TAHCCP2) mRNA, complete cds.
BC021118 - Homo sapiens paroxysmal nonkinesigenic dyskinesia, mRNA (cDNA clone IMAGE:4861213), complete cds.
AL080092 - Homo sapiens mRNA; cDNA DKFZp564N1362 (from clone DKFZp564N1362).
JD529005 - Sequence 510029 from Patent EP1572962.
EU831670 - Synthetic construct Homo sapiens clone HAIB:100066699; DKFZo003A0420 paroxysmal nonkinesigenic dyskinesia protein (PNKD) gene, encodes complete protein.
EU831585 - Synthetic construct Homo sapiens clone HAIB:100066614; DKFZo007A0419 paroxysmal nonkinesigenic dyskinesia protein (PNKD) gene, encodes complete protein.
KJ906108 - Synthetic construct Homo sapiens clone ccsbBroadEn_15778 PNKD gene, encodes complete protein.
CU676836 - Synthetic construct Homo sapiens gateway clone IMAGE:100021831 5' read PNKD mRNA.
MA619196 - JP 2018138019-A/191122: Polycomb-Associated Non-Coding RNAs.
AY358753 - Homo sapiens clone DNA96894 AWQG2491 (UNQ2491) mRNA, complete cds.
CU678300 - Synthetic construct Homo sapiens gateway clone IMAGE:100017105 5' read PNKD mRNA.
KJ893497 - Synthetic construct Homo sapiens clone ccsbBroadEn_02891 PNKD gene, encodes complete protein.
AM393075 - Synthetic construct Homo sapiens clone IMAGE:100002024 for hypothetical protein (PNKD gene).
AM393168 - Synthetic construct Homo sapiens clone IMAGE:100002020 for hypothetical protein (PNKD gene).
BC002937 - Homo sapiens paroxysmal nonkinesigenic dyskinesia, mRNA (cDNA clone MGC:10635 IMAGE:3956630), complete cds.
AK309308 - Homo sapiens cDNA, FLJ99349.
AL137675 - Homo sapiens mRNA; cDNA DKFZp434O1772 (from clone DKFZp434O1772).
LF318596 - JP 2014500723-A/126099: Polycomb-Associated Non-Coding RNAs.
LF318597 - JP 2014500723-A/126100: Polycomb-Associated Non-Coding RNAs.
DQ598158 - Homo sapiens piRNA piR-36224, complete sequence.
BC007543 - Homo sapiens paroxysmal nonkinesiogenic dyskinesia, mRNA (cDNA clone IMAGE:2959415).
LF318600 - JP 2014500723-A/126103: Polycomb-Associated Non-Coding RNAs.
LF318601 - JP 2014500723-A/126104: Polycomb-Associated Non-Coding RNAs.
JD405704 - Sequence 386728 from Patent EP1572962.
JD164597 - Sequence 145621 from Patent EP1572962.
JD148111 - Sequence 129135 from Patent EP1572962.
JD115450 - Sequence 96474 from Patent EP1572962.
LF318602 - JP 2014500723-A/126105: Polycomb-Associated Non-Coding RNAs.
JD423526 - Sequence 404550 from Patent EP1572962.
JD208516 - Sequence 189540 from Patent EP1572962.
JD217246 - Sequence 198270 from Patent EP1572962.
JD128469 - Sequence 109493 from Patent EP1572962.
JD057639 - Sequence 38663 from Patent EP1572962.
JD488201 - Sequence 469225 from Patent EP1572962.
JD060646 - Sequence 41670 from Patent EP1572962.
JD151169 - Sequence 132193 from Patent EP1572962.
JD023468 - Sequence 4492 from Patent EP1572962.
JD024584 - Sequence 5608 from Patent EP1572962.
JD104564 - Sequence 85588 from Patent EP1572962.
JD033128 - Sequence 14152 from Patent EP1572962.
JD427298 - Sequence 408322 from Patent EP1572962.
JD354744 - Sequence 335768 from Patent EP1572962.
JD480116 - Sequence 461140 from Patent EP1572962.
JD126373 - Sequence 107397 from Patent EP1572962.
JD347563 - Sequence 328587 from Patent EP1572962.
JD121427 - Sequence 102451 from Patent EP1572962.
JD367986 - Sequence 349010 from Patent EP1572962.
JD208519 - Sequence 189543 from Patent EP1572962.
JD293010 - Sequence 274034 from Patent EP1572962.
JD269952 - Sequence 250976 from Patent EP1572962.
JD281164 - Sequence 262188 from Patent EP1572962.
JD210708 - Sequence 191732 from Patent EP1572962.
AY358680 - Homo sapiens clone DNA60281 AWQG2491 (UNQ2491) mRNA, complete cds.
JD093619 - Sequence 74643 from Patent EP1572962.
JD403965 - Sequence 384989 from Patent EP1572962.
JD104197 - Sequence 85221 from Patent EP1572962.
JD386708 - Sequence 367732 from Patent EP1572962.
JD340385 - Sequence 321409 from Patent EP1572962.
JD494235 - Sequence 475259 from Patent EP1572962.
JD371670 - Sequence 352694 from Patent EP1572962.
JD423654 - Sequence 404678 from Patent EP1572962.
JD138686 - Sequence 119710 from Patent EP1572962.
JD346349 - Sequence 327373 from Patent EP1572962.
JD334747 - Sequence 315771 from Patent EP1572962.
JD399379 - Sequence 380403 from Patent EP1572962.
JD427154 - Sequence 408178 from Patent EP1572962.
LF318603 - JP 2014500723-A/126106: Polycomb-Associated Non-Coding RNAs.
JD131947 - Sequence 112971 from Patent EP1572962.
JD147952 - Sequence 128976 from Patent EP1572962.
JD235566 - Sequence 216590 from Patent EP1572962.
JD270767 - Sequence 251791 from Patent EP1572962.
JD389646 - Sequence 370670 from Patent EP1572962.
LF318604 - JP 2014500723-A/126107: Polycomb-Associated Non-Coding RNAs.
JD402313 - Sequence 383337 from Patent EP1572962.
JD253668 - Sequence 234692 from Patent EP1572962.
JD423649 - Sequence 404673 from Patent EP1572962.
JD390357 - Sequence 371381 from Patent EP1572962.
JD191113 - Sequence 172137 from Patent EP1572962.
JD208302 - Sequence 189326 from Patent EP1572962.
JD185117 - Sequence 166141 from Patent EP1572962.
JD041633 - Sequence 22657 from Patent EP1572962.
JD391172 - Sequence 372196 from Patent EP1572962.
JD191461 - Sequence 172485 from Patent EP1572962.
JD285693 - Sequence 266717 from Patent EP1572962.
JD345793 - Sequence 326817 from Patent EP1572962.
JD241911 - Sequence 222935 from Patent EP1572962.
MA554173 - JP 2018138019-A/126099: Polycomb-Associated Non-Coding RNAs.
MA554174 - JP 2018138019-A/126100: Polycomb-Associated Non-Coding RNAs.
MA554177 - JP 2018138019-A/126103: Polycomb-Associated Non-Coding RNAs.
MA554178 - JP 2018138019-A/126104: Polycomb-Associated Non-Coding RNAs.
MA554179 - JP 2018138019-A/126105: Polycomb-Associated Non-Coding RNAs.
MA554180 - JP 2018138019-A/126106: Polycomb-Associated Non-Coding RNAs.
MA554181 - JP 2018138019-A/126107: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K1F2, ENST00000273077.1, ENST00000273077.2, ENST00000273077.3, ENST00000273077.4, ENST00000273077.5, ENST00000273077.6, ENST00000273077.7, ENST00000273077.8, FKSG19, KIAA1184, MR1, NM_015488, PNKD_HUMAN, Q8N490, Q96A48, Q9BU26, Q9NSX4, Q9ULN6, Q9Y4T1, TAHCCP2, uc317jax.1, uc317jax.2, UNQ2491/PRO5778
UCSC ID: ENST00000273077.9_6
RefSeq Accession: NM_015488.5
Protein: Q8N490 (aka PNKD_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PNKD:
dystonia-ov (Hereditary Dystonia Overview)
pnknd (Familial Paroxysmal Nonkinesigenic Dyskinesia)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.