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

Gene ID: 25953, updated on 3-Apr-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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Location:
2q35
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218270519..218346793)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (218756220..218832888)
105.20220307 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

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. 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
  2. A case of familial paroxysmal nonkinesigenic dyskinesia due to mutation of the PNKD gene in Chinese Mainland. Liang S, et al. Brain Res, 2015 Jan 21. PMID 25107857
  3. Clinicopathological and prognostic significance of myofibrillogenesis regulator-1 protein expression in pancreatic ductal adenocarcinoma. Zhao CY, et al. Tumour Biol, 2013 Oct. PMID 23696030
  4. Myofibrillogenesis regulator-1 overexpression is associated with poor prognosis of gastric cancer patients. Guo J, et al. World J Gastroenterol, 2012 Oct 14. PMID 23082061, Free PMC Article
  5. Familial paroxysmal nonkinesigenic dyskinesia: clinical and genetic analysis of a Taiwanese family. Yeh TH, et al. J Neurol Sci, 2012 Dec 15. PMID 22967746

See all (73) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. MR-1S is highly expressed in ovarian cancer cells and tissues.
    Title: [Expression of a novel biomarker, MR-1S, in ovarian carcinoma and its biological significance].
Submit: New GeneRIF Correction See all GeneRIFs (20)

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)

Genotypes

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 
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_2023_10

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

  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.

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