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    PNLDC1 PARN like ribonuclease domain containing exonuclease 1 [ Homo sapiens (human) ]

    Gene ID: 154197, updated on 11-Apr-2024

    Summary

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    Official Symbol
    PNLDC1provided by HGNC
    Official Full Name
    PARN like ribonuclease domain containing exonuclease 1provided by HGNC
    Primary source
    HGNC:HGNC:21185
    See related
    Ensembl:ENSG00000146453 MIM:619529; AllianceGenome:HGNC:21185
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SPGF57; Trimmer; HsPNLDC1
    Summary
    Enables poly(A)-specific ribonuclease activity. Involved in nuclear-transcribed mRNA poly(A) tail shortening. Located in endoplasmic reticulum. Implicated in spermatogenic failure. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Restricted expression toward testis (RPKM 4.8) See more
    Orthologs
    mouse all
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    Genomic context

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    See PNLDC1 in Genome Data Viewer
    Location:
    6q25.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (159799455..159820704)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (161045047..161066381)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (160221308..160241736)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:160209832-160210496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:160210497-160211160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25393 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160215999-160216870 Neighboring gene small nucleolar RNA, H/ACA box 29 Neighboring gene t-complex 1 Neighboring gene mitochondrial ribosomal protein L18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:160240240-160240966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160242614-160243420 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160251537-160252270 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:160296296-160296948 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:160339473-160340672 Neighboring gene MAS1 proto-oncogene, G protein-coupled receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160399030-160400020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:160401011-160402001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25399 Neighboring gene Sharpr-MPRA regulatory region 15614 Neighboring gene Sharpr-MPRA regulatory region 12427 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:160408528-160409102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160417106-160417992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160417993-160418878 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:160419578-160420777 Neighboring gene insulin like growth factor 2 receptor Neighboring gene antisense of IGF2R non-protein coding RNA

    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. Variant PNLDC1, Defective piRNA Processing, and Azoospermia. Nagirnaja L, et al. N Engl J Med, 2021 Aug 19. PMID 34347949, Free PMC Article
    2. PNLDC1, mouse pre-piRNA Trimmer, is required for meiotic and post-meiotic male germ cell development. Nishimura T, et al. EMBO Rep, 2018 Mar. PMID 29444933, Free PMC Article
    3. A balanced translocation disrupting BCL2L10 and PNLDC1 segregates with affective psychosis. Bouwkamp CG, et al. Am J Med Genet B Neuropsychiatr Genet, 2017 Apr. PMID 27260655, Free PMC Article
    4. A risk model of gene signatures for predicting platinum response and survival in ovarian cancer. Chen S, et al. J Ovarian Res, 2022 Mar 31. PMID 35361267, Free PMC Article
    5. Mammalian PNLDC1 is a novel poly(A) specific exonuclease with discrete expression during early development. Anastasakis D, et al. Nucleic Acids Res, 2016 Oct 14. PMID 27515512, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The role of homozygous LOF variant of the PNLDC1 gene in oligo-astheno-teratozoospermia (OAT) and male infertility.
      Title: The role of homozygous LOF variant of the PNLDC1 gene in oligo-astheno-teratozoospermia (OAT) and male infertility.
    2. A risk model of gene signatures for predicting platinum response and survival in ovarian cancer.
      Title: A risk model of gene signatures for predicting platinum response and survival in ovarian cancer.
    3. we describe the identification of a structural genetic variant segregating with affective psychosis in a family with multiple members suffering from bipolar I disorder. Using whole-genome sequencing, we delineated the translocation breakpoints as corresponding intragenic events disrupting BCL2L10 and PNLDC1. These data warrant further consideration for BCL2L10 and PNLDC1 as novel candidates for affective psychosis.
      Title: A balanced translocation disrupting BCL2L10 and PNLDC1 segregates with affective psychosis.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    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
    Spermatogenic failure 57
    MedGen: C5561988 OMIM: 619528 GeneReviews: Not available
    		Compare labs

    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

    • FLJ40240, MGC138451

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5'-RNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(A)-specific ribonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in blastocyst formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear-transcribed mRNA poly(A) tail shortening IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear-transcribed mRNA poly(A) tail shortening IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in piRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in priRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in siRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    poly(A)-specific ribonuclease PNLDC1
    Names
    PARN like, ribonuclease domain containing 1
    PARN-like domain-containing protein 1
    poly(A)-specific ribonuclease (PARN)-like domain containing 1
    poly(A)-specific ribonuclease PARN-like domain-containing protein 1
    poly(A)-specific ribonuclease domain-containing protein 1
    NP_001258791.1
    NP_775787.1
    XP_011533793.1
    XP_011533795.1
    XP_016865801.1
    XP_016865802.1
    XP_016865803.1
    XP_016865804.1
    XP_016865805.1
    XP_024302107.1
    XP_054210331.1
    XP_054210332.1
    XP_054210333.1
    XP_054210334.1
    XP_054210335.1
    XP_054210336.1
    XP_054210337.1
    XP_054210338.1

    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.

    mRNA and Protein(s)

    1. NM_001271862.2 → NP_001258791.1  poly(A)-specific ribonuclease PNLDC1 isoform 1

      See identical proteins and their annotated locations for NP_001258791.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK093139, AK097559, BM666663
      Consensus CDS
      CCDS5271.2
      UniProtKB/Swiss-Prot
      Q8NA58
      Related
      ENSP00000376007.3, ENST00000392167.4
      Conserved Domains (1) summary
      pfam04857
      Location:3 → 373
      CAF1; CAF1 family ribonuclease

    2. NM_173516.3 → NP_775787.1  poly(A)-specific ribonuclease PNLDC1 isoform 2

      See identical proteins and their annotated locations for NP_775787.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK097559, BM666663
      Consensus CDS
      CCDS64561.1
      UniProtKB/Swiss-Prot
      Q5TAP7, Q8N7X5, Q8NA58
      Related
      ENSP00000476448.1, ENST00000610273.5
      Conserved Domains (1) summary
      pfam04857
      Location:11 → 362
      CAF1; CAF1 family ribonuclease

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      159799455..159820704
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024446339.2 → XP_024302107.1  poly(A)-specific ribonuclease PNLDC1 isoform X8

      Conserved Domains (1) summary
      pfam04857
      Location:59 → 293
      CAF1; CAF1 family ribonuclease

    2. XM_017010312.3 → XP_016865801.1  poly(A)-specific ribonuclease PNLDC1 isoform X1

    3. XM_017010314.3 → XP_016865803.1  poly(A)-specific ribonuclease PNLDC1 isoform X4

    4. XM_017010313.3 → XP_016865802.1  poly(A)-specific ribonuclease PNLDC1 isoform X2

    5. XM_017010316.2 → XP_016865805.1  poly(A)-specific ribonuclease PNLDC1 isoform X6

    6. XM_011535491.3 → XP_011533793.1  poly(A)-specific ribonuclease PNLDC1 isoform X3

      See identical proteins and their annotated locations for XP_011533793.1

      UniProtKB/Swiss-Prot
      Q5TAP7, Q8N7X5, Q8NA58
      Conserved Domains (1) summary
      pfam04857
      Location:11 → 362
      CAF1; CAF1 family ribonuclease

    7. XM_017010315.3 → XP_016865804.1  poly(A)-specific ribonuclease PNLDC1 isoform X5

    8. XM_011535493.3 → XP_011533795.1  poly(A)-specific ribonuclease PNLDC1 isoform X7

      Conserved Domains (1) summary
      pfam04857
      Location:30 → 246
      CAF1; CAF1 family ribonuclease

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      161045047..161066381
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354363.1 → XP_054210338.1  poly(A)-specific ribonuclease PNLDC1 isoform X8

    2. XM_054354359.1 → XP_054210334.1  poly(A)-specific ribonuclease PNLDC1 isoform X4

    3. XM_054354356.1 → XP_054210331.1  poly(A)-specific ribonuclease PNLDC1 isoform X1

    4. XM_054354357.1 → XP_054210332.1  poly(A)-specific ribonuclease PNLDC1 isoform X2

    5. XM_054354361.1 → XP_054210336.1  poly(A)-specific ribonuclease PNLDC1 isoform X6

    6. XM_054354358.1 → XP_054210333.1  poly(A)-specific ribonuclease PNLDC1 isoform X3

      UniProtKB/Swiss-Prot
      Q5TAP7, Q8N7X5, Q8NA58

    7. XM_054354360.1 → XP_054210335.1  poly(A)-specific ribonuclease PNLDC1 isoform X5

    8. XM_054354362.1 → XP_054210337.1  poly(A)-specific ribonuclease PNLDC1 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NA58.2 GenPept UniProtKB/Swiss-Prot:Q8NA58

    Gene LinkOut

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

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