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

Gene ID: 154197, updated on 10-Dec-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; piRNA processing; and spermatogenesis. Located in endoplasmic reticulum. Implicated in spermatogenic failure 57. [provided by Alliance of Genome Resources, Dec 2024]
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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (159799455..159820704)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (161045047..161066381)
RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. The role of homozygous LOF variant of the PNLDC1 gene in oligo-astheno-teratozoospermia (OAT) and male infertility. Cheng ZX, et al. Asian J Androl, 2023 Nov 1. PMID 37282384, Free PMC Article
  2. Variant PNLDC1, Defective piRNA Processing, and Azoospermia. Nagirnaja L, et al. N Engl J Med, 2021 Aug 19. PMID 34347949, Free PMC Article
  3. 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
  4. 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
  5. 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

See all (16) 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)

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_2024_08

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

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