PNLDC1 (PARN like ribonuclease domain containing exonuclease 1)

Gene

• Entrez ID: 154197
• Gene name: PARN like ribonuclease domain containing exonuclease 1
• Gene symbol: PNLDC1
• Synonyms (NCBI Gene): HsPNLDC1, SPGF57, Trimmer
• Chromosome: 6
• Chromosome location: 6q25.3

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017523	hsa-miR-335-5p	Microarray	18185580

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000175	Function	3'-5'-RNA exonuclease activity	IBA
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA
GO:0000289	Process	Nuclear-transcribed mRNA poly(A) tail shortening	IBA
GO:0000289	Process	Nuclear-transcribed mRNA poly(A) tail shortening	IDA	27515512
GO:0000289	Process	Nuclear-transcribed mRNA poly(A) tail shortening	IEA
GO:0001825	Process	Blastocyst formation	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0004518	Function	Nuclease activity	IEA
GO:0004527	Function	Exonuclease activity	IEA
GO:0004535	Function	Poly(A)-specific ribonuclease activity	IDA	27515512
GO:0004535	Function	Poly(A)-specific ribonuclease activity	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IDA	27515512
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0007283	Process	Spermatogenesis	IMP	34347949
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0032502	Process	Developmental process	IEA
GO:0034587	Process	PiRNA processing	IMP	34347949
GO:0046872	Function	Metal ion binding	IEA
GO:1990431	Process	PriRNA 3'-end processing	IBA
GO:1990432	Process	SiRNA 3'-end processing	IBA

Other IDs

• MIM: 619529
• HGNC: 21185
• e!Ensembl: ENSG00000146453

Protein

• UniProt ID: Q8NA58
• Protein name: Poly(A)-specific ribonuclease PNLDC1 (EC 3.1.13.4) (PARN-like domain-containing protein 1) (Poly(A)-specific ribonuclease domain-containing protein 1) (HsPNLDC1)
• Protein function: 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails (PubMed:27515512). Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is al
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04857	CAF1	10 → 362	CAF1 family ribonuclease	Family

• Sequence:

  MFCTRGLLFFAFLAGLDIEFTGLRSNLSGPQQISLFDLPSEWYLKTRQSVQQFTVCQIGL
  SVFSAIEGEANKYIAHSCNFYLFPTTFGILDSEFSFQASSVQFLNQYGFNYNKFLKNGIP
  YMNEEQEKKIRHDILTGNWRVRSSPDKDQIKVVIDEVTRWLELAKEGDWMTLPGITGFQA
  FEVQLVLRQALPNIWTVLKDEGVVVKKVSKQHRWYLQNTSCDRESCWKENILLSARGFSV
  FFQMLVKAQKPLVGHNMMMDLLHLHEKFFRPLPESYDQFKQNIHSLFPVLIDTKSVTKDI
  WKEMNFPRVSNLSEVYEVLNSDLNPTKNSGPEIVHASRCEKYVETKCPHEAAYDAFLCGS
  VLLKVAHLLLQKIYHIDPVPESSFPQYLDVLAPYVNQVNLIRAGVPKINFSGPDYPSIRP
  PILILSVKRWPGVSEQQVYHKFQNLCKFDVRRLTRSQFLLLTNKFKDARNILKEYRDHPT
  LCISLYRYWRHSPNVNCLLQVCGIVTAWALLAFILGRSGT

• Sequence length: 520

Pathways

KEGG:

RNA degradation

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Male infertility	Likely pathogenic	rs1474478174	RCV004573395	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Male infertility with azoospermia or oligozoospermia due to single gene mutation	Pathogenic	rs2115028353, rs763048743, rs200629089	RCV001564024 RCV001564026 RCV001564023	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Non-obstructive azoospermia	Likely pathogenic	rs1781557432	RCV002260402	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oligospermia	Likely pathogenic	rs1781557432	RCV002260403	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spermatogenic failure 57	Pathogenic; Likely pathogenic	rs754159168, rs2115028353, rs763048743, rs200629089, rs1254456989, rs2483206286	RCV002246420 RCV002246418 RCV002246419 RCV002246417 RCV001845057 RCV003990519	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TESTICULAR AZOOSPERMIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Affective Disorders, Psychotic	Affective Psychosis	BEFREE	27260655		★☆☆☆☆ Found in Text Mining only
Asthenozoospermia	Asthenozoospermia	Pubtator	36960498	Associate	★☆☆☆☆ Found in Text Mining only
Azoospermia	Azoospermia	Pubtator	34347949	Associate	★☆☆☆☆ Found in Text Mining only
Azoospermia Nonobstructive	Nonobstructive azoospermia	Pubtator	34347949, 36960498, 39223739	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	34080453	Associate	★☆☆☆☆ Found in Text Mining only
Infertility	Infertility	Pubtator	36960498	Associate	★☆☆☆☆ Found in Text Mining only
Infertility Male	Male infertility	Pubtator	34347949, 36960498	Associate	★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	36960498	Associate	★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	35361267	Associate	★☆☆☆☆ Found in Text Mining only
Teratozoospermia	Teratozoospermia	Pubtator	36960498	Associate	★☆☆☆☆ Found in Text Mining only