Gene Gene information from NCBI Gene database. Download as csv Download as pdf
Entrez ID	154197
Gene name	PARN like ribonuclease domain containing exonuclease 1
Gene symbol	PNLDC1
Synonyms (NCBI Gene)	HsPNLDC1SPGF57Trimmer
Chromosome	6
Chromosome location	6q25.3

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

26 Show/Hide all (26)

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

MIM	HGNC	e!Ensembl
619529	21185	ENSG00000146453

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

Interactions

View interactions

KEGG Pathway
RNA degradation

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)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
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 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CORONARY ARTERY DISEASE	—	GWAS catalog	35285134	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	38072966	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TESTICULAR AZOOSPERMIA	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining Show/Hide Text Mining Associations (10)
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

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
SHOC1	4	["Male infertility","Male infertility single gene azoospermia","Spermatogenic failure","Testicular azoospermia"]	[]	8	["Disgenet (Male infertility)","Disgenet (Male infertility single gene azoospermia)","Orphanet (Male infertility single gene azoospermia)","Disgenet (Spermatogenic failure)","GWAS catalog (Spermatogenic failure)","HPO (Spermatogenic failure)","ClinVar (Spermatogenic failure)","Disgenet (Testicular azoospermia)"]
ZMYND15	4	["Male infertility","Male infertility single gene azoospermia","Spermatogenic failure","Testicular azoospermia"]	[]	7	["Disgenet (Male infertility)","Disgenet (Male infertility single gene azoospermia)","Orphanet (Male infertility single gene azoospermia)","Disgenet (Spermatogenic failure)","HPO (Spermatogenic failure)","ClinVar (Spermatogenic failure)","Disgenet (Testicular azoospermia)"]
M1AP	4	["Male infertility","Male infertility single gene azoospermia","Spermatogenic failure","Testicular azoospermia"]	[]	7	["Disgenet (Male infertility)","Disgenet (Male infertility single gene azoospermia)","Disgenet (Spermatogenic failure)","GWAS catalog (Spermatogenic failure)","HPO (Spermatogenic failure)","ClinVar (Spermatogenic failure)","Disgenet (Testicular azoospermia)"]
TERB2	3	["Male infertility single gene azoospermia","Spermatogenic failure","Testicular azoospermia"]	[]	6	["Disgenet (Male infertility single gene azoospermia)","Orphanet (Male infertility single gene azoospermia)","Disgenet (Spermatogenic failure)","HPO (Spermatogenic failure)","ClinVar (Spermatogenic failure)","Disgenet (Testicular azoospermia)"]
KLHL10	3	["Male infertility single gene azoospermia","Spermatogenic failure","Testicular azoospermia"]	[]	6	["Disgenet (Male infertility single gene azoospermia)","Orphanet (Male infertility single gene azoospermia)","Disgenet (Spermatogenic failure)","HPO (Spermatogenic failure)","ClinVar (Spermatogenic failure)","Disgenet (Testicular azoospermia)"]

PNLDC1 (PARN like ribonuclease domain containing exonuclease 1)

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