PNLDC1
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Also known as FLJ40240dJ195P10.2Trimmer
Summary
PNLDC1 (PARN like ribonuclease domain containing exonuclease 1, HGNC:21185) is a protein-coding gene on chromosome 6q25.3, encoding Poly(A)-specific ribonuclease PNLDC1 (Q8NA58). 3’-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails.
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.
Source: NCBI Gene 154197 — RefSeq curated summary.
At a glance
- Gene–disease (curated): spermatogenic failure 57 (Strong, GenCC)
- GWAS associations: 1
- Clinical variants (ClinVar): 89 total — 5 pathogenic, 4 likely-pathogenic
- Phenotypes (HPO): 11
- MANE Select transcript:
NM_001271862
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:21185 |
| Approved symbol | PNLDC1 |
| Name | PARN like ribonuclease domain containing exonuclease 1 |
| Location | 6q25.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ40240, dJ195P10.2, Trimmer |
| Ensembl gene | ENSG00000146453 |
| Ensembl biotype | protein_coding |
| OMIM | 619529 |
| Entrez | 154197 |
Gene structure
Transcript identifiers
Ensembl transcripts: 8 — 3 nonsense_mediated_decay, 3 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron
ENST00000275275, ENST00000392167, ENST00000609334, ENST00000609658, ENST00000610041, ENST00000610048, ENST00000610273, ENST00000943611
RefSeq mRNA: 2 — MANE Select: NM_001271862
NM_001271862, NM_173516
CCDS: CCDS5271, CCDS64561
Canonical transcript exons
ENST00000392167 — 19 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001510939 | 159800772 | 159800829 |
| ENSE00001813612 | 159800276 | 159800383 |
| ENSE00003702547 | 159818555 | 159818654 |
| ENSE00003702669 | 159817109 | 159817151 |
| ENSE00003703297 | 159811701 | 159811786 |
| ENSE00003703351 | 159818946 | 159819121 |
| ENSE00003703729 | 159815969 | 159816033 |
| ENSE00003704185 | 159819254 | 159819352 |
| ENSE00003705091 | 159801113 | 159801186 |
| ENSE00003705540 | 159805983 | 159806083 |
| ENSE00003705798 | 159808740 | 159808816 |
| ENSE00003706789 | 159803965 | 159804088 |
| ENSE00003707260 | 159809015 | 159809158 |
| ENSE00003708595 | 159803271 | 159803310 |
| ENSE00003708693 | 159813601 | 159813656 |
| ENSE00003710622 | 159816543 | 159816596 |
| ENSE00003710892 | 159810026 | 159810095 |
| ENSE00003711057 | 159804549 | 159804637 |
| ENSE00003850341 | 159820454 | 159820704 |
Expression profiles
Bgee: expression breadth ubiquitous, 155 present calls, max score 91.96.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2212 / max 49.5116, expressed in 61 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 70998 | 0.2212 | 61 |
Top tissues by expression
239 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| oocyte | CL:0000023 | 91.96 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 87.84 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 86.32 | gold quality |
| secondary oocyte | CL:0000655 | 86.22 | gold quality |
| right testis | UBERON:0004534 | 80.42 | gold quality |
| left testis | UBERON:0004533 | 80.32 | gold quality |
| testis | UBERON:0000473 | 79.32 | gold quality |
| upper leg skin | UBERON:0004262 | 76.75 | gold quality |
| caudate nucleus | UBERON:0001873 | 70.64 | gold quality |
| putamen | UBERON:0001874 | 69.12 | gold quality |
| prefrontal cortex | UBERON:0000451 | 68.29 | gold quality |
| right frontal lobe | UBERON:0002810 | 68.02 | gold quality |
| bronchial epithelial cell | CL:0002328 | 66.61 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 66.04 | gold quality |
| bronchus | UBERON:0002185 | 65.43 | gold quality |
| nucleus accumbens | UBERON:0001882 | 64.23 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 64.16 | gold quality |
| frontal cortex | UBERON:0001870 | 63.21 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 63.11 | gold quality |
| sperm | CL:0000019 | 61.94 | gold quality |
| mammalian vulva | UBERON:0000997 | 61.27 | gold quality |
| right uterine tube | UBERON:0001302 | 61.00 | gold quality |
| neocortex | UBERON:0001950 | 60.87 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 60.09 | gold quality |
| adult organism | UBERON:0007023 | 59.15 | gold quality |
| body of pancreas | UBERON:0001150 | 58.91 | gold quality |
| cerebral cortex | UBERON:0000956 | 58.04 | gold quality |
| forebrain | UBERON:0001890 | 57.67 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 57.41 | gold quality |
| right coronary artery | UBERON:0001625 | 56.57 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 4.10 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
10 targeting PNLDC1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-6508-5P | 99.92 | 70.67 | 2465 |
| HSA-MIR-8067 | 99.86 | 69.59 | 2260 |
| HSA-MIR-29A-5P | 99.08 | 68.59 | 1813 |
| HSA-MIR-5000-3P | 98.79 | 65.63 | 1251 |
| HSA-MIR-4436A | 98.05 | 64.83 | 1140 |
| HSA-MIR-4521 | 97.73 | 67.64 | 684 |
| HSA-MIR-3144-5P | 97.64 | 65.45 | 646 |
| HSA-MIR-3169 | 96.40 | 67.58 | 698 |
| HSA-MIR-4740-5P | 96.25 | 67.96 | 726 |
| HSA-MIR-4693-3P | 95.23 | 65.92 | 735 |
Literature-anchored findings (GeneRIF, showing 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. (PMID:27260655)
- A risk model of gene signatures for predicting platinum response and survival in ovarian cancer. (PMID:35361267)
- The role of homozygous LOF variant of the PNLDC1 gene in oligo-astheno-teratozoospermia (OAT) and male infertility. (PMID:37282384)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Pnldc1 | ENSMUSG00000073460 |
| rattus_norvegicus | Pnldc1 | ENSRNOG00000023140 |
| caenorhabditis_elegans | WBGENE00010734 |
Paralogs (2): TOE1 (ENSG00000132773), PARN (ENSG00000140694)
Protein
Protein identifiers
Poly(A)-specific ribonuclease PNLDC1 — Q8NA58 (reviewed: Q8NA58)
Alternative names: PARN-like domain-containing protein 1, Poly(A)-specific ribonuclease domain-containing protein 1
All UniProt accessions (2): Q8NA58, V9GYA0
UniProt curated annotations — full annotation on UniProt →
Function. 3’-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. May act as a regulator of multipotency in embryonic stem cells. Is a critical factor for proper spermatogenesis, involved in pre-piRNAs processing to generate mature piRNAs.
Subcellular location. Endoplasmic reticulum membrane.
Disease relevance. Spermatogenic failure 57 (SPGF57) [MIM:619528] An autosomal recessive male infertility disorder characterized by non-obstructive azoospermia, due to error-prone meiosis and spermatogenic arrest at the late pachytene stage. The disease is caused by variants affecting the gene represented in this entry.
Similarity. Belongs to the CAF1 family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q8NA58-1 | 1 | yes |
| Q8NA58-2 | 2 |
RefSeq proteins (2): NP_001258791, NP_775787 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR006941 | RNase_CAF1 | Family |
| IPR012337 | RNaseH-like_sf | Homologous_superfamily |
| IPR036397 | RNaseH_sf | Homologous_superfamily |
| IPR051181 | CAF1_poly(A)_ribonucleases | Family |
Pfam: PF04857
Enzyme classification (BRENDA):
- EC 3.1.13.4 — poly(A)-specific ribonuclease (BRENDA: 15 organisms, 67 substrates, 89 inhibitors, 9 Km, 5 kcat entries)
Substrate kinetics (BRENDA)
2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.
| Substrate | Km (mM) | Measurements |
|---|---|---|
| POLY(A) RNA | — | 7 |
| POLY(A) | 0.0051 | 1 |
UniProt features (11 total): binding site 4, sequence variant 3, chain 1, transmembrane region 1, site 1, splice variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8NA58-F1 | 90.16 | 0.65 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Catalytic / active sites (1): 294 (interaction with poly(a))
Ligand- & substrate-binding residues (4): 17; 19; 260; 354
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 101 (showing top):
GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GSE45365_NK_CELL_VS_BCELL_DN, RNGTGGGC_UNKNOWN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOMF_RNA_NUCLEASE_ACTIVITY, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOMF_NUCLEASE_ACTIVITY, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_MALE_GAMETE_GENERATION, GOBP_BLASTOCYST_FORMATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, chr6q25, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS
GO Biological Process (8): nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184), nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289), blastocyst formation (GO:0001825), spermatogenesis (GO:0007283), piRNA processing (GO:0034587), priRNA 3’-end processing (GO:1990431), siRNA 3’-end processing (GO:1990432), developmental process (GO:0032502)
GO Molecular Function (8): 3’-5’-RNA exonuclease activity (GO:0000175), RNA binding (GO:0003723), poly(A)-specific ribonuclease activity (GO:0004535), metal ion binding (GO:0046872), nucleic acid binding (GO:0003676), nuclease activity (GO:0004518), exonuclease activity (GO:0004527), hydrolase activity (GO:0016787)
GO Cellular Component (4): nucleus (GO:0005634), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| nuclear-transcribed mRNA catabolic process | 2 |
| regulatory ncRNA 3’-end processing | 2 |
| intracellular membrane-bounded organelle | 2 |
| nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 1 |
| blastocyst development | 1 |
| anatomical structure formation involved in morphogenesis | 1 |
| developmental process involved in reproduction | 1 |
| male gamete generation | 1 |
| regulatory ncRNA processing | 1 |
| biological_process | 1 |
| 3’-5’ exonuclease activity | 1 |
| RNA exonuclease activity, producing 5’-phosphomonoesters | 1 |
| nucleic acid binding | 1 |
| 3’-5’-RNA exonuclease activity | 1 |
| cation binding | 1 |
| binding | 1 |
| catalytic activity, acting on a nucleic acid | 1 |
| nuclease activity | 1 |
| hydrolase activity, acting on ester bonds | 1 |
| catalytic activity | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| organelle membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| endoplasmic reticulum subcompartment | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
756 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| PNLDC1 | TENT2 | Q6PIY7 | 883 |
| PNLDC1 | SYMPK | Q92797 | 766 |
| PNLDC1 | TDRKH | Q9Y2W6 | 737 |
| PNLDC1 | PLD6 | Q8N2A8 | 731 |
| PNLDC1 | NGDN | Q8NEJ9 | 705 |
| PNLDC1 | HENMT1 | Q5T8I9 | 686 |
| PNLDC1 | PAPOLG | Q9BWT3 | 611 |
| PNLDC1 | PAPOLA | P51003 | 608 |
| PNLDC1 | PAPOLB | Q9NRJ5 | 608 |
| PNLDC1 | PABPC1L | Q4VXU2 | 602 |
| PNLDC1 | TDRD5 | Q8NAT2 | 593 |
| PNLDC1 | NOCT | Q9UK39 | 578 |
| PNLDC1 | MOV10L1 | Q9BXT6 | 554 |
| PNLDC1 | CSTF1 | Q05048 | 553 |
| PNLDC1 | CPEB1 | Q9BZB8 | 543 |
IntAct
2 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| PNLDC1 | C1QL1 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (23): TRPM7 (Affinity Capture-MS), ALG9 (Affinity Capture-MS), LMF2 (Affinity Capture-MS), C1QL1 (Affinity Capture-MS), DPY19L4 (Affinity Capture-MS), FAM69A (Affinity Capture-MS), CSGALNACT2 (Affinity Capture-MS), GLB1L2 (Affinity Capture-MS), TSPAN10 (Affinity Capture-MS), AMIGO1 (Affinity Capture-MS), GALNT12 (Affinity Capture-MS), SIDT2 (Affinity Capture-MS), PNLDC1 (Affinity Capture-MS), TRPM7 (Affinity Capture-MS), GLB1L2 (Affinity Capture-MS)
ESM2 similar proteins: A1L1C2, A1L1G9, A3KNW0, A4QP72, B1H1N7, B2RXZ1, B3DLB3, O00329, O35405, O35904, O70572, P51839, Q0P6H9, Q0V8L6, Q28DT3, Q2KJJ8, Q3U3W5, Q3UY23, Q4R583, Q501S4, Q5FVH2, Q5R4Y7, Q5R6R6, Q5U3T0, Q5ZHN9, Q60750, Q640M6, Q642A7, Q7SXA9, Q7ZVS8, Q80Y81, Q8BG07, Q8BWQ4, Q8C0L6, Q8CGS5, Q8HY87, Q8IV08, Q8K2P2, Q8NA58, Q8NFF5
Diamond homologs: B2RXZ1, Q5R6R6, Q5RAR6, Q8NA58, Q9D2E2, Q17QN2, Q96GM8
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
89 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 5 |
| Likely pathogenic | 4 |
| Uncertain significance | 56 |
| Likely benign | 9 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (9)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1184261 | NM_001271862.2(PNLDC1):c.1387C>T (p.Arg463Ter) | Pathogenic |
| 1184262 | NM_001271862.2(PNLDC1):c.283C>T (p.Pro95Ser) | Pathogenic |
| 1184264 | NM_001271862.2(PNLDC1):c.640-2A>T | Pathogenic |
| 1184272 | NM_001271862.2(PNLDC1):c.136dup (p.Leu46fs) | Pathogenic |
| 1343825 | NM_001271862.2(PNLDC1):c.172C>G (p.Arg58Gly) | Pathogenic |
| 1330303 | NM_001271862.2(PNLDC1):c.743G>A (p.Gly248Asp) | Likely pathogenic |
| 3024496 | NM_001271862.2(PNLDC1):c.1058A>G (p.Tyr353Cys) | Likely pathogenic |
| 3065442 | NM_001271862.2(PNLDC1):c.1257+2T>C | Likely pathogenic |
| 4292143 | NM_001271862.2(PNLDC1):c.563-2A>G | Likely pathogenic |
SpliceAI
3272 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 6:159800368:G:GT | donor_gain | 1.0000 |
| 6:159800414:G:GT | donor_gain | 1.0000 |
| 6:159804534:T:TA | acceptor_gain | 1.0000 |
| 6:159804540:T:A | acceptor_gain | 1.0000 |
| 6:159804546:A:AG | acceptor_gain | 1.0000 |
| 6:159804547:A:AG | acceptor_gain | 1.0000 |
| 6:159804548:G:GC | acceptor_gain | 1.0000 |
| 6:159804548:GTTT:G | acceptor_gain | 1.0000 |
| 6:159805967:A:AG | acceptor_gain | 1.0000 |
| 6:159805968:T:G | acceptor_gain | 1.0000 |
| 6:159805975:A:AG | acceptor_gain | 1.0000 |
| 6:159805976:T:G | acceptor_gain | 1.0000 |
| 6:159805979:TCA:T | acceptor_loss | 1.0000 |
| 6:159805980:CA:C | acceptor_loss | 1.0000 |
| 6:159805981:A:AG | acceptor_gain | 1.0000 |
| 6:159805981:AGC:A | acceptor_loss | 1.0000 |
| 6:159805982:G:GG | acceptor_gain | 1.0000 |
| 6:159805982:GC:G | acceptor_gain | 1.0000 |
| 6:159805982:GCT:G | acceptor_gain | 1.0000 |
| 6:159805982:GCTC:G | acceptor_gain | 1.0000 |
| 6:159805982:GCTCT:G | acceptor_gain | 1.0000 |
| 6:159806050:G:GT | donor_gain | 1.0000 |
| 6:159806051:A:T | donor_gain | 1.0000 |
| 6:159806080:ACTG:A | donor_loss | 1.0000 |
| 6:159806081:CTGG:C | donor_loss | 1.0000 |
| 6:159806083:GG:G | donor_loss | 1.0000 |
| 6:159806084:G:GG | donor_gain | 1.0000 |
| 6:159806085:T:G | donor_loss | 1.0000 |
| 6:159815964:A:AG | acceptor_gain | 1.0000 |
| 6:159815967:A:AG | acceptor_gain | 1.0000 |
AlphaMissense
3529 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 6:159804056:T:C | F103L | 0.997 |
| 6:159804058:T:A | F103L | 0.997 |
| 6:159804058:T:G | F103L | 0.997 |
| 6:159811720:G:C | K280N | 0.997 |
| 6:159811720:G:T | K280N | 0.997 |
| 6:159811754:G:C | D292H | 0.997 |
| 6:159810057:T:C | L261P | 0.996 |
| 6:159801138:T:G | Y43D | 0.995 |
| 6:159810036:G:A | G254E | 0.995 |
| 6:159810054:A:C | D260A | 0.995 |
| 6:159810066:T:C | L264P | 0.995 |
| 6:159811755:A:C | D292A | 0.995 |
| 6:159811755:A:T | D292V | 0.995 |
| 6:159811762:G:C | K294N | 0.995 |
| 6:159811762:G:T | K294N | 0.995 |
| 6:159816578:G:C | A355P | 0.995 |
| 6:159803271:G:A | G59E | 0.994 |
| 6:159810040:T:A | H255Q | 0.994 |
| 6:159810040:T:G | H255Q | 0.994 |
| 6:159816589:T:G | C358W | 0.994 |
| 6:159810038:C:G | H255D | 0.993 |
| 6:159810043:T:A | N256K | 0.993 |
| 6:159810043:T:G | N256K | 0.993 |
| 6:159811756:T:A | D292E | 0.993 |
| 6:159811756:T:G | D292E | 0.993 |
| 6:159816576:A:C | D354A | 0.993 |
| 6:159801168:T:C | F53L | 0.992 |
| 6:159801170:T:A | F53L | 0.992 |
| 6:159801170:T:G | F53L | 0.992 |
| 6:159804074:T:C | F109L | 0.992 |
dbSNP variants (sampled 300 via entrez): RS1000375524 (6:159812048 C>G,T), RS1000503558 (6:159817553 A>G), RS1001060955 (6:159811762 G>A), RS1001233865 (6:159800428 C>A,G), RS1001326318 (6:159816279 T>C), RS1001439489 (6:159807407 A>G), RS1001472455 (6:159818813 A>G,T), RS1001489685 (6:159807081 T>A), RS1001663515 (6:159813062 G>A,T), RS1001697237 (6:159802131 A>G), RS1001778930 (6:159813400 G>A,T), RS1002088444 (6:159820505 A>G), RS1002340610 (6:159800215 C>A,T), RS1002445140 (6:159808669 C>G,T), RS1002495949 (6:159808392 A>G)
Disease associations
OMIM: gene MIM:619529 | disease phenotypes: MIM:619528
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| spermatogenic failure 57 | Strong | Autosomal recessive |
Mondo (3): spermatogenic failure 57 (MONDO:0030439), oligospermia (MONDO:0001913), male infertility (MONDO:0005372)
Orphanet (1): Male infertility with azoospermia or oligozoospermia due to single gene mutation (Orphanet:399805)
HPO phenotypes
11 total (12 of 11 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000027 | Azoospermia |
| HP:0000118 | Phenotypic abnormality |
| HP:0000837 | Increased circulating gonadotropin level |
| HP:0003251 | Male infertility |
| HP:0008669 | Abnormal spermatogenesis |
| HP:0008734 | Decreased testicular size |
| HP:0011462 | Young adult onset |
| HP:0011961 | Non-obstructive azoospermia |
| HP:0011962 | Obstructive azoospermia |
| HP:0031038 | Spermatogenesis maturation arrest |
| HP:0000798 | Oligozoospermia |
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST003127_12 | Lipoprotein (a) levels | 5.000000e-11 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0006925 | lipoprotein A measurement |
MeSH disease descriptors (2)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D007248 | Infertility, Male | C12.100.500.430; C12.100.750.700; C12.200.294.430 |
| D009845 | Oligospermia | C12.100.500.430.508; C12.100.750.700.508; C12.200.294.430.508 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
15 total (human), top 15 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Copper | affects cotreatment, decreases expression, affects binding | 2 |
| aristolochic acid I | increases expression | 1 |
| bisphenol A | decreases methylation | 1 |
| 2-methyl-4-isothiazolin-3-one | increases expression | 1 |
| sodium arsenite | increases expression | 1 |
| licochalcone B | increases expression | 1 |
| (+)-JQ1 compound | increases expression | 1 |
| PCI 5002 | increases expression, affects cotreatment | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Disulfiram | affects binding, decreases expression | 1 |
| Nickel | decreases expression | 1 |
| Tobacco Smoke Pollution | affects expression | 1 |
| Zinc | affects cotreatment, increases expression | 1 |
| Aflatoxin B1 | increases methylation | 1 |
| Lactic Acid | decreases expression | 1 |
Cellosaurus cell lines
1 cell lines: 1 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_D8TF | Ubigene HCT 116 PNLDC1 KO | Cancer cell line | Male |
Clinical trials (associated diseases)
149 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT02307994 | PHASE4 | UNKNOWN | Clinical Research on Effectiveness and Safety of Treatment of Severe Oligospermia or Azoospermia With uFSH |
| NCT05320536 | PHASE4 | UNKNOWN | A Clinical Study of Gulingji Capsule in the Treatment of Idiopathic Oligospermia, Asthenia, and Teratozoospermia |
| NCT06260007 | PHASE4 | RECRUITING | Efficacy and Safety Study of Products Based on Tribulus Terrestris, L. in Men With Oligospermia |
| NCT02202382 | PHASE4 | COMPLETED | Effects of Korean Red Ginseng on Male Infertility |
| NCT02204826 | PHASE4 | COMPLETED | Effects of Korean Red Ginseng on Semen Parameters in Male Infertility Patients: a Randomized, Placebo-controlled, Double-blind Clinical Study |
| NCT03802864 | PHASE4 | COMPLETED | Post-operative Pain Control of Testicular Sperm Extraction Using Liposomal Bupivacaine |
| NCT06100432 | PHASE4 | ACTIVE_NOT_RECRUITING | Effect of Eurycoma Longifolia (DLBS5055) and Multivitamins (Vitamin C+Vitamin E+ β-carotene) for Infertile Males |
| NCT07523022 | PHASE4 | ENROLLING_BY_INVITATION | Comparison of the Effect of Gonadotropin and Clomiphene Citrate Treatment on Sperm Parameters and the Outcome of Assisted Reproductive Procedures in Subfertile Men Based on the APHRODITE Groups |
| NCT00440180 | PHASE3 | TERMINATED | Aromatase Inhibitors in the Treatment of Male Infertility |
| NCT00975117 | PHASE3 | COMPLETED | Spermotrend in the Treatment of Male Infertility |
| NCT01407432 | PHASE3 | COMPLETED | Impact of Folates in the Care of the Male Infertility |
| NCT01895816 | PHASE3 | COMPLETED | Herbal Tonic Fertile Supplement(ZO2C5) |
| NCT02605070 | PHASE3 | TERMINATED | Pilot Study on the Effects of FSH Treatment on the Epigenetic Characteristics of Spermatozoa in Infertile Patients With Severe Oligozoospermia |
| NCT07402759 | PHASE3 | ACTIVE_NOT_RECRUITING | Impact of tdrd9 Gene Mutations in the Therapeutic Response to L-carnitine in Oligoasthenozoospermic Men |
| NCT01409837 | PHASE2 | COMPLETED | The Effect and Safety of Lisinopril in Non-hypertensive Men With Infertility From Low Sperm Count |
| NCT02234206 | PHASE2 | COMPLETED | A Clinical Trial to Study the Safety and Efficacy of Chandrakanthi Choornam in Patients With Low Sperm Count |
| NCT07481370 | PHASE2 | ENROLLING_BY_INVITATION | Isotretinoin vs hCG for Male Infertility Due to Low or Absent Sperm |
| NCT01880086 | PHASE2 | COMPLETED | Clomiphene Citrate for the Treatment of Low Testosterone Associated With Chronic Opioid Pain Medication Administration |
| NCT02061384 | PHASE2 | COMPLETED | RA-2 13-cis Retinoic Acid (Isotretinoin) |
| NCT02421887 | PHASE2 | COMPLETED | Males, Antioxidants, and Infertility Trial |
| NCT05200663 | PHASE2 | UNKNOWN | Efficacy Comparison of Tamoxifen and Tamoxifen With Antioxidants on Semen Quality of Male With Idiopathic Infertility |
| NCT05290558 | PHASE2 | ACTIVE_NOT_RECRUITING | The Therapeutic Effects of Bu Shen Yi Jing Pill on Semen Quality in Sub Fertile Males: a Randomized Controlled Trial |
| NCT06091969 | PHASE2 | NOT_YET_RECRUITING | Supplementation for Male Subfertility |
| NCT05158114 | PHASE1 | WITHDRAWN | Safety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for Testicular Injury and Oligospermia |
| NCT01595308 | PHASE1 | COMPLETED | A Pilot Study to Evaluate the Effect of Pomegranate Juice on Semen Parameters in Healthy Male Volunteers |
| NCT02122211 | PHASE1 | COMPLETED | Choline Dehydrogenase and Sperm Function: Effects of Betaine |
| NCT02575924 | PHASE1 | UNKNOWN | Influence of Culture Media on Clinical Outcomes in Poor Responders or Severe Male Infertility |
| NCT02063256 | PHASE2/PHASE3 | UNKNOWN | 7 NUTS Study. Diet Modification and Male Fertility. |
| NCT06869863 | PHASE1/PHASE2 | RECRUITING | Study of Tolerability, Safety, Pharmacokinetics, Pharmacodynamics and Preliminary Efficacy of the Medicinal Product MediReg® |
| NCT00479960 | EARLY_PHASE1 | UNKNOWN | A Preliminary Study on Effect of Omega-3 on Human Sperm |
| NCT06342856 | EARLY_PHASE1 | UNKNOWN | Evaluation of Treatment With Coenzyme Q10 and L-Carnitine on Semen Parameters in Infertile Men With Idiopathic Oligoasthenoteratospermia |
| NCT00548977 | Not specified | COMPLETED | Genetic Studies Spermatogenic Failure |
| NCT01239186 | Not specified | COMPLETED | Identification and Characterization of the Methylation Abnormalities on Whole Genome Among Infertile Men |
| NCT01509482 | Not specified | COMPLETED | Insulin Resistance in Idiopathic Oligospermia and Azoospermia |
| NCT01520584 | Not specified | UNKNOWN | Supplement Intake in Infertile Men;the Effect on Sperm Parameters,Fertilization Rate and Embryo Quality |
| NCT01828710 | Not specified | COMPLETED | Myo-inositol on Human Semen Parameters |
| NCT01856361 | Not specified | TERMINATED | Ramipril for the Treatment of Oligospermia |
| NCT02155179 | Not specified | COMPLETED | Sperm Pathology Samples and Morphokinetics |
| NCT03898752 | Not specified | COMPLETED | Is Oxidative Stress in Semen Reduced by Lifestyle Intervention |
| NCT04349345 | Not specified | COMPLETED | Seminal Fluid’s Changes Over 20 Years |
Related Atlas pages
- Associated diseases: spermatogenic failure 57
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): male infertility, oligospermia, spermatogenic failure 57