TBC1D25
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Summary
TBC1D25 (TBC1 domain family member 25, HGNC:8092) is a protein-coding gene on chromosome Xp11.23, encoding TBC1 domain family member 25 (Q3MII6). Acts as a GTPase-activating protein specific for RAB33B.
This gene encodes a protein with a TBC domain and functions as a Rab GTPase activating protein. The encoded protein is involved in the fusion of autophagosomes with endosomes and lysosomes. This gene was previously known as ornithine aminotransferase-like 1, but has no similarity to ornithine aminotransferase.
Source: NCBI Gene 4943 — RefSeq curated summary.
At a glance
- Clinical variants (ClinVar): 95 total — 1 likely-pathogenic
- Phenotypes (HPO): 1
- MANE Select transcript:
NM_002536
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:8092 |
| Approved symbol | TBC1D25 |
| Name | TBC1 domain family member 25 |
| Location | Xp11.23 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000068354 |
| Ensembl biotype | protein_coding |
| OMIM | 311240 |
| Entrez | 4943 |
Gene structure
Transcript identifiers
Ensembl transcripts: 11 — 8 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay
ENST00000376771, ENST00000418627, ENST00000476141, ENST00000481090, ENST00000494495, ENST00000858094, ENST00000858095, ENST00000858096, ENST00000858097, ENST00000941579, ENST00000941580
RefSeq mRNA: 5 — MANE Select: NM_002536
NM_001348262, NM_001348263, NM_001348264, NM_001348265, NM_002536
CCDS: CCDS35242
Canonical transcript exons
ENST00000376771 — 6 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001471631 | 48559614 | 48562609 |
| ENSE00001817600 | 48539714 | 48539920 |
| ENSE00003509057 | 48544869 | 48545023 |
| ENSE00003559308 | 48559158 | 48559346 |
| ENSE00003609249 | 48558897 | 48559024 |
| ENSE00003711017 | 48541333 | 48541442 |
Expression profiles
Bgee: expression breadth ubiquitous, 188 present calls, max score 88.89.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.5594 / max 64.1693, expressed in 1778 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 196257 | 8.5594 | 1778 |
Top tissues by expression
234 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| ileal mucosa | UBERON:0000331 | 88.89 | gold quality |
| tibialis anterior | UBERON:0001385 | 87.44 | silver quality |
| granulocyte | CL:0000094 | 86.02 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 85.96 | gold quality |
| upper arm skin | UBERON:0004263 | 85.25 | gold quality |
| vena cava | UBERON:0004087 | 84.98 | silver quality |
| nasal cavity epithelium | UBERON:0005384 | 84.61 | gold quality |
| kidney epithelium | UBERON:0004819 | 84.54 | gold quality |
| endothelial cell | CL:0000115 | 84.46 | gold quality |
| blood | UBERON:0000178 | 84.35 | gold quality |
| apex of heart | UBERON:0002098 | 83.83 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 83.62 | gold quality |
| cortical plate | UBERON:0005343 | 83.59 | gold quality |
| pancreatic ductal cell | CL:0002079 | 83.49 | silver quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 83.45 | gold quality |
| cerebellar cortex | UBERON:0002129 | 83.37 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 83.31 | gold quality |
| prefrontal cortex | UBERON:0000451 | 83.06 | gold quality |
| heart left ventricle | UBERON:0002084 | 83.06 | gold quality |
| cerebellum | UBERON:0002037 | 82.97 | gold quality |
| gastrocnemius | UBERON:0001388 | 82.93 | gold quality |
| cardiac ventricle | UBERON:0002082 | 82.91 | gold quality |
| deltoid | UBERON:0001476 | 82.48 | silver quality |
| muscle of leg | UBERON:0001383 | 82.42 | gold quality |
| popliteal artery | UBERON:0002250 | 82.28 | gold quality |
| cerebellar vermis | UBERON:0004720 | 82.27 | gold quality |
| tibial artery | UBERON:0007610 | 82.27 | gold quality |
| right atrium auricular region | UBERON:0006631 | 82.25 | gold quality |
| cardiac atrium | UBERON:0002081 | 82.14 | gold quality |
| mucosa of stomach | UBERON:0001199 | 82.12 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-100618 | yes | 158.00 |
| E-ANND-3 | yes | 2.87 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
64 targeting TBC1D25, 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-4534 | 99.99 | 66.58 | 1907 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-196A-1-3P | 99.99 | 72.15 | 2772 |
| HSA-MIR-3692-3P | 99.98 | 70.27 | 2139 |
| HSA-MIR-19A-3P | 99.98 | 75.33 | 2762 |
| HSA-MIR-19B-3P | 99.98 | 75.44 | 2754 |
| HSA-MIR-6825-5P | 99.96 | 69.81 | 3431 |
| HSA-MIR-570-3P | 99.96 | 72.41 | 4910 |
| HSA-MIR-3912-5P | 99.95 | 66.11 | 925 |
| HSA-MIR-8082 | 99.95 | 67.27 | 1170 |
| HSA-MIR-4697-3P | 99.89 | 67.09 | 1123 |
| HSA-MIR-12119 | 99.87 | 68.35 | 1653 |
| HSA-MIR-4739 | 99.84 | 65.25 | 1832 |
| HSA-MIR-1321 | 99.84 | 65.30 | 1811 |
| HSA-MIR-4756-5P | 99.84 | 64.98 | 1809 |
| HSA-MIR-7110-5P | 99.80 | 67.84 | 1712 |
| HSA-MIR-548AG | 99.77 | 69.25 | 1492 |
| HSA-MIR-548AI | 99.69 | 69.24 | 1494 |
| HSA-MIR-548BA | 99.69 | 69.14 | 1514 |
| HSA-MIR-570-5P | 99.69 | 69.24 | 1494 |
| HSA-MIR-4470 | 99.66 | 69.35 | 1767 |
| HSA-MIR-6887-3P | 99.66 | 67.83 | 1778 |
| HSA-MIR-10393-5P | 99.65 | 68.01 | 1368 |
| HSA-MIR-3175 | 99.65 | 66.30 | 2031 |
| HSA-MIR-4516 | 99.61 | 67.78 | 3390 |
| HSA-MIR-888-3P | 99.53 | 69.77 | 1057 |
| HSA-MIR-1207-5P | 99.49 | 69.11 | 2983 |
| HSA-MIR-128-1-5P | 99.33 | 60.46 | 332 |
| HSA-MIR-128-2-5P | 99.33 | 60.83 | 311 |
| HSA-MIR-6808-5P | 99.31 | 66.23 | 2150 |
Literature-anchored findings (GeneRIF, showing 4)
- Our study showed that adenovirus-mediated antisense ODC and expression inhibits tumor cell growth through blocking the polyamine synthesis pathway. (PMID:17558447)
- Studies indicate that each of the 4 genes was associated with at least one main outcome: anxiety (SAT1, SMS), mood disorders (SAT1, SMOX), and suicide attempts (SAT1, OATL1). (PMID:21152090)
- Rab33b, OATL1 and Myo6 have roles in nanoparticle trafficking in HeLa cells (PMID:27374232)
- RabGAP TBC1D25 is involved in human osteoclast activity. (PMID:33353759)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | tbc1d25 | ENSDARG00000075333 |
| mus_musculus | Tbc1d25 | ENSMUSG00000039201 |
| rattus_norvegicus | Tbc1d25 | ENSRNOG00000005303 |
| drosophila_melanogaster | CG8155 | FBGN0034009 |
Paralogs (45): RABGAP1 (ENSG00000011454), TBC1D22A (ENSG00000054611), TBC1D22B (ENSG00000065491), TBC1D1 (ENSG00000065882), EVI5 (ENSG00000067208), TBC1D2 (ENSG00000095383), TBC1D10A (ENSG00000099992), SGSM3 (ENSG00000100359), TBC1D17 (ENSG00000104946), TBC1D13 (ENSG00000107021), TBC1D12 (ENSG00000108239), TBC1D9 (ENSG00000109436), TBC1D30 (ENSG00000111490), TBC1D15 (ENSG00000121749), TBC1D5 (ENSG00000131374), TBC1D14 (ENSG00000132405), TBC1D8B (ENSG00000133138), TBC1D4 (ENSG00000136111), GRTP1 (ENSG00000139835), SGSM2 (ENSG00000141258), EVI5L (ENSG00000142459), TBCK (ENSG00000145348), USP6NL (ENSG00000148429), RABGAP1L (ENSG00000152061), SGSM1 (ENSG00000167037), TBC1D21 (ENSG00000167139), TBC1D2B (ENSG00000167202), TBC1D16 (ENSG00000167291), TBC1D10B (ENSG00000169221), TBC1D10C (ENSG00000175463), TBC1D28 (ENSG00000189375), TBC1D9B (ENSG00000197226), TBC1D8 (ENSG00000204634), TBC1D26 (ENSG00000214946), TBC1D3G (ENSG00000260287), TBC1D3K (ENSG00000273513), TBC1D3H (ENSG00000274226), TBC1D3D (ENSG00000274419), TBC1D3L (ENSG00000274512), TBC1D3 (ENSG00000274611)
Protein
Protein identifiers
TBC1 domain family member 25 — Q3MII6 (reviewed: Q3MII6)
All UniProt accessions (3): Q3MII6, B4DF03, C9JMI8
UniProt curated annotations — full annotation on UniProt →
Function. Acts as a GTPase-activating protein specific for RAB33B. Involved in the regulation of autophagosome maturation, the process in which autophagosomes fuse with endosomes and lysosomes.
Subunit / interactions. Interacts (via N-terminus) with MAP1LC3B, GABARAP and GABARAPL2.
Subcellular location. Cytoplasm. Cytoplasmic vesicle. Autophagosome.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q3MII6-1 | 1 | yes |
| Q3MII6-2 | 2 |
RefSeq proteins (5): NP_001335191, NP_001335192, NP_001335193, NP_001335194, NP_002527* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000195 | Rab-GAP-TBC_dom | Domain |
| IPR035969 | Rab-GAP_TBC_sf | Homologous_superfamily |
Pfam: PF00566
UniProt features (15 total): modified residue 3, splice variant 2, mutagenesis site 2, region of interest 2, compositionally biased region 2, chain 1, domain 1, sequence variant 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q3MII6-F1 | 71.10 | 0.48 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (3): 140, 160, 506
Mutagenesis-validated functional residues (2):
| Position | Phenotype |
|---|---|
| 134–135 | severely affects interaction with gabarap. does not localize at autophagosomes. |
| 136 | abolishes interaction with gabarap. does not localize at autophagosomes. |
Function
Pathways and Gene Ontology
Reactome pathways
4 pathways
| ID | Pathway |
|---|---|
| R-HSA-8854214 | TBC/RABGAPs |
| R-HSA-199991 | Membrane Trafficking |
| R-HSA-5653656 | Vesicle-mediated transport |
| R-HSA-9007101 | Rab regulation of trafficking |
MSigDB gene sets: 85 (showing top):
GOBP_REGULATION_OF_AUTOPHAGY, REACTOME_MEMBRANE_TRAFFICKING, GOBP_MACROAUTOPHAGY, WANG_LMO4_TARGETS_DN, GOBP_REGULATION_OF_CATABOLIC_PROCESS, ATCATGA_MIR433, CAAGGAT_MIR362, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_DISASSEMBLY, GOCC_AUTOPHAGOSOME, GOMF_ENZYME_ACTIVATOR_ACTIVITY, GOMF_NUCLEOSIDE_TRIPHOSPHATASE_REGULATOR_ACTIVITY, CTGTTAC_MIR194, GOMF_ENZYME_REGULATOR_ACTIVITY, CACTGCC_MIR34A_MIR34C_MIR449, chrXp11
GO Biological Process (2): autophagy (GO:0006914), regulation of autophagosome maturation (GO:1901096)
GO Molecular Function (4): GTPase activator activity (GO:0005096), protein binding (GO:0005515), transaminase activity (GO:0008483), transferase activity (GO:0016740)
GO Cellular Component (3): autophagosome (GO:0005776), cytoplasmic vesicle (GO:0031410), cytoplasm (GO:0005737)
Reactome top-level categories
Rollup of top-3 pathways:
| Category | Pathways |
|---|---|
| Rab regulation of trafficking | 1 |
| Vesicle-mediated transport | 1 |
| Membrane Trafficking | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| catabolic process | 1 |
| transmembrane transport | 1 |
| process utilizing autophagic mechanism | 1 |
| regulation of macroautophagy | 1 |
| regulation of organelle organization | 1 |
| regulation of protein-containing complex disassembly | 1 |
| autophagosome maturation | 1 |
| GTPase activity | 1 |
| enzyme activator activity | 1 |
| GTPase regulator activity | 1 |
| binding | 1 |
| transferase activity, transferring nitrogenous groups | 1 |
| catalytic activity | 1 |
| vacuole | 1 |
| cytoplasm | 1 |
| intracellular vesicle | 1 |
| intracellular anatomical structure | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
992 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| TBC1D25 | GABARAPL2 | P60520 | 897 |
| TBC1D25 | F5GZY7 | F5GZY7 | 882 |
| TBC1D25 | USP6 | P35125 | 812 |
| TBC1D25 | CDC16 | Q13042 | 810 |
| TBC1D25 | TFE3 | P19532 | 803 |
| TBC1D25 | RAB33B | Q9H082 | 770 |
| TBC1D25 | ELK1 | P19419 | 761 |
| TBC1D25 | OAT | P04181 | 735 |
| TBC1D25 | ASPSCR1 | Q9BZE9 | 697 |
| TBC1D25 | KCNH3 | Q9ULD8 | 684 |
| TBC1D25 | PRCC | Q92733 | 669 |
| TBC1D25 | RBMY1D | P0C7P1 | 652 |
| TBC1D25 | TBC1D5 | Q92609 | 650 |
| TBC1D25 | RBM3 | P98179 | 645 |
| TBC1D25 | TIMP1 | P01033 | 635 |
IntAct
77 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| GABARAPL2 | TBC1D25 | psi-mi:“MI:0915”(physical association) | 0.740 |
| TBC1D25 | GABARAPL1 | psi-mi:“MI:0915”(physical association) | 0.740 |
| GYPA | TCAF2 | psi-mi:“MI:0914”(association) | 0.640 |
| YWHAH | PLEKHG3 | psi-mi:“MI:0914”(association) | 0.610 |
| ATF4 | TBC1D25 | psi-mi:“MI:0915”(physical association) | 0.590 |
| TBC1D25 | TRIML2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TBC1D25 | LGALS14 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TBC1D25 | MAP1LC3C | psi-mi:“MI:0915”(physical association) | 0.560 |
| TBC1D25 | RUSC1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TBC1D25 | KCNIP1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| RAB2A | TBC1D25 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TBC1D25 | LARP1B | psi-mi:“MI:0915”(physical association) | 0.560 |
| TBC1D25 | FAM9B | psi-mi:“MI:0915”(physical association) | 0.560 |
| TBC1D25 | LMNTD2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TBC1D25 | GABARAP | psi-mi:“MI:0914”(association) | 0.530 |
| YWHAB | PLEKHG3 | psi-mi:“MI:0914”(association) | 0.480 |
| TBC1D25 | SMC3 | psi-mi:“MI:0915”(physical association) | 0.400 |
| HMGB2 | TBC1D25 | psi-mi:“MI:0915”(physical association) | 0.370 |
| PCCA | TBC1D25 | psi-mi:“MI:0914”(association) | 0.350 |
| CREB3L2 | PLEKHG3 | psi-mi:“MI:0914”(association) | 0.350 |
| TBC1D25 | DCLK1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| TBC1D25 | SIPA1L1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| TBC1D25 | GIGYF1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| TBC1D25 | AFDN | psi-mi:“MI:0915”(physical association) | 0.000 |
| EIF4E2 | TBC1D25 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SRGAP2 | TBC1D25 | psi-mi:“MI:0915”(physical association) | 0.000 |
| CDC25B | TBC1D25 | psi-mi:“MI:0915”(physical association) | 0.000 |
| CDK16 | TBC1D25 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (76): TBC1D25 (Reconstituted Complex), TBC1D25 (Reconstituted Complex), TBC1D25 (Affinity Capture-MS), GABARAPL1 (Affinity Capture-MS), GABARAP (Affinity Capture-MS), GABARAPL2 (Affinity Capture-MS), OMA1 (Affinity Capture-MS), TBC1D25 (Affinity Capture-MS), FAM110A (Affinity Capture-MS), TBC1D25 (Affinity Capture-MS), TBC1D25 (Affinity Capture-MS), TBC1D25 (Affinity Capture-MS), FAM110B (Affinity Capture-MS), TBC1D25 (Affinity Capture-MS), TBC1D25 (Affinity Capture-MS)
ESM2 similar proteins: A0A8I3NFE2, A0FI79, A1A5B6, A4D2P6, D7PF45, F1LXF1, O15357, O60346, O75808, P11274, P49796, P52734, P53349, P59672, P70268, P78524, P98174, Q0QWG9, Q13233, Q13905, Q16825, Q3MII6, Q50H33, Q5RDA9, Q62925, Q63433, Q6NS60, Q6P549, Q6PDJ6, Q6WVG3, Q7Z5H3, Q8BL80, Q8BUP8, Q8N2R8, Q8TF61, Q8VHK2, Q8WXD9, Q924W7, Q92625, Q96CX2
Diamond homologs: A1A5B6, O43147, P09379, P48365, Q2NKQ1, Q3MII6, Q6FWI1, Q80U12, Q8BPQ7, Q8BYH7, Q8TBP0, Q8TC07, Q94BY9, Q9CXF4, Q9HA65, Q9UUH7, I2HAA0, Q09830, Q6BU76, Q28CB1, Q8R3D1, Q9NVG8, P48566, Q12344, O95759, O97790, Q5ZJ17, Q60949, Q86TI0, Q8BYJ6, Q9D9D3, Q9Z1A9
SIGNOR signaling
1 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| GABARAP | up-regulates | TBC1D25 | binding |
Disease & clinical
Clinical variants and AI predictions
ClinVar
95 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 1 |
| Uncertain significance | 46 |
| Likely benign | 2 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 816940 | NM_002536.4(TBC1D25):c.4609C>T | Likely pathogenic |
SpliceAI
963 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| X:48541439:GTGG:G | donor_gain | 1.0000 |
| X:48545024:G:GG | donor_gain | 1.0000 |
| X:48559156:AGGT:A | acceptor_gain | 1.0000 |
| X:48559156:AGGTG:A | acceptor_gain | 1.0000 |
| X:48559157:GGT:G | acceptor_gain | 1.0000 |
| X:48559157:GGTG:G | acceptor_gain | 1.0000 |
| X:48559157:GGTGG:G | acceptor_gain | 1.0000 |
| X:48559342:GAAAG:G | donor_gain | 1.0000 |
| X:48559345:AG:A | donor_gain | 1.0000 |
| X:48559346:GG:G | donor_gain | 1.0000 |
| X:48559346:GGT:G | donor_loss | 1.0000 |
| X:48559347:G:GA | donor_loss | 1.0000 |
| X:48559347:G:GG | donor_gain | 1.0000 |
| X:48559607:T:TA | acceptor_gain | 1.0000 |
| X:48559608:G:A | acceptor_gain | 1.0000 |
| X:48559609:GGCA:G | acceptor_loss | 1.0000 |
| X:48559610:GCA:G | acceptor_loss | 1.0000 |
| X:48559612:A:AG | acceptor_gain | 1.0000 |
| X:48559612:AG:A | acceptor_gain | 1.0000 |
| X:48559612:AGGT:A | acceptor_gain | 1.0000 |
| X:48559612:AGGTG:A | acceptor_gain | 1.0000 |
| X:48559613:G:A | acceptor_loss | 1.0000 |
| X:48559613:G:GT | acceptor_gain | 1.0000 |
| X:48559613:GG:G | acceptor_gain | 1.0000 |
| X:48559613:GGT:G | acceptor_gain | 1.0000 |
| X:48559613:GGTG:G | acceptor_gain | 1.0000 |
| X:48559613:GGTGG:G | acceptor_gain | 1.0000 |
| X:48541332:GAAAT:G | acceptor_gain | 0.9900 |
| X:48541441:GG:G | donor_gain | 0.9900 |
| X:48541442:GG:G | donor_gain | 0.9900 |
AlphaMissense
4441 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| X:48541370:T:C | F54S | 1.000 |
| X:48558914:T:A | W136R | 1.000 |
| X:48558914:T:C | W136R | 1.000 |
| X:48559620:T:A | W238R | 1.000 |
| X:48559620:T:C | W238R | 1.000 |
| X:48559771:T:A | V288D | 1.000 |
| X:48559779:G:C | D291H | 1.000 |
| X:48559780:A:C | D291A | 1.000 |
| X:48559780:A:G | D291G | 1.000 |
| X:48559780:A:T | D291V | 1.000 |
| X:48559781:T:A | D291E | 1.000 |
| X:48559781:T:G | D291E | 1.000 |
| X:48559905:G:C | G333R | 1.000 |
| X:48559911:A:C | S335R | 1.000 |
| X:48559913:T:A | S335R | 1.000 |
| X:48559913:T:G | S335R | 1.000 |
| X:48559915:A:G | D336G | 1.000 |
| X:48560092:T:C | L395P | 1.000 |
| X:48560126:T:G | C406W | 1.000 |
| X:48560133:T:A | W409R | 1.000 |
| X:48560133:T:C | W409R | 1.000 |
| X:48560199:T:A | W431R | 1.000 |
| X:48560199:T:C | W431R | 1.000 |
| X:48539910:T:A | V38D | 0.999 |
| X:48541369:T:C | F54L | 0.999 |
| X:48541370:T:G | F54C | 0.999 |
| X:48541371:T:A | F54L | 0.999 |
| X:48541371:T:G | F54L | 0.999 |
| X:48541373:C:A | A55D | 0.999 |
| X:48541376:T:A | V56E | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000001287 (X:48541796 G>A), RS1000143427 (X:48562407 A>G), RS1000433336 (X:48561917 G>A), RS1000483857 (X:48553955 C>T), RS1000597228 (X:48543833 G>A), RS1001112677 (X:48544393 C>T), RS1001597535 (X:48546370 G>A), RS1001719064 (X:48546546 C>G,T), RS1001932783 (X:48556553 G>C), RS1002602212 (X:48548769 A>G), RS1002627996 (X:48539630 C>T), RS1002708510 (X:48549344 C>T), RS1002774423 (X:48538955 C>G,T), RS1003222126 (X:48541663 C>A), RS1003495778 (X:48558473 G>C)
Disease associations
OMIM: gene MIM:311240 | disease phenotypes:
GenCC curated gene-disease
Mondo (1): oligospermia (MONDO:0001913)
Orphanet (0):
HPO phenotypes
1 total (1 of 1 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000798 | Oligozoospermia |
GWAS associations
0 associations (top):
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| 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
16 total (human), top 16 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | decreases expression, increases abundance, increases expression | 2 |
| Benzo(a)pyrene | affects methylation, increases methylation | 2 |
| FR900359 | decreases phosphorylation | 1 |
| triphenyl phosphate | affects expression | 1 |
| 2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline | increases expression | 1 |
| pinosylvin | increases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| acyline | decreases expression | 1 |
| abrine | increases expression | 1 |
| Arsenic | increases abundance, increases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Methotrexate | decreases expression | 1 |
| Progesterone | increases expression | 1 |
| Smoke | decreases expression | 1 |
| Urethane | increases expression | 1 |
| 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide | increases expression | 1 |
Clinical trials (associated diseases)
26 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 |
| NCT00440180 | PHASE3 | TERMINATED | Aromatase Inhibitors in the Treatment of Male Infertility |
| 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 |
| NCT05158114 | PHASE1 | WITHDRAWN | Safety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for Testicular Injury and Oligospermia |
| 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 |
| NCT04795440 | Not specified | COMPLETED | Comparison of ICSI Outcomes in Cycles Using Testicular and Ejaculate Sperm From Couples With High SDF |
| NCT05506722 | Not specified | UNKNOWN | Using of Testes Shocker in Improving the Spermatogenesis and Sperms Activity |
| NCT05842239 | Not specified | RECRUITING | Hyperbaric Oxygen Therapy for Men Suffering From Infertility Due to Oligospermia. |
| NCT06202469 | Not specified | COMPLETED | Creatine and Ubiquinol for Sperm Quality |
| NCT07357701 | Not specified | RECRUITING | Identifying Genome Variants in Non-Obstructive Azoospermia (NOA) or Primary Ovarian Insufficiency (POI) |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): oligospermia