LIN9
gene geneOn this page
Also known as TGS
Summary
LIN9 (lin-9 DREAM MuvB core complex component, HGNC:30830) is a protein-coding gene on chromosome 1q42.12, encoding Protein lin-9 homolog (Q5TKA1). Acts as a tumor suppressor.
This gene encodes a tumor suppressor protein that inhibits DNA synthesis and oncogenic transformation through association with the retinoblastoma 1 protein. The encoded protein also interacts with a complex of other cell cycle regulators to repress cell cycle-dependent gene expression in non-dividing cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.
Source: NCBI Gene 286826 — RefSeq curated summary.
At a glance
- GWAS associations: 6
- Clinical variants (ClinVar): 61 total
- MANE Select transcript:
NM_001366245
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:30830 |
| Approved symbol | LIN9 |
| Name | lin-9 DREAM MuvB core complex component |
| Location | 1q42.12 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | TGS |
| Ensembl gene | ENSG00000183814 |
| Ensembl biotype | protein_coding |
| OMIM | 609375 |
| Entrez | 286826 |
Gene structure
Transcript identifiers
Ensembl transcripts: 12 — 12 protein_coding
ENST00000328205, ENST00000359525, ENST00000366808, ENST00000460719, ENST00000481685, ENST00000681046, ENST00000899464, ENST00000899465, ENST00000899466, ENST00000899467, ENST00000918994, ENST00000918995
RefSeq mRNA: 9 — MANE Select: NM_001366245
NM_001270409, NM_001270410, NM_001366237, NM_001366238, NM_001366239, NM_001366240, NM_001366241, NM_001366245, NM_173083
CCDS: CCDS1553, CCDS91164, CCDS91165
Canonical transcript exons
ENST00000681046 — 15 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001292598 | 226277775 | 226277932 |
| ENSE00001293826 | 226266213 | 226266332 |
| ENSE00001300920 | 226295842 | 226295946 |
| ENSE00001306222 | 226250839 | 226250919 |
| ENSE00001312187 | 226286333 | 226286458 |
| ENSE00001313449 | 226267957 | 226268090 |
| ENSE00001321890 | 226287664 | 226287797 |
| ENSE00001324549 | 226265533 | 226265634 |
| ENSE00001337987 | 226233096 | 226233193 |
| ENSE00001337989 | 226233344 | 226233523 |
| ENSE00001337990 | 226238971 | 226239096 |
| ENSE00001442658 | 226231157 | 226232606 |
| ENSE00003498432 | 226301173 | 226301205 |
| ENSE00003593168 | 226297719 | 226297813 |
| ENSE00003912496 | 226309109 | 226309164 |
Expression profiles
Bgee: expression breadth ubiquitous, 185 present calls, max score 86.67.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.5988 / max 149.6492, expressed in 1348 samples.
FANTOM5 promoters (2 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 17748 | 5.5462 | 1338 |
| 17750 | 0.0526 | 13 |
Top tissues by expression
231 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| ventricular zone | UBERON:0003053 | 86.67 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 85.34 | gold quality |
| ganglionic eminence | UBERON:0004023 | 84.35 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 83.77 | gold quality |
| heart left ventricle | UBERON:0002084 | 79.42 | gold quality |
| cardiac ventricle | UBERON:0002082 | 79.24 | gold quality |
| secondary oocyte | CL:0000655 | 79.07 | silver quality |
| heart right ventricle | UBERON:0002080 | 78.28 | silver quality |
| oocyte | CL:0000023 | 77.32 | gold quality |
| heart | UBERON:0000948 | 75.96 | gold quality |
| apex of heart | UBERON:0002098 | 75.71 | gold quality |
| cortical plate | UBERON:0005343 | 75.66 | gold quality |
| calcaneal tendon | UBERON:0003701 | 75.35 | gold quality |
| rectum | UBERON:0001052 | 73.70 | gold quality |
| right atrium auricular region | UBERON:0006631 | 73.02 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 73.00 | gold quality |
| cardiac atrium | UBERON:0002081 | 72.01 | gold quality |
| stromal cell of endometrium | CL:0002255 | 71.17 | gold quality |
| testis | UBERON:0000473 | 70.36 | gold quality |
| muscle of leg | UBERON:0001383 | 70.22 | gold quality |
| islet of Langerhans | UBERON:0000006 | 70.08 | gold quality |
| gastrocnemius | UBERON:0001388 | 69.87 | gold quality |
| vermiform appendix | UBERON:0001154 | 69.77 | gold quality |
| bone marrow cell | CL:0002092 | 69.72 | silver quality |
| right testis | UBERON:0004534 | 69.65 | gold quality |
| lymph node | UBERON:0000029 | 69.39 | gold quality |
| ovary | UBERON:0000992 | 69.04 | gold quality |
| left testis | UBERON:0004533 | 68.86 | gold quality |
| leukocyte | CL:0000738 | 68.62 | gold quality |
| esophagus mucosa | UBERON:0002469 | 68.53 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 10.95 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
100 targeting LIN9, 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-4795-3P | 100.00 | 74.62 | 4024 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-126-5P | 100.00 | 72.71 | 3180 |
| HSA-MIR-340-5P | 100.00 | 72.50 | 4437 |
| HSA-LET-7A-3P | 100.00 | 74.03 | 3932 |
| HSA-LET-7B-3P | 100.00 | 74.08 | 3913 |
| HSA-LET-7F-1-3P | 100.00 | 74.02 | 3928 |
| HSA-MIR-98-3P | 100.00 | 74.08 | 3907 |
| HSA-MIR-5011-5P | 100.00 | 83.46 | 5820 |
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-196A-1-3P | 99.99 | 72.15 | 2772 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-19A-3P | 99.98 | 75.33 | 2762 |
| HSA-MIR-19B-3P | 99.98 | 75.44 | 2754 |
| HSA-MIR-4803 | 99.98 | 71.99 | 3117 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-LET-7F-2-3P | 99.98 | 70.98 | 2588 |
| HSA-MIR-1185-1-3P | 99.98 | 71.04 | 2593 |
| HSA-MIR-1185-2-3P | 99.98 | 71.04 | 2593 |
| HSA-MIR-4789-5P | 99.98 | 70.76 | 2721 |
| HSA-MIR-12136 | 99.98 | 72.81 | 5713 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-302C-5P | 99.97 | 72.56 | 3642 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-3688-3P | 99.97 | 72.02 | 2834 |
| HSA-MIR-3065-5P | 99.97 | 71.56 | 3281 |
Literature-anchored findings (GeneRIF, showing 12)
- Human Lin-9 has tumor-suppressing activities and the ability of hLin-9 to inhibit transformation is mediated through its association with pRB. (PMID:15538385)
- Mutation of BARA/LIN-9 restores the expression of E2F target genes. (PMID:16730350)
- Mip/LIN-9 is required for the expression of B-Myb, and both proteins collaborate in the control of the cell cycle progression via the regulation of S phase and cyclin A, cyclin B, and CDK1 (PMID:17098733)
- human LIN-9, together with B-MYB, has a critical role in the activation of genes that are essential for progression into mitosis (PMID:17159899)
- The repressor complex that Mip/LIN-9 forms with p107 takes functional precedence over the transcriptional activation linked to the Mip/LIN-9 and B-Myb interaction. (PMID:17563750)
- inactivation of LIN9, a subunit of DREAM, results in premature senescence, which can be overcome by the SV40 large T (LT) antigen (PMID:21860417)
- Study links hTRM9L and tRNA modifications to inhibition of tumour growth via LIN9 and HIF1-alpha-dependent mechanisms. (PMID:23381944)
- Results show that E7 interacts with the B-Myb, FoxM1 and LIN9 components of this activator complex, leading to cooperative transcriptional activation of mitotic genes in primary cells and E7 recruitment to the corresponding promoters. (PMID:24141769)
- LIN-9 phosphorylation on threonine-96 is required for transcriptional activation of LIN-9 target genes and promotes cell cycle progression. (PMID:24475316)
- The MuvB multiprotein complex, together with B-MYB and FOXM1 (MMB-FOXM1) regulate the expression of mitotic kinesins in breast cancer cells. (PMID:28061449)
- High LIN9 expression is associated with Triple-negative breast cancers. (PMID:28807940)
- LIN9 and NEK2 Are Core Regulators of Mitotic Fidelity That Can Be Therapeutically Targeted to Overcome Taxane Resistance. (PMID:32054769)
Cross-species orthologs
6 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | lin9 | ENSDARG00000028475 |
| mus_musculus | Lin9 | ENSMUSG00000058729 |
| rattus_norvegicus | Lin9 | ENSRNOG00000023304 |
| drosophila_melanogaster | aly | FBGN0004372 |
| drosophila_melanogaster | mip130 | FBGN0023509 |
| caenorhabditis_elegans | WBGENE00002998 |
Protein
Protein identifiers
Protein lin-9 homolog — Q5TKA1 (reviewed: Q5TKA1)
Alternative names: Beta subunit-associated regulator of apoptosis, TUDOR gene similar protein, Type I interferon receptor beta chain-associated protein, pRB-associated protein
All UniProt accessions (5): Q5TKA1, B1B047, C9J5J4, H0Y322, H7C4T7
UniProt curated annotations — full annotation on UniProt →
Function. Acts as a tumor suppressor. Inhibits DNA synthesis. Its ability to inhibit oncogenic transformation is mediated through its association with RB1. Plays a role in the expression of genes required for the G1/S transition.
Subunit / interactions. Component of the DREAM complex (also named LINC complex) at least composed of E2F4, E2F5, LIN9, LIN37, LIN52, LIN54, MYBL1, MYBL2, RBL1, RBL2, RBBP4, TFDP1 and TFDP2. The complex exists in quiescent cells where it represses cell cycle-dependent genes. It dissociates in S phase when LIN9, LIN37, LIN52 and LIN54 form a subcomplex that binds to MYBL2. Interacts with RB1.
Subcellular location. Nucleus. Nucleoplasm.
Tissue specificity. Expressed in thymus and testis.
Similarity. Belongs to the lin-9 family.
Isoforms (3)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q5TKA1-1 | 1, Lin9-L, Long form | yes |
| Q5TKA1-2 | 2 | |
| Q5TKA1-3 | 3, Lin9-S, Short form |
RefSeq proteins (9): NP_001257338, NP_001257339, NP_001353166, NP_001353167, NP_001353168, NP_001353169, NP_001353170, NP_001353174, NP_775106 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR010561 | LIN-9/ALY1 | Family |
| IPR033471 | DIRP | Domain |
| IPR045831 | LIN9_C | Domain |
Pfam: PF06584, PF19438
UniProt features (36 total): helix 10, modified residue 7, strand 7, turn 3, splice variant 2, sequence conflict 2, initiator methionine 1, chain 1, cross-link 1, region of interest 1, coiled-coil region 1
Structure
Experimental structures (PDB)
3 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 6C48 | X-RAY DIFFRACTION | 2.32 |
| 7N40 | X-RAY DIFFRACTION | 2.55 |
| 7R1D | ELECTRON MICROSCOPY | 3.5 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q5TKA1-F1 | 71.21 | 0.28 |
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 (8): 321, 21, 2, 65, 95, 96, 304, 309
Function
Pathways and Gene Ontology
Reactome pathways
14 pathways
| ID | Pathway |
|---|---|
| R-HSA-1362277 | Transcription of E2F targets under negative control by DREAM complex |
| R-HSA-1362300 | Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 |
| R-HSA-1538133 | G0 and Early G1 |
| R-HSA-156711 | Polo-like kinase mediated events |
| R-HSA-69202 | Cyclin E associated events during G1/S transition |
| R-HSA-69205 | G1/S-Specific Transcription |
| R-HSA-69656 | Cyclin A:Cdk2-associated events at S phase entry |
| R-HSA-1640170 | Cell Cycle |
| R-HSA-453274 | Mitotic G2-G2/M phases |
| R-HSA-453279 | Mitotic G1 phase and G1/S transition |
| R-HSA-69206 | G1/S Transition |
| R-HSA-69242 | S Phase |
| R-HSA-69275 | G2/M Transition |
| R-HSA-69278 | Cell Cycle, Mitotic |
MSigDB gene sets: 196 (showing top):
RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, TAATAAT_MIR126, REACTOME_G1_S_SPECIFIC_TRANSCRIPTION, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, TATTATA_MIR374, LE_EGR2_TARGETS_UP, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_DNA_BIOSYNTHETIC_PROCESS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FISCHER_DREAM_TARGETS, BERENJENO_TRANSFORMED_BY_RHOA_UP, TTTGCAC_MIR19A_MIR19B, DURCHDEWALD_SKIN_CARCINOGENESIS_DN, GOCC_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATOR_COMPLEX
GO Biological Process (4): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), regulation of cell cycle (GO:0051726), DNA biosynthetic process (GO:0071897)
GO Molecular Function (2): DNA binding (GO:0003677), protein binding (GO:0005515)
GO Cellular Component (3): nucleoplasm (GO:0005654), transcription repressor complex (GO:0017053), nucleus (GO:0005634)
Reactome top-level categories
Rollup of top-8 pathways:
| Category | Pathways |
|---|---|
| Cell Cycle, Mitotic | 3 |
| G0 and Early G1 | 2 |
| Mitotic G1 phase and G1/S transition | 2 |
| G1/S Transition | 2 |
| G2/M Transition | 1 |
| S Phase | 1 |
| Mitotic G2-G2/M phases | 1 |
| Cell Cycle | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| gene expression | 1 |
| RNA biosynthetic process | 1 |
| regulation of DNA-templated transcription | 1 |
| transcription by RNA polymerase II | 1 |
| cell cycle | 1 |
| regulation of cellular process | 1 |
| DNA metabolic process | 1 |
| nucleic acid biosynthetic process | 1 |
| nucleic acid binding | 1 |
| binding | 1 |
| nuclear lumen | 1 |
| cellular anatomical structure | 1 |
| transcription regulator complex | 1 |
| intracellular membrane-bounded organelle | 1 |
Protein interactions and networks
STRING
944 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| LIN9 | LIN37 | Q96GY3 | 999 |
| LIN9 | RBBP4 | P31149 | 999 |
| LIN9 | LIN54 | Q6MZP7 | 999 |
| LIN9 | LIN52 | Q52LA3 | 998 |
| LIN9 | MYBL2 | P10244 | 994 |
| LIN9 | E2F4 | Q16254 | 939 |
| LIN9 | RBL2 | Q08999 | 897 |
| LIN9 | FOXM1 | Q08050 | 753 |
| LIN9 | RB1 | P06400 | 740 |
| LIN9 | E2F5 | Q15329 | 701 |
| LIN9 | MYBL1 | P10243 | 679 |
| LIN9 | MSI1 | O43347 | 665 |
| LIN9 | DPP6 | P42658 | 638 |
| LIN9 | RBBP7 | Q16576 | 625 |
| LIN9 | E2F1 | Q01094 | 608 |
IntAct
81 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CDK2 | CCNE2 | psi-mi:“MI:0914”(association) | 0.940 |
| RBBP7 | CDK2AP1 | psi-mi:“MI:0914”(association) | 0.840 |
| RBBP4 | CDK2AP1 | psi-mi:“MI:0914”(association) | 0.790 |
| LIN37 | RBL2 | psi-mi:“MI:0914”(association) | 0.770 |
| LIN37 | MYBL2 | psi-mi:“MI:0914”(association) | 0.730 |
| LIN9 | MYBL2 | psi-mi:“MI:0914”(association) | 0.720 |
| LIN9 | MYBL2 | psi-mi:“MI:0915”(physical association) | 0.720 |
| MYBL2 | LIN9 | psi-mi:“MI:0915”(physical association) | 0.720 |
| LIN9 | RBL2 | psi-mi:“MI:0914”(association) | 0.700 |
| LIN9 | RBL2 | psi-mi:“MI:0915”(physical association) | 0.700 |
| RBL2 | LIN9 | psi-mi:“MI:0914”(association) | 0.700 |
| E2F4 | LIN9 | psi-mi:“MI:0915”(physical association) | 0.670 |
| LIN54 | RBL2 | psi-mi:“MI:0914”(association) | 0.620 |
| TCF19 | E2F6 | psi-mi:“MI:0914”(association) | 0.620 |
| LIN54 | MYBL2 | psi-mi:“MI:0914”(association) | 0.560 |
| RBL2 | LIN52 | psi-mi:“MI:0914”(association) | 0.560 |
BioGRID (208): LIN9 (Affinity Capture-RNA), LIN9 (Affinity Capture-RNA), LIN9 (Affinity Capture-RNA), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), LIN9 (Proximity Label-MS), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), MYBL2 (Affinity Capture-Western), LIN9 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), MYBL2 (Affinity Capture-MS), LIN54 (Affinity Capture-MS)
ESM2 similar proteins: A0AUQ6, A2BE76, O14645, O18973, O35427, O35473, O55003, O88447, O88597, P50503, Q05B58, Q12983, Q13901, Q14457, Q14AM7, Q14CZ0, Q28HY5, Q32KN2, Q32PE4, Q4A1L3, Q4A1L4, Q4A1L5, Q4R3K5, Q4R8N2, Q4RLT3, Q52LA3, Q5JSJ4, Q5NVP8, Q5R878, Q5RBU4, Q5TKA1, Q5ZHS3, Q5ZJQ3, Q68FJ8, Q6DKA1, Q6GMH0, Q6GP52, Q6PAX8, Q6X4M3, Q7TSU0
Diamond homologs: P30630, Q4R8N2, Q5RHQ8, Q5TKA1, Q6A331, Q6A333, Q8C735, Q6A332
SIGNOR signaling
2 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| CDK3 | up-regulates | LIN9 | phosphorylation |
| CyclinE1/CDK3 | “up-regulates activity” | LIN9 | phosphorylation |
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 73 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| G0 and Early G1 | 11 | 80.5× | 1e-16 |
| Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 | 8 | 80.1× | 3e-12 |
| Transcription of E2F targets under negative control by DREAM complex | 8 | 72.5× | 6e-12 |
| Polo-like kinase mediated events | 6 | 63.4× | 2e-08 |
| Cyclin E associated events during G1/S transition | 10 | 47.6× | 1e-12 |
| G1/S-Specific Transcription | 8 | 47.6× | 3e-10 |
| Cyclin A:Cdk2-associated events at S phase entry | 10 | 44.3× | 2e-12 |
| G1/S Transition | 6 | 23.3× | 1e-05 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| G1/S transition of mitotic cell cycle | 6 | 17.2× | 2e-04 |
| chromatin remodeling | 8 | 8.3× | 5e-04 |
| transcription by RNA polymerase II | 8 | 8.1× | 5e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
61 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 43 |
| Likely benign | 0 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2294 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:226233092:TTAC:T | donor_loss | 1.0000 |
| 1:226233093:TA:T | donor_loss | 1.0000 |
| 1:226233094:ACCTG:A | donor_loss | 1.0000 |
| 1:226233095:CCT:C | donor_loss | 1.0000 |
| 1:226233189:AGACA:A | acceptor_gain | 1.0000 |
| 1:226233190:GACA:G | acceptor_gain | 1.0000 |
| 1:226233191:ACA:A | acceptor_gain | 1.0000 |
| 1:226233192:CA:C | acceptor_gain | 1.0000 |
| 1:226233192:CAC:C | acceptor_gain | 1.0000 |
| 1:226233193:ACTAA:A | acceptor_loss | 1.0000 |
| 1:226233194:C:CC | acceptor_gain | 1.0000 |
| 1:226234555:T:TA | donor_gain | 1.0000 |
| 1:226238966:CTTA:C | donor_loss | 1.0000 |
| 1:226238967:TTA:T | donor_loss | 1.0000 |
| 1:226238968:TAC:T | donor_loss | 1.0000 |
| 1:226238969:A:AC | donor_gain | 1.0000 |
| 1:226238969:AC:A | donor_gain | 1.0000 |
| 1:226238969:ACCT:A | donor_gain | 1.0000 |
| 1:226238969:ACCTC:A | donor_loss | 1.0000 |
| 1:226238970:C:CT | donor_gain | 1.0000 |
| 1:226238970:CC:C | donor_gain | 1.0000 |
| 1:226238970:CCT:C | donor_gain | 1.0000 |
| 1:226238970:CCTC:C | donor_gain | 1.0000 |
| 1:226238970:CCTCA:C | donor_gain | 1.0000 |
| 1:226239092:GATTT:G | acceptor_gain | 1.0000 |
| 1:226239093:ATTT:A | acceptor_gain | 1.0000 |
| 1:226239094:TTT:T | acceptor_gain | 1.0000 |
| 1:226239095:TT:T | acceptor_gain | 1.0000 |
| 1:226239096:TCTGA:T | acceptor_loss | 1.0000 |
| 1:226239097:C:CC | acceptor_gain | 1.0000 |
AlphaMissense
0 scored. Top likely-pathogenic:
dbSNP variants (sampled 300 via entrez): RS1000015635 (1:226242792 C>T), RS1000063352 (1:226272721 C>T), RS1000110835 (1:226302913 C>T), RS1000149119 (1:226281776 C>T), RS1000201485 (1:226306004 T>C), RS1000217648 (1:226255064 A>C), RS1000244189 (1:226281574 G>C), RS1000307871 (1:226306248 C>T), RS1000392661 (1:226293828 T>A), RS1000407826 (1:226268111 T>C), RS1000429070 (1:226255289 T>C), RS1000490239 (1:226300181 G>A,C,T), RS1000516214 (1:226305027 G>A), RS1000544749 (1:226261140 A>T), RS1000545526 (1:226256616 T>C)
Disease associations
OMIM: gene MIM:609375 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
6 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST009257_10 | Caudate nucleus volume | 2.000000e-06 |
| GCST010105_147 | Nicotine dependence symptom count | 6.000000e-06 |
| GCST010816_6 | Gut microbiota beta diversity (weighted UniFrac distance) | 8.000000e-06 |
| GCST012489_97 | Heel bone mineral density x serum urate levels interaction | 9.000000e-09 |
| GCST90002390_340 | Mean corpuscular hemoglobin | 3.000000e-11 |
| GCST90002395_508 | Mean platelet volume | 5.000000e-12 |
EFO canonical traits (6, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004830 | caudate nucleus volume |
| EFO:0009262 | nicotine dependence symptom count |
| EFO:0007874 | gut microbiome measurement |
| EFO:0004531 | urate measurement |
| EFO:0009270 | heel bone mineral density |
| EFO:0004527 | mean corpuscular hemoglobin |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
32 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects expression, decreases expression | 4 |
| aristolochic acid I | decreases expression | 1 |
| FR900359 | affects phosphorylation | 1 |
| dicrotophos | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| propionaldehyde | decreases expression | 1 |
| bisphenol A | increases methylation | 1 |
| arsenite | decreases reaction, affects binding | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | decreases expression | 1 |
| potassium chromate(VI) | affects cotreatment, decreases expression | 1 |
| aflatoxin B2 | decreases methylation | 1 |
| coumarin | increases phosphorylation | 1 |
| epigallocatechin gallate | affects cotreatment, decreases expression | 1 |
| 2-palmitoylglycerol | increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Ethanol | decreases expression | 1 |
| Atrazine | decreases expression | 1 |
| Benzo(a)pyrene | increases methylation | 1 |
| Caffeine | affects phosphorylation | 1 |
| Calcitriol | decreases expression, affects cotreatment | 1 |
| Cisplatin | increases expression | 1 |
| Dichlorodiphenyl Dichloroethylene | increases expression | 1 |
| Lead | affects expression | 1 |
| Lucanthone | decreases expression | 1 |
| Testosterone | decreases expression, affects cotreatment | 1 |
| Tetrachlorodibenzodioxin | affects expression | 1 |
| Thimerosal | increases expression | 1 |
| Tobacco Smoke Pollution | decreases expression | 1 |
| Tretinoin | decreases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.