TRIM9

Summary

TRIM9 (tripartite motif containing 9, HGNC:16288) is a protein-coding gene on chromosome 14q22.1, encoding E3 ubiquitin-protein ligase TRIM9 (Q9C026). E3 ubiquitin-protein ligase which ubiquitinates itself in cooperation with an E2 enzyme UBE2D2/UBC4 and serves as a targeting signal for proteasomal degradation.

The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies. Its function has not been identified. Alternate splicing of this gene generates two transcript variants encoding different isoforms.

Source: NCBI Gene 114088 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 67 total
• MANE Select transcript: NM_001387360

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16288
Approved symbol	TRIM9
Name	tripartite motif containing 9
Location	14q22.1
Locus type	gene with protein product
Status	Approved
Aliases	SPRING, RNF91
Ensembl gene	ENSG00000100505
Ensembl biotype	protein_coding
OMIM	606555
Entrez	114088

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000298355, ENST00000338969, ENST00000360392, ENST00000555170, ENST00000555933, ENST00000557456, ENST00000684578, ENST00000910718, ENST00000910719, ENST00000910720, ENST00000910721, ENST00000910722, ENST00000910723, ENST00000910724, ENST00000917874, ENST00000968505

RefSeq mRNA: 23 — MANE Select: NM_001387360 NM_001387360, NM_001387361, NM_001387362, NM_001387363, NM_001387364, NM_001387365, NM_001387366, NM_001387367, NM_001387368, NM_001387369, NM_001387370, NM_001387371, NM_001387372, NM_001387373, NM_001387374, NM_001387375, NM_001387376, NM_001387377, NM_001387378, NM_001387379, NM_001387380, NM_015163, NM_052978

CCDS: CCDS45105, CCDS91879, CCDS9703

Canonical transcript exons

ENST00000684578 — 13 exons

Exon	Start	End
ENSE00000657201	50981800	50982103
ENSE00000657203	50998050	50998188
ENSE00000657205	51000683	51000840
ENSE00000657206	51009080	51009233
ENSE00000657207	51010384	51010494
ENSE00001094099	51025265	51025360
ENSE00001094103	51022835	51022957
ENSE00001367396	50979387	50979549
ENSE00001372688	50982942	50982965
ENSE00003523579	50983380	50983421
ENSE00003667123	50985956	50986144
ENSE00003917584	51094118	51095105
ENSE00003917819	50975266	50977353

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 99.49.

FANTOM5 (CAGE): breadth broad, TPM avg 10.1883 / max 541.8684, expressed in 663 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
143186	8.6854	591
143188	0.7193	167
143190	0.4593	116
143189	0.2845	95
143187	0.0398	27

Top tissues by expression

290 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	99.49	gold quality
cerebellar hemisphere	UBERON:0002245	99.35	gold quality
cerebellar cortex	UBERON:0002129	99.30	gold quality
cerebellum	UBERON:0002037	99.00	gold quality
right frontal lobe	UBERON:0002810	98.16	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.12	gold quality
primary visual cortex	UBERON:0002436	97.98	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.44	gold quality
CA1 field of hippocampus	UBERON:0003881	97.33	gold quality
occipital lobe	UBERON:0002021	96.97	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	96.61	gold quality
middle temporal gyrus	UBERON:0002771	96.58	gold quality
ventricular zone	UBERON:0003053	96.43	gold quality
nucleus accumbens	UBERON:0001882	96.41	gold quality
caudate nucleus	UBERON:0001873	95.78	gold quality
frontal cortex	UBERON:0001870	95.37	gold quality
neocortex	UBERON:0001950	95.35	gold quality
frontal lobe	UBERON:0016525	95.35	gold quality
cingulate cortex	UBERON:0003027	95.31	gold quality
endothelial cell	CL:0000115	95.28	gold quality
prefrontal cortex	UBERON:0000451	95.26	gold quality
anterior cingulate cortex	UBERON:0009835	95.25	gold quality
cerebral cortex	UBERON:0000956	95.16	gold quality
telencephalon	UBERON:0001893	95.14	gold quality
putamen	UBERON:0001874	95.07	gold quality
amygdala	UBERON:0001876	95.00	gold quality
brain	UBERON:0000955	94.87	gold quality
central nervous system	UBERON:0001017	94.68	gold quality
forebrain	UBERON:0001890	94.60	gold quality
Ammon’s horn	UBERON:0001954	94.54	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-11	yes	58.17
E-GEOD-84465	yes	22.49
E-ANND-3	no	5.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

147 targeting TRIM9, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515

Literature-anchored findings (GeneRIF, showing 10)

• These results suggest that TRIM9 plays an important role in the regulation of neuronal functions and participates in pathological process of Lewy body disease through its ligase activity. (PMID:20085810)
• TRIM9 is a brain-specific negative regulator of the NF-kappaB pro-inflammatory signalling pathway. (PMID:25190485)
• TRIM9s undergoes Lys-63-linked auto-polyubiquitination and serves as a platform to bridge GSK3beta to TBK1, leading to the activation of IRF3 signaling. (PMID:26915459)
• Authors demonstrate that tripartite motif protein 9 (TRIM9)-dependent ubiquitination of DCC blocks the interaction with and phosphorylation of FAK. (PMID:28701345)
• TRIM9s promotes the K63-linked ubiquitination of MKK6 at Lys82, thus inhibiting the degradative K48-linked ubiquitination of MKK6 at the same lysine. MKK6 could also stabilize TRIM9s by promoting the phosphorylation of TRIM9s at Ser76/80 via p38, thereby blocking the ubiquitin-proteasome pathway. (PMID:29669288)
• Findings reveal that TRIM9 is essential for resolving NF-kappaB-dependent neuroinflammation to promote recovery and repair after brain injury. (PMID:30970257)
• TRIM9 overexpression promotes uterine leiomyoma cell proliferation and inhibits cell apoptosis via NF-kappaB signaling pathway. (PMID:32679146)
• Targeting TRIM9 by miR-218-5p Restricts Cell Proliferation and Epithelial-Mesenchymal Transition in Non-Small Cell Lung Cancer. (PMID:36889762)
• TRIM9 Interacts with ZEB1 to Suppress Esophageal Cancer by Promoting ZEB1 Protein Degradation via the UPP Pathway. (PMID:37124931)
• A new SPRING in lipid metabolism. (PMID:37548386)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	trim9	ENSDARG00000039123
mus_musculus	Trim9	ENSMUSG00000021071
rattus_norvegicus	Trim9	ENSRNOG00000007031

Paralogs (80): MID2 (ENSG00000080561), MID1 (ENSG00000101871), MEFV (ENSG00000103313), TRIM35 (ENSG00000104228), TRIM14 (ENSG00000106785), TRIM37 (ENSG00000108395), TRIM2 (ENSG00000109654), TRIM3 (ENSG00000110171), TRIM38 (ENSG00000112343), TRIM62 (ENSG00000116525), TRIM67 (ENSG00000119283), TRIM32 (ENSG00000119401), BSPRY (ENSG00000119411), TRIM25 (ENSG00000121060), TRIM6 (ENSG00000121236), TRIM24 (ENSG00000122779), TRIM51 (ENSG00000124900), TRIM28 (ENSG00000130726), TRIM21 (ENSG00000132109), TRIM5 (ENSG00000132256), TRIM22 (ENSG00000132274), TRIM47 (ENSG00000132481), TRIM45 (ENSG00000134253), TRIM29 (ENSG00000137699), TRIM54 (ENSG00000138100), PML (ENSG00000140464), TRIM65 (ENSG00000141569), TRIM43B (ENSG00000144010), TRIM43 (ENSG00000144015), TRIM7 (ENSG00000146054), TRIM41 (ENSG00000146063), TRIM50 (ENSG00000146755), TRIM4 (ENSG00000146833), TRIM55 (ENSG00000147573), TRIM48 (ENSG00000150244), TRIM36 (ENSG00000152503), TRIM11 (ENSG00000154370), TRIM74 (ENSG00000155428), TRIM42 (ENSG00000155890), TRIM63 (ENSG00000158022)

Protein

Protein identifiers

E3 ubiquitin-protein ligase TRIM9 — Q9C026 (reviewed: Q9C026)

Alternative names: RING finger protein 91, RING-type E3 ubiquitin transferase TRIM9, Tripartite motif-containing protein 9

All UniProt accessions (2): Q9C026, A0A804HIL7

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase which ubiquitinates itself in cooperation with an E2 enzyme UBE2D2/UBC4 and serves as a targeting signal for proteasomal degradation. May play a role in regulation of neuronal functions and may also participate in the formation or breakdown of abnormal inclusions in neurodegenerative disorders. May act as a regulator of synaptic vesicle exocytosis by controlling the availability of SNAP25 for the SNARE complex formation.

Subunit / interactions. Interacts with SNAP25.

Subcellular location. Cytoplasm. Cell projection. Dendrite. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle. Synapse. Cytoskeleton.

Tissue specificity. Brain. Highly expressed in the cerebral cortex (at protein level). Severely decreased in the affected brain areas in Parkinson disease and dementia with Lewy bodies.

Post-translational modifications. Auto-ubiquitinated. Poly-ubiquitinated in cultured cells, whereas it is monoubiquitinated in vitro.

Domain organisation. The coiled coil domain mediates the interaction with the N-terminal t-SNARE domain of SNAP25.

Pathway. Protein modification; protein ubiquitination.

Miscellaneous. May be due to a competing donor splice site, to exon inclusion and to intron retention. May be due to intron retention.

Similarity. Belongs to the TRIM/RBCC family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9C026-1	1, Beta	yes
Q9C026-4	4
Q9C026-5	5

RefSeq proteins (23): NP_001374289, NP_001374290, NP_001374291, NP_001374292, NP_001374293, NP_001374294, NP_001374295, NP_001374296, NP_001374297, NP_001374298, NP_001374299, NP_001374300, NP_001374301, NP_001374302, NP_001374303, NP_001374304, NP_001374305, NP_001374306, NP_001374307, NP_001374308, NP_001374309, NP_055978, NP_443210 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000315	Znf_B-box	Domain
IPR001841	Znf_RING	Domain
IPR001870	B30.2/SPRY	Domain
IPR003649	Bbox_C	Domain
IPR003877	SPRY_dom	Domain
IPR003961	FN3_dom	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR013783	Ig-like_fold	Homologous_superfamily
IPR017903	COS_domain	Domain
IPR017907	Znf_RING_CS	Conserved_site
IPR018957	Znf_C3HC4_RING-type	Domain
IPR036116	FN3_sf	Homologous_superfamily
IPR043136	B30.2/SPRY_sf	Homologous_superfamily
IPR049582	TRIM9_Bbox1	Domain
IPR050617	E3_ligase_FN3/SPRY	Family

Pfam: PF00041, PF00097, PF00622, PF00643, PF22586

UniProt features (51 total): strand 20, binding site 8, splice variant 5, modified residue 4, domain 3, zinc finger region 3, sequence conflict 2, turn 2, chain 1, sequence variant 1, helix 1, coiled-coil region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7B2S	X-RAY DIFFRACTION	1.5
2DB8	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9C026-F1	83.51	0.58

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 193; 198; 229; 232; 252; 258; 168; 171

Post-translational modifications (4): 41, 44, 46, 49

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation

MSigDB gene sets: 170 (showing top): BENPORATH_ES_WITH_H3K27ME3, LUCAS_HNF4A_TARGETS_DN, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, AGGCACT_MIR5153P, MODULE_66, SMID_BREAST_CANCER_LUMINAL_B_UP, BACH2_01, MODULE_99, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP, TGANTCA_AP1_C, TGACATY_UNKNOWN

GO Biological Process (2): protein ubiquitination (GO:0016567), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (7): zinc ion binding (GO:0008270), protein domain specific binding (GO:0019904), protein homodimerization activity (GO:0042803), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (7): cytoplasm (GO:0005737), cytoskeleton (GO:0005856), synaptic vesicle (GO:0008021), dendrite (GO:0030425), cytoplasmic vesicle (GO:0031410), cell projection (GO:0042995), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Class I MHC mediated antigen processing & presentation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
protein modification by small protein conjugation	1
ubiquitin-dependent protein catabolic process	1
proteasomal protein catabolic process	1
transition metal ion binding	1
protein binding	1
identical protein binding	1
protein dimerization activity	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein ligase activity	1
binding	1
catalytic activity	1
cation binding	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
exocytic vesicle	1
presynapse	1
neuron projection	1
dendritic tree	1
cytoplasm	1
intracellular vesicle	1
cell junction	1

Protein interactions and networks

STRING

1718 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRIM9	BBOX1	O75936	862
TRIM9	TRAT1	Q6PIZ9	862
TRIM9	TRIM17	Q9Y577	793
TRIM9	SNAP25	P13795	731
TRIM9	UBE2G2	P56554	712
TRIM9	VASP	P50552	701
TRIM9	DCC	P43146	693
TRIM9	TRIM32	Q13049	640
TRIM9	BTRC	Q9Y297	640
TRIM9	TRIM68	Q6AZZ1	563
TRIM9	CACTIN	Q8WUQ7	561
TRIM9	NTN1	O95631	537
TRIM9	TRIM44	Q96DX7	525
TRIM9	TRIM39	Q9HCM9	509
TRIM9	G3V2F7	G3V2F7	505

IntAct

128 interactions, top by confidence:

A	B	Type	Score
TRIM9	BTRC	psi-mi:“MI:0915”(physical association)	0.830
BTRC	TRIM9	psi-mi:“MI:0915”(physical association)	0.830
RELL2	OXSR1	psi-mi:“MI:0914”(association)	0.830
TRIM9	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
SPG21	TRIM9	psi-mi:“MI:0915”(physical association)	0.720
TRIM9	SPG21	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	TRIM9	psi-mi:“MI:0915”(physical association)	0.720
VASP	TRIM9	psi-mi:“MI:0915”(physical association)	0.670
NFKB1	NFKBIE	psi-mi:“MI:2364”(proximity)	0.600
CSNK1D	TRIM9	psi-mi:“MI:0915”(physical association)	0.560
TRIM9	NFKBID	psi-mi:“MI:0915”(physical association)	0.560
GFM2	TRIM9	psi-mi:“MI:0915”(physical association)	0.560
MUL1	TRIM9	psi-mi:“MI:0915”(physical association)	0.560
TRIM9	TSSK3	psi-mi:“MI:0915”(physical association)	0.560
TRIM9	EVL	psi-mi:“MI:0915”(physical association)	0.560
TRIM9	AP3M1	psi-mi:“MI:0915”(physical association)	0.560
TRIM9	GFM2	psi-mi:“MI:0915”(physical association)	0.560
TRIM9	MUL1	psi-mi:“MI:0915”(physical association)	0.560
TSSK3	TRIM9	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (295): BTRC (Affinity Capture-MS), ACTA2 (Affinity Capture-MS), FBXW11 (Affinity Capture-MS), BTRC (Affinity Capture-Western), FBXW11 (Affinity Capture-Western), TRIM9 (Affinity Capture-Western), TRIM9 (Affinity Capture-Western), TRIM9 (Affinity Capture-MS), TRIM9 (Affinity Capture-MS), TRIM9 (Two-hybrid), TRIM9 (Two-hybrid), TRIM9 (Two-hybrid), TRIM9 (Two-hybrid), TRIM9 (Two-hybrid), TRIM9 (Two-hybrid)

ESM2 similar proteins: A1L0Y2, A2ALK8, A2ARP1, A2Z8S0, A4IFG2, A8XT88, B1AVZ0, B3M1E1, B3P4N5, B4GZ20, B4HJC0, B4KA23, B4LVS8, B4NKI9, B4PVH6, B4QVW6, M9MRI4, O35242, O76050, P0C644, P26045, Q18223, Q29B63, Q29RQ5, Q3MHZ2, Q3UJK4, Q571F5, Q5M870, Q5NCX5, Q5PQR3, Q5R881, Q6PFW1, Q6PJ21, Q75G68, Q8BVR6, Q8C726, Q8CJC5, Q8R516, Q91YL3, Q91ZY8

Diamond homologs: A0A0G2JXN2, A0JN74, A0JPQ4, A5D7F8, A5D8S5, A6NGJ6, A6NI03, B6VQ60, E1BD59, F6ZQ54, G3X8Y1, O60858, P15533, P86449, Q03601, Q1ACD6, Q1ACD7, Q28E95, Q29RQ5, Q2KHN1, Q2YEM8, Q2YEM9, Q32L60, Q38HM4, Q3TL54, Q3ZEE5, Q503I2, Q505D9, Q5C8T6, Q5C8T8, Q5C8U3, Q5D7H7, Q5D7I2, Q5D7I3, Q5EBN2, Q5M7V1, Q5M929, Q5PQN5, Q5RBR0, Q5RKG6

SIGNOR signaling

4 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	TRIM9	ubiquitination
TRIM9	“down-regulates quantity by destabilization”	TRIM9	ubiquitination
UBE2D2	“up-regulates activity”	TRIM9	binding
TRIM9	“down-regulates quantity”	VASP	ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 80 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
Translocation of SLC2A4 (GLUT4) to the plasma membrane	5	15.1×	4e-03
Regulation of PLK1 Activity at G2/M Transition	6	14.9×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
protein destabilization	6	24.6×	1e-04
protein polyubiquitination	6	9.8×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

67 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	59
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2319 predictions. Top by Δscore:

Variant	Effect	Δscore
14:50979381:GCTTA:G	donor_loss	1.0000
14:50979382:CTTA:C	donor_loss	1.0000
14:50979383:TTACC:T	donor_loss	1.0000
14:50979384:TA:T	donor_loss	1.0000
14:50979385:A:T	donor_loss	1.0000
14:50979386:C:CT	donor_loss	1.0000
14:51010380:TTA:T	donor_loss	1.0000
14:51010381:TAC:T	donor_loss	1.0000
14:51010382:A:AT	donor_loss	1.0000
14:51022830:CTCA:C	donor_loss	1.0000
14:51022831:TCA:T	donor_loss	1.0000
14:51022832:CA:C	donor_loss	1.0000
14:51022833:A:AT	donor_loss	1.0000
14:51022834:C:CT	donor_loss	1.0000
14:51025260:CATA:C	donor_loss	1.0000
14:51025261:ATAC:A	donor_loss	1.0000
14:51025262:TACCT:T	donor_loss	1.0000
14:51025263:A:AG	donor_loss	1.0000
14:51025264:C:A	donor_loss	1.0000
14:51025356:TGGCT:T	acceptor_gain	1.0000
14:50979545:CAGTT:C	acceptor_gain	0.9900
14:50979550:C:CC	acceptor_gain	0.9900
14:50981794:GGGTA:G	donor_loss	0.9900
14:50981795:GGTAC:G	donor_loss	0.9900
14:50981796:GTAC:G	donor_loss	0.9900
14:50981797:TA:T	donor_loss	0.9900
14:50981798:ACCTG:A	donor_loss	0.9900
14:50981799:C:CT	donor_loss	0.9900
14:50982100:GCCA:G	acceptor_gain	0.9900
14:50982100:GCCAC:G	acceptor_loss	0.9900

AlphaMissense

5258 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:50979405:G:C	S684R	1.000
14:50979405:G:T	S684R	1.000
14:50979407:T:G	S684R	1.000
14:50979412:G:T	A682E	1.000
14:50979505:A:G	L651P	1.000
14:50979549:T:A	R636S	1.000
14:50979549:T:G	R636S	1.000
14:50981800:C:G	R636T	1.000
14:50981808:G:C	H633Q	1.000
14:50981808:G:T	H633Q	1.000
14:50981810:G:C	H633D	1.000
14:50981829:C:A	W626C	1.000
14:50981829:C:G	W626C	1.000
14:50981831:A:G	W626R	1.000
14:50981831:A:T	W626R	1.000
14:50981832:G:C	S625R	1.000
14:50981832:G:T	S625R	1.000
14:50981834:T:G	S625R	1.000
14:50981836:C:G	R624P	1.000
14:50981845:T:A	D621V	1.000
14:50981846:C:G	D621H	1.000
14:50981852:A:G	Y619H	1.000
14:50981858:C:G	A617P	1.000
14:50981878:C:A	G610V	1.000
14:50981878:C:T	G610E	1.000
14:50981879:C:G	G610R	1.000
14:50981879:C:T	G610R	1.000
14:50981881:A:G	L609S	1.000
14:50981911:G:T	A599D	1.000
14:50981917:C:T	G597D	1.000

dbSNP variants (sampled 300 via entrez): RS1000011370 (14:51057855 G>A,C), RS1000033057 (14:51066487 C>G,T), RS1000048087 (14:51027407 G>A,T), RS1000205997 (14:51008800 A>G), RS1000236939 (14:51030316 C>A), RS1000270255 (14:51060574 C>T), RS1000299984 (14:51050536 T>A), RS1000315372 (14:51079568 T>C,G), RS1000385696 (14:51033648 G>A,C,T), RS1000402233 (14:51071293 T>C), RS1000407071 (14:51066724 A>G), RS1000414485 (14:51012126 G>A,C), RS1000457334 (14:51008778 A>G), RS1000462902 (14:51002908 T>G), RS1000472124 (14:51094405 T>A)

Disease associations

OMIM: gene MIM:606555 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002211_4	Psychosis (atypical)	8.000000e-07
GCST002826_6	Urate levels (BMI interaction)	9.000000e-06
GCST003445_12	Response to cyclophosphamide in systemic lupus erythematosus with lupus nephritis	7.000000e-06
GCST005173_47	Coronary artery calcified atherosclerotic plaque (130 HU threshold) in type 2 diabetes	9.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004531	urate measurement
EFO:0004723	coronary artery calcification

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	6
trichostatin A	affects cotreatment, increases expression	3
Vorinostat	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
sotorasib	decreases expression, affects cotreatment	1
terbufos	increases methylation	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
tobacco tar	decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Irinotecan	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Carbamazepine	affects expression	1
Doxorubicin	increases expression	1
Fonofos	increases methylation	1
Endosulfan	decreases expression	1
Nickel	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TU61	HAP1 TRIM9 (-) 1	Cancer cell line	Male
CVCL_TU62	HAP1 TRIM9 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.