TRIM39

Summary

TRIM39 (tripartite motif containing 39, HGNC:10065) is a protein-coding gene on chromosome 6p22.1, encoding E3 ubiquitin-protein ligase TRIM39 (Q9HCM9). E3 ubiquitin-protein ligase.

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 function of this protein has not been identified. This gene lies within the major histocompatibility complex class I region on chromosome 6. Alternate splicing results in two transcript variants encoding different isoforms.

Source: NCBI Gene 56658 — RefSeq curated summary.

At a glance

• GWAS associations: 22
• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_001369521

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10065
Approved symbol	TRIM39
Name	tripartite motif containing 39
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204599
Ensembl biotype	protein_coding
OMIM	605700
Entrez	56658

Gene structure

Transcript identifiers

Ensembl transcripts: 37 — 37 protein_coding

ENST00000376656, ENST00000376659, ENST00000396547, ENST00000396548, ENST00000396551, ENST00000420746, ENST00000428404, ENST00000428555, ENST00000428728, ENST00000440271, ENST00000458516, ENST00000883577, ENST00000883578, ENST00000883579, ENST00000883580, ENST00000883581, ENST00000883582, ENST00000883583, ENST00000883584, ENST00000883585, ENST00000883586, ENST00000883587, ENST00000883588, ENST00000883589, ENST00000929418, ENST00000929419, ENST00000929420, ENST00000929421, ENST00000929422, ENST00000929423, ENST00000929424, ENST00000929425, ENST00000944928, ENST00000944929, ENST00000944930, ENST00000944931, ENST00000944932

RefSeq mRNA: 5 — MANE Select: NM_001369521 NM_001369521, NM_001369522, NM_001369523, NM_021253, NM_172016

CCDS: CCDS34377, CCDS34378

Canonical transcript exons

ENST00000396551 — 8 exons

Exon	Start	End
ENSE00001773189	30341712	30343729
ENSE00002510808	30328889	30329041
ENSE00002522130	30329311	30329770
ENSE00003490105	30330781	30330876
ENSE00003506162	30335745	30335975
ENSE00003553555	30339908	30339930
ENSE00003571317	30340505	30340620
ENSE00003978192	30326927	30326995

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 87.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.1424 / max 325.1018, expressed in 1750 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66713	3.5277	1560
66714	2.0422	1032
66716	0.7601	308
66712	0.5425	206
66715	0.2119	68
66717	0.0580	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	87.39	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.86	gold quality
left testis	UBERON:0004533	85.69	gold quality
testis	UBERON:0000473	85.67	gold quality
blood	UBERON:0000178	85.43	gold quality
right testis	UBERON:0004534	85.41	gold quality
calcaneal tendon	UBERON:0003701	85.22	gold quality
popliteal artery	UBERON:0002250	84.97	gold quality
tibial artery	UBERON:0007610	84.97	gold quality
mucosa of stomach	UBERON:0001199	84.87	gold quality
lower esophagus mucosa	UBERON:0035834	84.73	gold quality
lower esophagus	UBERON:0013473	84.51	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.51	gold quality
sural nerve	UBERON:0015488	84.41	gold quality
gastrocnemius	UBERON:0001388	84.09	gold quality
descending thoracic aorta	UBERON:0002345	83.91	gold quality
muscle of leg	UBERON:0001383	83.90	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	83.84	gold quality
bone marrow	UBERON:0002371	83.77	gold quality
pituitary gland	UBERON:0000007	83.68	gold quality
muscle layer of sigmoid colon	UBERON:0035805	83.67	gold quality
esophagus	UBERON:0001043	83.58	gold quality
adenohypophysis	UBERON:0002196	83.51	gold quality
smooth muscle tissue	UBERON:0001135	83.11	gold quality
esophagus mucosa	UBERON:0002469	83.11	gold quality
thoracic aorta	UBERON:0001515	83.05	gold quality
fallopian tube	UBERON:0003889	82.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.94	gold quality
ascending aorta	UBERON:0001496	82.90	gold quality
urinary bladder	UBERON:0001255	82.89	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

88 targeting TRIM39, 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-3064-3P	100.00	70.09	1254
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-6722-3P	99.45	67.62	1919

Literature-anchored findings (GeneRIF, showing 9)

• Data suggest that TRIM39 can promote apoptosis signalling through stabilization of MOAP-1. (PMID:19100260)
• these findings suggest that RNF39 and TRIM39 are involved in the etiology of Behcet’s disease. (PMID:20875797)
• TRIM39 has a role in regulating cell cycle progression and the balance between cytostasis and apoptosis after DNA damage via stabilizing p21 (PMID:23213251)
• analysis of ubiquitylation of p53 by the APC/C inhibitor Trim39 (PMID:23213260)
• TRIM39R, but not TRIM39B, regulates type I interferon response (PMID:23707810)
• TRIM39 negatively regulates the NFkappaB signaling pathway possibly via stabilization of cactin. (PMID:26363554)
• Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci. (PMID:33311639)
• TRIM39 deficiency inhibits tumor progression and autophagic flux in colorectal cancer via suppressing the activity of Rab7. (PMID:33846303)
• TRIM39 is a poor prognostic factor for patients with estrogen receptor-positive breast cancer and promotes cell cycle progression. (PMID:35174936)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Trim39	ENSMUSG00000045409
rattus_norvegicus	Trim39	ENSRNOG00000000785

Paralogs (80): MID2 (ENSG00000080561), TRIM9 (ENSG00000100505), 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)

Protein

Protein identifiers

E3 ubiquitin-protein ligase TRIM39 — Q9HCM9 (reviewed: Q9HCM9)

Alternative names: RING finger protein 23, RING-type E3 ubiquitin transferase TRIM39, Testis-abundant finger protein, Tripartite motif-containing protein 39

All UniProt accessions (8): A0A024RCP5, A2AAZ2, A2AAZ3, A2AAZ4, A2AAZ5, A2AAZ6, Q9HCM9, H0Y735

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase. May facilitate apoptosis by inhibiting APC/C-Cdh1-mediated poly-ubiquitination and subsequent proteasome-mediated degradation of the pro-apoptotic protein MOAP1. Regulates the G1/S transition of the cell cycle and DNA damage-induced G2 arrest by stabilizing CDKN1A/p21. Positively regulates CDKN1A/p21 stability by competing with DTL for CDKN1A/p21 binding, therefore disrupting DCX(DTL) E3 ubiquitin ligase complex-mediated CDKN1A/p21 ubiquitination and degradation. Regulates the G1/S transition of the cell cycle and DNA damage-induced G2 arrest by stabilizing CDKN1A/p21. Positively regulates CDKN1A/p21 stability by competing with DTL for CDKN1A/p21 binding, therefore disrupting DCX(DTL) E3 ubiquitin ligase complex-mediated CDKN1A/p21 ubiquitination and degradation. Negatively regulates the canonical NF-kappa-B signaling pathway via stabilization of CACTIN in an ubiquitination-independent manner.

Subunit / interactions. Isoform 1 interacts with MOAP1. Isoform 1 and isoform 2 interact with CDKN1A. Isoform 2 interacts (via domain B box-type) with CACTIN.

Subcellular location. Cytoplasm. Cytosol. Mitochondrion. Nucleus Nucleus.

Tissue specificity. Ubiquitous; highly expressed in brain, heart, kidney, liver, skeletal muscle, spleen and testis.

Post-translational modifications. Autoubiquitinated.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the TRIM/RBCC family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9HCM9-1	1, TIM39alpha	yes
Q9HCM9-2	2, TIM39beta

RefSeq proteins (5): NP_001356450, NP_001356451, NP_001356452, NP_067076, NP_742013 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000315	Znf_B-box	Domain
IPR001841	Znf_RING	Domain
IPR001870	B30.2/SPRY	Domain
IPR003877	SPRY_dom	Domain
IPR003879	Butyrophylin_SPRY	Domain
IPR006574	PRY	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR017907	Znf_RING_CS	Conserved_site
IPR035033	PRY/SPRY_TRIM39	Domain
IPR043136	B30.2/SPRY_sf	Homologous_superfamily
IPR050143	TRIM/RBCC	Family

Pfam: PF00622, PF00643, PF13765, PF15227

UniProt features (22 total): binding site 4, strand 4, sequence conflict 2, helix 2, turn 2, zinc finger region 2, region of interest 2, chain 1, domain 1, splice variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
2DID	SOLUTION NMR
2DIF	SOLUTION NMR
2ECJ	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HCM9-F1	85.03	0.54

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 (4): 135; 107; 110; 129

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 196 (showing top): GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, GOBP_MITOTIC_G2_M_TRANSITION_CHECKPOINT, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, EFC_Q6, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_REGULATION_OF_CELL_CYCLE_G2_M_PHASE_TRANSITION

GO Biological Process (11): apoptotic process (GO:0006915), mitotic G2 DNA damage checkpoint signaling (GO:0007095), regulation of gene expression (GO:0010468), protein ubiquitination (GO:0016567), negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435), negative regulation of canonical NF-kappaB signal transduction (GO:0043124), innate immune response (GO:0045087), protein stabilization (GO:0050821), regulation of cell cycle G1/S phase transition (GO:1902806), negative regulation of ubiquitin-dependent protein catabolic process (GO:2000059), positive regulation of apoptotic signaling pathway (GO:2001235)

GO Molecular Function (6): zinc ion binding (GO:0008270), identical protein binding (GO:0042802), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cytosol (GO:0005829)

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
apoptotic signaling pathway	2
intracellular membrane-bounded organelle	2
cellular anatomical structure	2
cytoplasm	2
programmed cell death	1
execution phase of apoptosis	1
mitotic G2 phase	1
mitotic DNA damage checkpoint signaling	1
mitotic G2/M transition checkpoint	1
gene expression	1
regulation of macromolecule biosynthetic process	1
protein modification by small protein conjugation	1
regulation of proteasomal ubiquitin-dependent protein catabolic process	1
proteasome-mediated ubiquitin-dependent protein catabolic process	1
negative regulation of proteasomal protein catabolic process	1
negative regulation of ubiquitin-dependent protein catabolic process	1
canonical NF-kappaB signal transduction	1
regulation of canonical NF-kappaB signal transduction	1
negative regulation of intracellular signal transduction	1
immune response	1
defense response to symbiont	1
regulation of protein stability	1
cell cycle G1/S phase transition	1
regulation of cell cycle phase transition	1
ubiquitin-dependent protein catabolic process	1
negative regulation of protein catabolic process	1
regulation of ubiquitin-dependent protein catabolic process	1
positive regulation of signal transduction	1
positive regulation of apoptotic process	1
regulation of apoptotic signaling pathway	1
transition metal ion binding	1
protein binding	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein ligase activity	1
binding	1
catalytic activity	1
cation binding	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

797 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRIM39	BBOX1	O75936	870
TRIM39	MOAP1	Q96BY2	729
TRIM39	PRKG1	P14619	725
TRIM39	CACTIN	Q8WUQ7	697
TRIM39	TRAT1	Q6PIZ9	655
TRIM39	TXN	P10599	544
TRIM39	PPP1R11	O60927	521
TRIM39	CCDC120	Q96HB5	513
TRIM39	BTBD9	Q96Q07	512
TRIM39	TRIM9	Q9C026	509
TRIM39	TADA3	O75528	496
TRIM39	TP53	P04637	485
TRIM39	PRY	O14603	480
TRIM39	RPP21	Q9H633	475
TRIM39	TRIM66	O15016	471

IntAct

212 interactions, top by confidence:

A	B	Type	Score
TRIM39	TRIM17	psi-mi:“MI:0915”(physical association)	0.860
TRIM17	TRIM39	psi-mi:“MI:0915”(physical association)	0.860
TRIM39	TRIM39	psi-mi:“MI:0915”(physical association)	0.810
TRIM39	UBE2D1	psi-mi:“MI:0915”(physical association)	0.800
UBE2D3	TRIM39	psi-mi:“MI:0915”(physical association)	0.800
TRIM39	UBE2E2	psi-mi:“MI:0915”(physical association)	0.800
TRIM39	UBE2D3	psi-mi:“MI:0915”(physical association)	0.800
UBE2D1	TRIM39	psi-mi:“MI:0915”(physical association)	0.800
UBE2E2	TRIM39	psi-mi:“MI:0915”(physical association)	0.800
TRIM39	UBE2E3	psi-mi:“MI:0915”(physical association)	0.740
UBXN6	TRIM39	psi-mi:“MI:0915”(physical association)	0.740

BioGRID (205): TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid), TRIM39 (Two-hybrid)

ESM2 similar proteins: A0JN74, A6NCK2, A6NGJ6, A6NI03, B1H278, K7N6K2, O00478, O00481, P14373, P19474, Q13410, Q1ACD5, Q1ACD6, Q1ACD7, Q1ACD8, Q1XHU0, Q2YEM8, Q2YEM9, Q3ZEE5, Q587N6, Q5C8T6, Q5C8T8, Q5C8U1, Q5D7I9, Q5D7J0, Q5D7J1, Q5NCC9, Q5R996, Q62158, Q6MFZ5, Q7YR33, Q7YRV4, Q80V85, Q8BGE7, Q8NG06, Q923T7, Q96BQ3, Q96F44, Q99PP6, Q99PQ2

Diamond homologs: A0A0G2JXN2, Q1XHU0, Q7TNM2, Q7Z4K8, Q80WG7, Q9HCM9, Q9NQ86, A0A2P1BRP3, A0A2P1BRQ0, A0ZSK3, A0ZSK4, B1H278, O95361, Q14142, Q1LY10, Q309B1, Q5BK82, Q5R760, Q6MFZ5, Q6P6S3, Q6UXG8, Q80X56, Q80YW5, Q8BVW3, Q8WV44, Q8WVV5, Q91453, Q96F44, Q98989, Q98993, Q99PP9, Q99PQ2, Q9ESN2, A0JN74, O19085, P14373, P19474, Q02084, Q5R7W8, Q62158

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	TRIM39	ubiquitination
TRIM39	“down-regulates quantity by destabilization”	TP53	ubiquitination
TRIM39	“up-regulates quantity by stabilization”	MOAP1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 107 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
Synthesis of active ubiquitin: roles of E1 and E2 enzymes	7	31.1×	4e-07
E3 ubiquitin ligases ubiquitinate target proteins	5	11.7×	4e-03
FCGR3A-mediated phagocytosis	5	11.3×	4e-03
Regulation of endogenous retroelements by KRAB-ZFP proteins	6	7.7×	5e-03
Antigen processing: Ubiquitination & Proteasome degradation	15	6.7×	7e-07

GO biological processes:

GO term	Partners	Fold	FDR
protein K11-linked ubiquitination	6	23.8×	2e-05
protein monoubiquitination	6	20.8×	4e-05
ephrin receptor signaling pathway	5	17.4×	6e-04
protein K63-linked ubiquitination	6	16.2×	1e-04
protein K48-linked ubiquitination	9	15.3×	2e-06
protein autoubiquitination	5	11.8×	3e-03
protein polyubiquitination	10	11.7×	2e-06
ubiquitin-dependent protein catabolic process	10	7.5×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2306 predictions. Top by Δscore:

Variant	Effect	Δscore
6:30328908:GAAAC:G	acceptor_gain	1.0000
6:30329039:GAG:G	donor_gain	1.0000
6:30335743:A:AG	acceptor_gain	1.0000
6:30335743:A:T	acceptor_loss	1.0000
6:30335744:G:GA	acceptor_loss	1.0000
6:30335744:G:GG	acceptor_gain	1.0000
6:30335744:GA:G	acceptor_gain	1.0000
6:30335744:GAGA:G	acceptor_gain	1.0000
6:30340487:T:G	acceptor_gain	1.0000
6:30340494:A:AG	acceptor_gain	1.0000
6:30340495:T:G	acceptor_gain	1.0000
6:30340500:CCTAG:C	acceptor_loss	1.0000
6:30340502:TAG:T	acceptor_loss	1.0000
6:30340503:A:AC	acceptor_loss	1.0000
6:30340503:A:AG	acceptor_gain	1.0000
6:30340503:AGAT:A	acceptor_gain	1.0000
6:30340503:AGATG:A	acceptor_loss	1.0000
6:30340504:G:A	acceptor_loss	1.0000
6:30340504:G:GT	acceptor_gain	1.0000
6:30340504:GA:G	acceptor_gain	1.0000
6:30340504:GAT:G	acceptor_gain	1.0000
6:30340504:GATG:G	acceptor_gain	1.0000
6:30340504:GATGT:G	acceptor_gain	1.0000
6:30340598:G:GT	donor_gain	1.0000
6:30340614:C:G	donor_gain	1.0000
6:30340617:ATTGG:A	donor_loss	1.0000
6:30340619:TGGTG:T	donor_loss	1.0000
6:30340621:G:GA	donor_loss	1.0000
6:30340621:G:GG	donor_gain	1.0000
6:30340622:TGA:T	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000247515 (6:30327440 A>G,T), RS1000849666 (6:30343376 T>G), RS1001018233 (6:30326345 A>T), RS1001032100 (6:30335575 G>A), RS1001134805 (6:30333465 C>G), RS1001255204 (6:30329056 A>G), RS1001479907 (6:30327836 T>A,C), RS1001482966 (6:30335335 T>A), RS1001659756 (6:30344072 G>A), RS1001683465 (6:30328535 A>G), RS1001796252 (6:30336980 G>A), RS1001846712 (6:30334779 G>A), RS1001995205 (6:30342662 A>G), RS1002015692 (6:30327200 C>T), RS1002444512 (6:30342629 C>T)

Disease associations

OMIM: gene MIM:605700 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

22 associations (top):

Study	Trait	p-value
GCST002884_2	Cutaneous lupus erythematosus	2.000000e-11
GCST002884_4	Cutaneous lupus erythematosus	2.000000e-11
GCST004521_114	Autism spectrum disorder or schizophrenia	3.000000e-17
GCST004521_121	Autism spectrum disorder or schizophrenia	3.000000e-13
GCST004521_132	Autism spectrum disorder or schizophrenia	2.000000e-09
GCST004521_171	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST004521_2	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_210	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_263	Autism spectrum disorder or schizophrenia	7.000000e-17
GCST004521_265	Autism spectrum disorder or schizophrenia	7.000000e-14
GCST004521_268	Autism spectrum disorder or schizophrenia	7.000000e-12
GCST004521_269	Autism spectrum disorder or schizophrenia	7.000000e-11
GCST004521_295	Autism spectrum disorder or schizophrenia	6.000000e-18
GCST004521_3	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_44	Autism spectrum disorder or schizophrenia	2.000000e-17
GCST004521_56	Autism spectrum disorder or schizophrenia	1.000000e-22
GCST004521_70	Autism spectrum disorder or schizophrenia	8.000000e-20
GCST004521_79	Autism spectrum disorder or schizophrenia	1.000000e-16
GCST005232_23	Neuroticism	8.000000e-09
GCST007993_27	Asthma (adult onset)	7.000000e-07
GCST007995_23	Asthma (childhood onset)	3.000000e-08
GCST012354_18	Anxiety	1.000000e-12

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007660	neuroticism measurement
EFO:1002011	adult onset asthma
EFO:0009863	anxiety measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases expression, affects cotreatment, decreases expression, increases abundance, increases oxidation (+1 more)	3
Ozone	increases abundance, affects expression, affects cotreatment, decreases expression, increases oxidation	3
methacrylaldehyde	affects cotreatment, decreases expression, increases oxidation, increases abundance	2
Acrolein	affects cotreatment, decreases expression, increases oxidation, increases abundance	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases oxidation, increases abundance	1
titanium dioxide	increases expression	1
sodium arsenite	increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
Temozolomide	increases expression	1
Arsenic	affects methylation	1
Benzene	increases expression	1
Benzo(a)pyrene	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Methylcholanthrene	affects binding, increases reaction	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	affects expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Gold Compounds	increases expression	1
Particulate Matter	increases abundance, increases expression	1
Volatile Organic Compounds	affects cotreatment, decreases expression, increases oxidation	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TU19	HAP1 TRIM39 (-) 1	Cancer cell line	Male
CVCL_TU20	HAP1 TRIM39 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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