TRIM42

Summary

TRIM42 (tripartite motif containing 42, HGNC:19014) is a protein-coding gene on chromosome 3q23, encoding Tripartite motif-containing protein 42 (Q8IWZ5).

This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region.

Source: NCBI Gene 287015 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 112 total
• MANE Select transcript: NM_152616

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19014
Approved symbol	TRIM42
Name	tripartite motif containing 42
Location	3q23
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40097, PPP1R40, T4A1
Ensembl gene	ENSG00000155890
Ensembl biotype	protein_coding
OMIM	620334
Entrez	287015

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000286349

RefSeq mRNA: 1 — MANE Select: NM_152616 NM_152616

CCDS: CCDS3113

Canonical transcript exons

ENST00000286349 — 5 exons

Exon	Start	End
ENSE00001023275	140682462	140683159
ENSE00001023277	140687722	140688542
ENSE00001077543	140678064	140678570
ENSE00001136757	140690968	140691192
ENSE00001246699	140700888	140701150

Expression profiles

Bgee: expression breadth broad, 15 present calls, max score 83.68.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0853 / max 78.0377, expressed in 4 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38856	0.0804	4
38855	0.0049	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.68	gold quality
left testis	UBERON:0004533	79.41	gold quality
right testis	UBERON:0004534	77.97	gold quality
testis	UBERON:0000473	77.05	gold quality
secondary oocyte	CL:0000655	63.03	gold quality
cerebellar vermis	UBERON:0004720	58.21	gold quality
adult organism	UBERON:0007023	55.89	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	52.15	gold quality
oocyte	CL:0000023	48.25	gold quality
thymus	UBERON:0002370	43.37	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
quadriceps femoris	UBERON:0001377	43.34	gold quality
middle temporal gyrus	UBERON:0002771	41.97	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
sperm	CL:0000019	40.97	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality
cartilage tissue	UBERON:0002418	40.06	gold quality
oviduct epithelium	UBERON:0004804	40.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting TRIM42, 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-6867-5P	100.00	82.21	3464
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-3618	99.69	68.57	1012
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-4635	98.74	67.63	1339
HSA-MIR-934	98.49	70.44	581

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Trim42	ENSMUSG00000032451
rattus_norvegicus	Trim42	ENSRNOG00000048975

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), TRIM63 (ENSG00000158022)

Protein

Protein identifiers

Tripartite motif-containing protein 42 — Q8IWZ5 (reviewed: Q8IWZ5)

All UniProt accessions (1): Q8IWZ5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the TRIM/RBCC family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IWZ5-1	1	yes
Q8IWZ5-2	2

RefSeq proteins (1): NP_689829* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000315	Znf_B-box	Domain
IPR001841	Znf_RING	Domain
IPR003961	FN3_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR017903	COS_domain	Domain
IPR017907	Znf_RING_CS	Conserved_site
IPR036116	FN3_sf	Homologous_superfamily
IPR042765	TRIM42_RING-HC	Domain
IPR051051	E3_ubiq-ligase_TRIM/RNF	Family

Pfam: PF00041, PF00643

UniProt features (17 total): binding site 4, sequence variant 3, zinc finger region 3, domain 2, splice variant 2, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IWZ5-F1	65.42	0.18

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): 318; 290; 293; 313

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY, GOMF_UBIQUITIN_LIKE_PROTEIN_LIGASE_ACTIVITY, CHENG_IMPRINTED_BY_ESTRADIOL, MIR6867_5P, MIR4261, MIR147B_5P, MIR934, GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_CONJUGATION, chr3q23, RTAAACA_FREAC2_01, GSE12003_4D_VS_8D_CULTURE_BM_PROGENITOR_UP

GO Biological Process (1): protein ubiquitination (GO:0016567)

GO Molecular Function (4): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein modification by small protein conjugation	1
transition metal ion binding	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein ligase activity	1
binding	1
cation binding	1

Protein interactions and networks

STRING

502 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRIM42	C10orf120	Q5SQS8	571
TRIM42	C5orf47	Q569G3	539
TRIM42	TRIM27	P14373	537
TRIM42	TRIM77	I1YAP6	502
TRIM42	ZPLD1	Q8TCW7	487
TRIM42	TRIM47	Q96LD4	480
TRIM42	CCDC27	Q2M243	477
TRIM42	TRIM69	Q86WT6	476
TRIM42	TGIF2LX	Q8IUE1	476
TRIM42	TRIM41	Q8WV44	472
TRIM42	SAXO1	Q8IYX7	468
TRIM42	TRIM23	P36406	461
TRIM42	TRIM64	A6NGJ6	460
TRIM42	TRIM4	Q9C037	457
TRIM42	SPRED3	Q2MJR0	454

IntAct

513 interactions, top by confidence:

A	B	Type	Score
TRIM42	HOXA1	psi-mi:“MI:0915”(physical association)	0.720
TRIM42	LONRF1	psi-mi:“MI:0915”(physical association)	0.720
KCTD9	TRIM42	psi-mi:“MI:0915”(physical association)	0.720
TRIM42	STK16	psi-mi:“MI:0915”(physical association)	0.720
EMD	TRIM42	psi-mi:“MI:0915”(physical association)	0.720
LONRF1	TRIM42	psi-mi:“MI:0915”(physical association)	0.720
TRIM42	KLHL38	psi-mi:“MI:0915”(physical association)	0.720
TRIM42	KCTD9	psi-mi:“MI:0915”(physical association)	0.720
KLHL38	TRIM42	psi-mi:“MI:0915”(physical association)	0.720
HOXA1	TRIM42	psi-mi:“MI:0915”(physical association)	0.720
TRIM42	YWHAQ	psi-mi:“MI:0915”(physical association)	0.670
YWHAQ	TRIM42	psi-mi:“MI:0915”(physical association)	0.670
KRT13	TRIM42	psi-mi:“MI:0915”(physical association)	0.560
TRIM42	GLI1	psi-mi:“MI:0915”(physical association)	0.560
TRIM27	TRIM42	psi-mi:“MI:0915”(physical association)	0.560
TRIM42	KRT15	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (158): TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid), TRIM42 (Two-hybrid)

ESM2 similar proteins: A0A7H0DN99, A0A8V8TMC4, D3YUJ3, I2HAA0, O01501, O13818, O14260, O14332, O17657, O42575, O43008, P06776, P0C7X3, P17214, P25009, P30645, P34624, P36034, P38729, P52924, P53053, P53124, Q03080, Q05930, Q07788, Q08C99, Q08CI4, Q09792, Q10326, Q10PQ9, Q22695, Q28EL0, Q4R871, Q5IBH7, Q5ICL9, Q5MJ70, Q5T2Q4, Q5U5D0, Q6NRF4, Q75D04

Diamond homologs: G4SLH0, Q6NWW9, Q8IWZ5, Q9D2H5, O95361, Q5R760

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	TRIM42	ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 59 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
Keratinization	8	13.5×	2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	103
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1113 predictions. Top by Δscore:

Variant	Effect	Δscore
3:140678571:G:GG	donor_gain	1.0000
3:140687720:A:AG	acceptor_gain	1.0000
3:140687721:G:GG	acceptor_gain	1.0000
3:140690962:CCATA:C	acceptor_loss	1.0000
3:140690963:CATA:C	acceptor_loss	1.0000
3:140690966:A:AC	acceptor_loss	1.0000
3:140690967:G:GT	acceptor_loss	1.0000
3:140678568:CTC:C	donor_gain	0.9900
3:140682460:A:AG	acceptor_gain	0.9900
3:140682461:G:GA	acceptor_gain	0.9900
3:140683150:TTCA:T	donor_gain	0.9900
3:140690688:C:CA	acceptor_gain	0.9900
3:140690966:A:AG	acceptor_gain	0.9900
3:140690967:G:GG	acceptor_gain	0.9900
3:140691127:GAA:G	donor_gain	0.9900
3:140691129:A:AG	donor_gain	0.9900
3:140691141:A:AG	donor_gain	0.9900
3:140691142:G:GG	donor_gain	0.9900
3:140691189:CAAG:C	donor_loss	0.9900
3:140691190:AAG:A	donor_loss	0.9900
3:140691191:AG:A	donor_loss	0.9900
3:140691192:G:GT	donor_loss	0.9900
3:140700882:TTGCA:T	acceptor_loss	0.9900
3:140700883:TGCAG:T	acceptor_loss	0.9900
3:140700884:GCAG:G	acceptor_loss	0.9900
3:140700885:CAGG:C	acceptor_loss	0.9900
3:140700886:A:G	acceptor_loss	0.9900
3:140700886:AGGT:A	acceptor_gain	0.9900
3:140700887:G:GA	acceptor_loss	0.9900
3:140700887:GGTG:G	acceptor_gain	0.9900

AlphaMissense

4861 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:140682682:T:C	C188R	0.999
3:140682988:T:C	C290R	0.999
3:140690974:T:A	W623R	0.999
3:140690974:T:C	W623R	0.999
3:140682684:C:G	C188W	0.998
3:140682691:T:C	C191R	0.998
3:140682832:T:C	C238R	0.998
3:140683048:T:C	C310R	0.998
3:140683050:C:G	C310W	0.998
3:140687979:G:C	A433P	0.998
3:140688006:T:C	F442L	0.998
3:140688008:C:A	F442L	0.998
3:140688008:C:G	F442L	0.998
3:140688010:T:C	L443P	0.998
3:140688018:G:C	A446P	0.998
3:140691175:T:A	W690R	0.998
3:140691175:T:C	W690R	0.998
3:140682556:T:C	C146R	0.997
3:140682601:T:C	C161R	0.997
3:140682602:G:A	C161Y	0.997
3:140682603:C:G	C161W	0.997
3:140682616:T:C	C166R	0.997
3:140682683:G:A	C188Y	0.997
3:140682691:T:A	C191S	0.997
3:140682692:G:A	C191Y	0.997
3:140682692:G:C	C191S	0.997
3:140682693:C:G	C191W	0.997
3:140682832:T:A	C238S	0.997
3:140682833:G:C	C238S	0.997
3:140682860:C:A	A247D	0.997

dbSNP variants (sampled 300 via entrez): RS1000153426 (3:140678929 G>A), RS1000432369 (3:140690140 T>C), RS1000615070 (3:140683414 G>C), RS1000670243 (3:140676717 A>G), RS1001056448 (3:140697070 C>T), RS1001217007 (3:140678168 C>A,T), RS1001699552 (3:140684881 T>C), RS1001716890 (3:140696758 A>G), RS1001717941 (3:140677618 A>G), RS1001928772 (3:140684260 G>A,T), RS1001935571 (3:140690053 C>T), RS1002017110 (3:140698280 G>A), RS1002178234 (3:140697417 G>A), RS1002186837 (3:140676278 T>C), RS1002403668 (3:140684582 AC>A)

Disease associations

OMIM: gene MIM:620334 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002306_50	Bipolar disorder (body mass index interaction)	7.000000e-09
GCST002685_7	Refractive astigmatism	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
perfluorooctanoic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
perfluorohexanesulfonic acid	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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