MEX3D

Summary

MEX3D (mex-3 RNA binding family member D, HGNC:16734) is a protein-coding gene on chromosome 19p13.3, encoding RNA-binding protein MEX3D (Q86XN8). RNA binding protein, may be involved in post-transcriptional regulatory mechanisms.

Enables mRNA 3’-UTR AU-rich region binding activity. Predicted to be involved in mRNA destabilization and mRNA localization resulting in post-transcriptional regulation of gene expression. Located in nucleus and perinuclear region of cytoplasm.

Source: NCBI Gene 399664 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 158 total
• MANE Select transcript: NM_203304

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16734
Approved symbol	MEX3D
Name	mex-3 RNA binding family member D
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	Tino, KIAA2031, OK/SW-cl.4, RNF193
Ensembl gene	ENSG00000181588
Ensembl biotype	protein_coding
OMIM	611009
Entrez	399664

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000402693, ENST00000605173

RefSeq mRNA: 2 — MANE Select: NM_203304 NM_001174118, NM_203304

CCDS: CCDS32865

Canonical transcript exons

ENST00000402693 — 2 exons

Exon	Start	End
ENSE00001546901	1554672	1556923
ENSE00001678957	1567464	1568325

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 94.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5365 / max 106.2228, expressed in 1520 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178039	6.0526	1508
178038	0.3046	141
178037	0.1794	55

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	94.54	gold quality
left testis	UBERON:0004533	94.53	gold quality
ganglionic eminence	UBERON:0004023	92.71	gold quality
testis	UBERON:0000473	90.01	gold quality
ventricular zone	UBERON:0003053	89.59	gold quality
secondary oocyte	CL:0000655	88.72	gold quality
cortical plate	UBERON:0005343	87.96	gold quality
stromal cell of endometrium	CL:0002255	82.36	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	80.54	gold quality
embryo	UBERON:0000922	80.07	gold quality
mucosa of transverse colon	UBERON:0004991	79.93	gold quality
sural nerve	UBERON:0015488	79.89	gold quality
left ovary	UBERON:0002119	79.68	gold quality
right ovary	UBERON:0002118	79.63	gold quality
body of uterus	UBERON:0009853	78.92	gold quality
skin of leg	UBERON:0001511	78.75	gold quality
skin of abdomen	UBERON:0001416	78.67	gold quality
ectocervix	UBERON:0012249	78.42	gold quality
right lung	UBERON:0002167	78.22	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.67	gold quality
spinal cord	UBERON:0002240	77.66	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	77.58	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.50	gold quality
endocervix	UBERON:0000458	77.47	gold quality
lower esophagus	UBERON:0013473	77.47	gold quality
left uterine tube	UBERON:0001303	77.30	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.03	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.94	gold quality
ascending aorta	UBERON:0001496	76.90	gold quality
decidua	UBERON:0002450	76.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

121 targeting MEX3D, 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-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3162-3P	100.00	65.37	363
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-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-4666A-3P	99.96	71.71	3434
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-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

Literature-anchored findings (GeneRIF, showing 2)

• Dysregulated gene expressions of MEX3D, FOS and BCL2 in human induced-neuronal (iN) cells from NF1 patients (PMID:29066822)
• MEX3D is an oncogenic driver in prostate cancer. (PMID:34455614)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Mex3d	ENSMUSG00000048696
rattus_norvegicus	Mex3d	ENSRNOG00000030830

Paralogs (3): MEX3C (ENSG00000176624), MEX3B (ENSG00000183496), MEX3A (ENSG00000254726)

Protein

Protein identifiers

RNA-binding protein MEX3D — Q86XN8 (reviewed: Q86XN8)

Alternative names: RING finger and KH domain-containing protein 1, RING finger protein 193, TINO

All UniProt accessions (2): Q86XN8, S4R446

UniProt curated annotations — full annotation on UniProt →

Function. RNA binding protein, may be involved in post-transcriptional regulatory mechanisms.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Ubiquitously expressed in all the cell lines and tissues tested.

Post-translational modifications. Phosphorylated.

Domain organisation. Binds RNA through its KH domains.

Isoforms (3)

UniProt ID	Names	Canonical?
Q86XN8-1	1	yes
Q86XN8-2	2, TINO
Q86XN8-3	3

RefSeq proteins (2): NP_001167589, NP_976049* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001841	Znf_RING	Domain
IPR004087	KH_dom	Domain
IPR004088	KH_dom_type_1	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR036612	KH_dom_type_1_sf	Homologous_superfamily
IPR047226	KH-I_MEX3_rpt2	Domain
IPR047227	MEX3	Family
IPR047228	KH-I_MEX3_rpt1	Domain

Pfam: PF00013, PF13920

UniProt features (28 total): compositionally biased region 7, strand 4, region of interest 4, helix 3, domain 2, modified residue 2, splice variant 2, turn 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2DGR	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86XN8-F1	61.58	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 (2): 510, 514

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): MYAATNNNNNNNGGC_UNKNOWN, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GGGTGGRR_PAX4_03, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, SOX9_B1, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, TGACATY_UNKNOWN, BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP, GFI1_01, GGCNNMSMYNTTG_UNKNOWN, GOBP_RNA_LOCALIZATION, CAIRO_LIVER_DEVELOPMENT_UP

GO Biological Process (2): mRNA localization resulting in post-transcriptional regulation of gene expression (GO:0010609), mRNA destabilization (GO:0061157)

GO Molecular Function (5): RNA binding (GO:0003723), zinc ion binding (GO:0008270), mRNA 3’-UTR AU-rich region binding (GO:0035925), nucleic acid binding (GO:0003676), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
intracellular mRNA localization	1
post-transcriptional regulation of gene expression	1
negative regulation of gene expression	1
regulation of mRNA stability	1
RNA destabilization	1
positive regulation of mRNA catabolic process	1
nucleic acid binding	1
transition metal ion binding	1
mRNA 3’-UTR binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

694 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MEX3D	HNRNPK	P61978	812
MEX3D	DCP1A	Q9NPI6	758
MEX3D	AGO1	Q9UL18	657
MEX3D	TRIM71	Q2Q1W2	602
MEX3D	CAPN3	P20807	577
MEX3D	TENT2	Q6PIY7	518
MEX3D	DAZ1	Q9NQZ3	507
MEX3D	TTN	Q8WZ42	474
MEX3D	UNC119	Q13432	461
MEX3D	LMBRD2	Q68DH5	424
MEX3D	SKIC3	Q6PGP7	422
MEX3D	DDX6	P26196	407
MEX3D	ATOSA	Q32MH5	389
MEX3D	SLURP1	P55000	380
MEX3D	CDX2	Q99626	380

IntAct

49 interactions, top by confidence:

A	B	Type	Score
ENPP6	SCAMP1	psi-mi:“MI:0914”(association)	0.640
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
ZAR1L	BCL2L11	psi-mi:“MI:0914”(association)	0.530
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
PLOD1	COL25A1	psi-mi:“MI:0914”(association)	0.350
PSMC3		psi-mi:“MI:0914”(association)	0.350
LMO2	APBB1	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
PLOD1	PLK4	psi-mi:“MI:0914”(association)	0.350
LMO2	POLR2D	psi-mi:“MI:0914”(association)	0.350
AJUBA	DTNB	psi-mi:“MI:0914”(association)	0.350
B4GALT2	LENG9	psi-mi:“MI:0914”(association)	0.350
NPAS1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
PLEKHG7	MROH6	psi-mi:“MI:0914”(association)	0.350
EEF1AKMT3	SMCHD1	psi-mi:“MI:0914”(association)	0.350
UBXN6	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
D2HGDH	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
SULT1C4	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
CRYBB3	ARHGAP32	psi-mi:“MI:0914”(association)	0.350
SENP3	IPO5	psi-mi:“MI:0914”(association)	0.350
PPARD	ACACB	psi-mi:“MI:0914”(association)	0.350
NPRL2	APAF1	psi-mi:“MI:0914”(association)	0.350

BioGRID (69): MEX3D (Affinity Capture-RNA), MEX3D (Affinity Capture-MS), MEX3D (Affinity Capture-MS), MEX3D (Affinity Capture-MS), MEX3D (Affinity Capture-MS), MEX3D (Protein-RNA), MEX3D (Affinity Capture-MS), MEX3D (Affinity Capture-MS), MEX3D (Proximity Label-MS), MEX3D (Proximity Label-MS), MEX3D (Proximity Label-MS), MEX3D (Proximity Label-MS), MEX3D (Proximity Label-MS), MEX3D (Affinity Capture-MS), MEX3D (Affinity Capture-MS)

ESM2 similar proteins: A0A2K3DDJ2, A2A9A2, A2VDX9, A2Y5N0, A4GRC6, A6QQ94, A8ICS9, A8ID95, A8INQ0, A8ITB0, A8ITV9, A8J666, A8JID5, F5A894, O83683, P09695, P09715, P14348, P17473, P24096, P28925, P30662, P54817, Q01JD1, Q08354, Q08355, Q08356, Q10MB4, Q2QPW2, Q49I55, Q49I57, Q4VKB4, Q5QD03, Q6AYU4, Q6F5E0, Q6L4N4, Q6S6U0, Q6SVX2, Q6SW04, Q7XT42

Diamond homologs: A1E2V0, A1L020, A1L3F4, A9JTP3, A9ULZ2, O08863, O62640, Q05A36, Q0MW30, Q13489, Q13490, Q3UE17, Q5U5Q3, Q62210, Q69Z36, Q6TEM9, Q6ZN04, Q7XI08, Q86XN8, Q8JHV9, Q90660, Q9SYH3, A8MQ27, P41436, Q5M870, Q8CJC5, A0A0B4KGY6, F4KDN0, O19049, O74919, P61978, P61979, P61980, Q32PX7, Q3T0D0, Q3U0V1, Q4R4M6, Q5R5H8, Q8UVD9, Q91WJ8

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	MEX3D	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	148
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

250 predictions. Top by Δscore:

Variant	Effect	Δscore
19:1556920:CAGC:C	acceptor_gain	1.0000
19:1556923:CCTG:C	acceptor_loss	1.0000
19:1556924:C:A	acceptor_loss	1.0000
19:1556930:G:T	acceptor_gain	1.0000
19:1567460:TCAC:T	donor_loss	1.0000
19:1567461:CACC:C	donor_loss	1.0000
19:1567462:A:T	donor_loss	1.0000
19:1567462:AC:A	donor_gain	1.0000
19:1567463:C:CA	donor_loss	1.0000
19:1567463:CC:C	donor_gain	1.0000
19:1556924:C:CC	acceptor_gain	0.9900
19:1556925:T:C	acceptor_loss	0.9900
19:1556929:C:CT	acceptor_gain	0.9900
19:1556929:C:T	acceptor_gain	0.9900
19:1567462:A:AC	donor_gain	0.9900
19:1567463:C:CC	donor_gain	0.9900
19:1556921:AGC:A	acceptor_gain	0.9800
19:1556922:GC:G	acceptor_gain	0.9800
19:1556923:CC:C	acceptor_gain	0.9800
19:1567462:ACC:A	donor_gain	0.9800
19:1567463:CCC:C	donor_gain	0.9800
19:1567476:CGAT:C	donor_gain	0.9800
19:1556919:GCAGC:G	acceptor_gain	0.9700
19:1556920:CAGCC:C	acceptor_gain	0.9700
19:1567463:CCCTG:C	donor_gain	0.9700
19:1567463:CCCT:C	donor_gain	0.9600
19:1556924:C:T	acceptor_gain	0.9400
19:1565970:C:CT	donor_gain	0.8400
19:1556921:AGCC:A	acceptor_gain	0.8300
19:1556922:GCCT:G	acceptor_gain	0.8200

AlphaMissense

4137 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:1555612:C:G	C636S	1.000
19:1555613:A:G	C636R	1.000
19:1555613:A:T	C636S	1.000
19:1555647:G:C	C624W	1.000
19:1555648:C:T	C624Y	1.000
19:1555649:A:G	C624R	1.000
19:1555656:G:C	C621W	1.000
19:1555657:C:T	C621Y	1.000
19:1555658:A:G	C621R	1.000
19:1555660:A:G	F620S	1.000
19:1555675:C:T	C615Y	1.000
19:1555676:A:G	C615R	1.000
19:1555721:A:G	C600R	1.000
19:1556506:A:T	I338N	1.000
19:1556510:G:C	H337D	1.000
19:1556518:A:C	I334S	1.000
19:1556518:A:T	I334N	1.000
19:1556554:C:A	G322V	1.000
19:1556554:C:T	G322E	1.000
19:1556555:C:A	G322W	1.000
19:1556555:C:G	G322R	1.000
19:1556555:C:T	G322R	1.000
19:1556560:A:T	V320D	1.000
19:1556565:G:C	F318L	1.000
19:1556565:G:T	F318L	1.000
19:1556566:A:C	F318C	1.000
19:1556566:A:G	F318S	1.000
19:1556567:A:C	F318V	1.000
19:1556567:A:G	F318L	1.000
19:1556590:G:T	P310H	1.000

dbSNP variants (sampled 300 via entrez): RS1000089885 (19:1555863 G>A,C,T), RS1000113099 (19:1559032 G>C), RS1000269120 (19:1563729 AC>A), RS1000318030 (19:1562875 C>T), RS1000437577 (19:1567407 C>T), RS1000440751 (19:1568170 G>A), RS1000473322 (19:1567973 C>A,G), RS1000687243 (19:1557195 G>A), RS1000691985 (19:1555208 A>C,G,T), RS1000743724 (19:1563549 G>A), RS1000891913 (19:1568849 G>T), RS1001163289 (19:1557422 C>A,G,T), RS1001275600 (19:1568877 C>T), RS1001352163 (19:1562443 T>C), RS1001635673 (19:1558480 C>T)

Disease associations

OMIM: gene MIM:611009 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cisplatin	decreases expression, increases expression	2
Smoke	increases abundance, decreases expression	2
Particulate Matter	increases expression, decreases expression, increases abundance	2
FR900359	decreases phosphorylation	1
methylmercuric chloride	increases expression	1
bisphenol A	decreases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
zinc chromate	increases abundance, decreases expression	1
pinosylvin	decreases expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
abrine	decreases expression	1
licochalcone B	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Bortezomib	decreases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Vehicle Emissions	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases expression	1
Caffeine	decreases phosphorylation	1
Doxorubicin	decreases expression	1
Endosulfan	decreases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Ribonucleotides	affects binding	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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