YBX3

Summary

YBX3 (Y-box binding protein 3, HGNC:2428) is a protein-coding gene on chromosome 12p13.2, encoding Y-box-binding protein 3 (P16989). Binds to the GM-CSF promoter.

Enables RNA binding activity. Involved in cellular hyperosmotic response; cellular response to tumor necrosis factor; and negative regulation of programmed cell death. Located in cytosol.

Source: NCBI Gene 8531 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 91 total
• Druggable target: yes
• Transcription factor: yes — 29 downstream targets (CollecTRI)
• MANE Select transcript: NM_003651

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2428
Approved symbol	YBX3
Name	Y-box binding protein 3
Location	12p13.2
Locus type	gene with protein product
Status	Approved
Aliases	dbpA, ZONAB, CSDA1
Ensembl gene	ENSG00000060138
Ensembl biotype	protein_coding
OMIM	603437
Entrez	8531

Gene structure

Transcript identifiers

Ensembl transcripts: 46 — 31 protein_coding, 9 protein_coding_CDS_not_defined, 6 retained_intron

ENST00000228251, ENST00000279550, ENST00000366286, ENST00000366290, ENST00000536107, ENST00000536823, ENST00000539204, ENST00000540447, ENST00000540747, ENST00000540975, ENST00000541351, ENST00000542002, ENST00000542641, ENST00000544501, ENST00000544504, ENST00000544622, ENST00000546164, ENST00000546298, ENST00000895010, ENST00000895011, ENST00000895012, ENST00000895013, ENST00000895014, ENST00000895015, ENST00000895016, ENST00000895017, ENST00000895018, ENST00000932591, ENST00000932592, ENST00000932593, ENST00000932594, ENST00000955201, ENST00000955202, ENST00000955203, ENST00000955204, ENST00000955205, ENST00000955206, ENST00000955207, ENST00000955208, ENST00000955209, ENST00000955210, ENST00000955211, ENST00000955212, ENST00000955213, ENST00000955214, ENST00000955215

RefSeq mRNA: 2 — MANE Select: NM_003651 NM_001145426, NM_003651

CCDS: CCDS44831, CCDS8630

Canonical transcript exons

ENST00000228251 — 10 exons

Exon	Start	End
ENSE00001208872	10699089	10699654
ENSE00002302711	10722850	10723323
ENSE00003486859	10715694	10715783
ENSE00003497534	10701254	10701353
ENSE00003522598	10718088	10718121
ENSE00003554552	10713211	10713333
ENSE00003572809	10704051	10704148
ENSE00003601328	10709908	10710114
ENSE00003656513	10719080	10719143
ENSE00003661596	10701960	10702134

Expression profiles

Bgee: expression breadth ubiquitous, 300 present calls, max score 99.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 94.7827 / max 7124.7536, expressed in 1809 samples.

FANTOM5 promoters (22 alternative TSS)

Promoter ID	TPM avg	Samples expressed
129567	90.0203	1809
129557	0.9709	596
129540	0.7142	306
129550	0.7008	233
129546	0.6360	315
129542	0.1908	63
129551	0.1875	38
129559	0.1724	50
129558	0.1686	45
129548	0.1585	36

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	99.93	gold quality
muscle of leg	UBERON:0001383	99.89	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	99.89	gold quality
hindlimb stylopod muscle	UBERON:0004252	99.88	gold quality
body of tongue	UBERON:0011876	99.88	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	99.86	gold quality
skeletal muscle tissue	UBERON:0001134	99.85	gold quality
vastus lateralis	UBERON:0001379	99.84	gold quality
muscle organ	UBERON:0001630	99.84	gold quality
skeletal muscle organ	UBERON:0014892	99.84	gold quality
tibialis anterior	UBERON:0001385	99.83	gold quality
biceps brachii	UBERON:0001507	99.83	gold quality
deltoid	UBERON:0001476	99.79	gold quality
triceps brachii	UBERON:0001509	99.77	gold quality
diaphragm	UBERON:0001103	99.75	gold quality
gluteal muscle	UBERON:0002000	99.75	gold quality
left testis	UBERON:0004533	99.74	gold quality
right testis	UBERON:0004534	99.72	gold quality
lower lobe of lung	UBERON:0008949	99.70	gold quality
parotid gland	UBERON:0001831	99.69	gold quality
penis	UBERON:0000989	99.68	gold quality
adult organism	UBERON:0007023	99.65	gold quality
pharyngeal mucosa	UBERON:0000355	99.64	gold quality
heart right ventricle	UBERON:0002080	99.62	gold quality
muscle tissue	UBERON:0002385	99.61	gold quality
trabecular bone tissue	UBERON:0002483	99.61	gold quality
upper leg skin	UBERON:0004262	99.61	gold quality
cauda epididymis	UBERON:0004360	99.60	gold quality
quadriceps femoris	UBERON:0001377	99.59	gold quality
skin of abdomen	UBERON:0001416	99.59	gold quality

Single-cell (SCXA)

Detected in 21 experiment(s), a significant marker in 19.

Experiment	Marker?	Max mean expression
E-CURD-122	yes	1925.56
E-MTAB-9221	yes	1077.22
E-HCAD-1	yes	216.59
E-HCAD-4	yes	63.62
E-HCAD-6	yes	62.59
E-MTAB-10287	yes	47.77
E-MTAB-7316	yes	35.52
E-MTAB-6701	yes	28.08
E-GEOD-81547	yes	24.82
E-MTAB-10042	yes	24.71
E-MTAB-8410	yes	20.03
E-MTAB-5061	yes	18.80
E-HCAD-9	yes	11.11
E-CURD-46	yes	11.00
E-ENAD-27	yes	6.84

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

29 targets.

Target	Regulation
ADAM2
APP
CAT	Unknown
CCND1	Unknown
CDK4
CUBN	Repression
EPHB4
ERBB2
F11R
FOS	Repression
GLB1
GSR
GTPBP1
HBG2	Repression
HSPA4
KCNA1
KRAS
LCT
LHB
LRP2
MUC1	Unknown
NEK1
PRM1
TAF8
TRIB3
VEGFA	Repression
VEGFC	Repression
YBX3
ZDHHC2

Upstream regulators (CollecTRI, top): E2F1, E2F4, MYC, YBX1, YBX3

miRNA regulators (miRDB)

79 targeting YBX3, 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-9-5P	100.00	72.28	2361
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
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-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-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349

Literature-anchored findings (GeneRIF, showing 23)

• human dbpA has a role in accelerating hepatocarcinogenesis (PMID:12239625)
• identification of complexes, binding to the vascular endothelial growth factor mRNA 5’- and 3’-UTR, that contain cold shock domain and polypyrimidine tract binding RNA binding proteins (PMID:14728692)
• ZONAB regulates the transcription of genes that are important for G1/S-phase progression and links tight junctions to the transcriptional control of key cell cycle regulators and epithelial cell differentiation. (PMID:16508013)
• The symplekin/ZONAB complex inhibits intestinal cell differentiation by the repression of AML1/Runx1. (PMID:19328795)
• The expression of human DBPA was upregulated in gastric cancer tissues and cell lines. siRNA treatment successfully silenced DBPA expression. (PMID:19749785)
• ZONAB is an important component of the mechanisms that sense epithelial density and participates in the complex transcriptional networks that regulate the switch between proliferation and differentiation (PMID:20133480)
• In human skeletal muscle cells, CSDA was upregulated during hypoxia when cells were damaged and apoptosis was induced. (PMID:21473684)
• DbpA promoter was methylated in 37.7% of HCC samples. (PMID:22159460)
• We demonstrate that ZONAB promotes cell survival in response to proinflammatory, hyperosmotic, and cytotoxic stress and that stress-induced ZONAB activation involves the Rho regulator GEF-H1. (PMID:22711822)
• In the prenatal brain, the cold shock domain protein A were found to be abundantly expressed in radial glial cells, neuroblasts and neurons. (PMID:24817634)
• Stratification according to Fuhrman grade disclosed higher YBX3 expression levels. (PMID:24885929)
• Data suggest that DNA binding protein A (dbpA) may be used as a therapeutic target in colorectal cancer (CRC). (PMID:27430286)
• dbpA knockdown in SW620 cells altered the expression of carcinogenesis-associated genes in Colorectal cancer. (PMID:27569444)
• Authors examined, for the first time in a Turkish population, the association between protamine gene alleles (PRM1 c.-190C>A, PRM1 c.197G>T, and PRM2 c.248C>T), and YBX2 (c.187T>C and c.1095 + 16A>G) and male infertility. (PMID:29227750)
• ZONAB is up-regulated in bladder cancer cell lines, which promotes invasion, demonstrating the important role it plays in tumorogenesis and cancer progression (PMID:30784285)
• YBX3 binds within the 3’ UTR of SLC7A5 to stabilize the transcript. (PMID:31189097)
• YB-3 substitutes YB-1 in global mRNA binding. (PMID:31944153)
• Y-Box-Binding Protein 3 (YBX3) Restricts Influenza A Virus by Interacting with Viral Ribonucleoprotein Complex and Imparing its Function. (PMID:32553055)
• Knockdown of DNA-binding protein A enhances the chemotherapy sensitivity of colorectal cancer via suppressing the Wnt/beta-catenin/Chk1 pathway. (PMID:32652867)
• Identification and verification of YBX3 and its regulatory gene HEIH as an oncogenic system: A multidimensional analysis in colon cancer. (PMID:36059530)
• Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma. (PMID:37418046)
• M6A-mediated-upregulation of lncRNA BLACAT3 promotes bladder cancer angiogenesis and hematogenous metastasis through YBX3 nuclear shuttling and enhancing NCF2 transcription. (PMID:37612524)
• The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5 mRNA in proliferating and differentiating skeletal muscle cells. (PMID:38159852)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ybx3	ENSMUSG00000030189
rattus_norvegicus	Ybx3	ENSRNOG00000005480
caenorhabditis_elegans		WBGENE00000472

Paralogs (4): YBX2 (ENSG00000006047), YBX1 (ENSG00000065978), LIN28A (ENSG00000131914), LIN28B (ENSG00000187772)

Protein

Protein identifiers

Y-box-binding protein 3 — P16989 (reviewed: P16989)

Alternative names: Cold shock domain-containing protein A, DNA-binding protein A, Single-strand DNA-binding protein NF-GMB

All UniProt accessions (2): P16989, A0A0D9SEI8

UniProt curated annotations — full annotation on UniProt →

Function. Binds to the GM-CSF promoter. Seems to act as a repressor. Also binds to full-length mRNA and to short RNA sequences containing the consensus site 5’-UCCAUCA-3’. May have a role in translation repression.

Subunit / interactions. Found in a mRNP complex with YBX2. Interacts with RRP1B.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Highly expressed in skeletal muscle and heart.

Isoforms (3)

UniProt ID	Names	Canonical?
P16989-1	1	yes
P16989-2	2
P16989-3	3

RefSeq proteins (2): NP_001138898, NP_003642* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002059	CSP_DNA-bd	Domain
IPR011129	CSD	Domain
IPR012340	NA-bd_OB-fold	Homologous_superfamily
IPR019844	CSD_CS	Conserved_site
IPR050181	Cold_shock_domain	Family

Pfam: PF00313

UniProt features (26 total): modified residue 13, compositionally biased region 5, splice variant 2, region of interest 2, initiator methionine 1, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P16989-F1	59.33	0.21

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 (13): 2, 2, 34, 134, 201, 203, 204, 251, 324, 326, 346, 369, 370

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 451 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, AAGCAAT_MIR137, GOBP_REGULATION_OF_SKELETAL_MUSCLE_TISSUE_DEVELOPMENT, GOBP_MUSCLE_TISSUE_DEVELOPMENT, GRUETZMANN_PANCREATIC_CANCER_DN, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_RESPONSE_TO_PEPTIDE, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, CMYB_01, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_3_UTR_MEDIATED_MRNA_STABILIZATION, GOBP_GROWTH, GOBP_MACROMOLECULE_CATABOLIC_PROCESS

GO Biological Process (19): negative regulation of transcription by RNA polymerase II (GO:0000122), in utero embryonic development (GO:0001701), apoptotic process (GO:0006915), spermatogenesis (GO:0007283), male gonad development (GO:0008584), fertilization (GO:0009566), regulation of gene expression (GO:0010468), ectopic germ cell programmed cell death (GO:0035234), positive regulation of organ growth (GO:0046622), negative regulation of skeletal muscle tissue development (GO:0048642), negative regulation of necroptotic process (GO:0060546), 3’-UTR-mediated mRNA stabilization (GO:0070935), cellular response to tumor necrosis factor (GO:0071356), cellular hyperosmotic response (GO:0071474), negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219), negative regulation of reproductive process (GO:2000242), positive regulation of cytoplasmic translation (GO:2000767), negative regulation of apoptotic process (GO:0043066), negative regulation of developmental process (GO:0051093)

GO Molecular Function (8): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), mRNA 3’-UTR binding (GO:0003730), small GTPase binding (GO:0031267), ribonucleoprotein complex binding (GO:0043021), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), bicellular tight junction (GO:0005923), synapse (GO:0045202), perinuclear region of cytoplasm (GO:0048471)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
developmental process involved in reproduction	2
reproductive process	2
negative regulation of biological process	2
binding	2
nucleic acid binding	2
cytoplasm	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
chordate embryonic development	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
male gamete generation	1
gonad development	1
development of primary male sexual characteristics	1
sexual reproduction	1
gene expression	1
regulation of macromolecule biosynthetic process	1
programmed cell death involved in cell development	1
organ growth	1
regulation of organ growth	1
positive regulation of developmental growth	1
positive regulation of multicellular organismal process	1
skeletal muscle tissue development	1
negative regulation of striated muscle tissue development	1
regulation of skeletal muscle tissue development	1
regulation of necroptotic process	1
negative regulation of programmed necrotic cell death	1
necroptotic process	1
mRNA stabilization	1
response to tumor necrosis factor	1
cellular response to cytokine stimulus	1
hyperosmotic response	1
cellular response to osmotic stress	1
intrinsic apoptotic signaling pathway in response to osmotic stress	1
regulation of intrinsic apoptotic signaling pathway in response to osmotic stress	1
negative regulation of intrinsic apoptotic signaling pathway	1
regulation of reproductive process	1

Protein interactions and networks

STRING

2212 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YBX3	DCN	P07585	991
YBX3	TJP1	Q07157	979
YBX3	RALA	P11233	738
YBX3	RALB	P11234	723
YBX3	TJP2	Q9UDY2	701
YBX3	YBX1	P16990	638
YBX3	OCLN	Q16625	632
YBX3	CCND1	P24385	626
YBX3	ARHGEF2	Q92974	621
YBX3	SYMPK	Q92797	599
YBX3	CGN	Q9P2M7	571
YBX3	SPN	P16150	557
YBX3	CSNK2A1	P19138	548
YBX3	HNRNPA1	P09651	533
YBX3	RAB3B	P20337	532

IntAct

253 interactions, top by confidence:

A	B	Type	Score
IFIT2	IFIT3	psi-mi:“MI:0914”(association)	0.780
H2AX	PPM1G	psi-mi:“MI:0914”(association)	0.730
HAUS6	HAUS5	psi-mi:“MI:0914”(association)	0.710
IGF2BP1	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
PPP1CA	YBX3	psi-mi:“MI:0915”(physical association)	0.540
PPP1CA	YBX3	psi-mi:“MI:0403”(colocalization)	0.540
E4F1	ZBTB24	psi-mi:“MI:0914”(association)	0.530
RPL6	MRPS14	psi-mi:“MI:0914”(association)	0.530
BHLHA15	RPLP0	psi-mi:“MI:0914”(association)	0.530
NCBP3	SAP18	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
YBX1	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
AGO1	AIP	psi-mi:“MI:0914”(association)	0.530
SNRNP70	GTPBP1	psi-mi:“MI:0914”(association)	0.530
ZC3HAV1	KHNYN	psi-mi:“MI:0914”(association)	0.530
THAP3	CASC3	psi-mi:“MI:0914”(association)	0.530
H2AC20	PPM1G	psi-mi:“MI:0914”(association)	0.530
SART3	NSA2	psi-mi:“MI:0914”(association)	0.530
MRPL2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
GSPT2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
RRP1B	NPM1	psi-mi:“MI:0914”(association)	0.510
UXT	YBX3	psi-mi:“MI:0915”(physical association)	0.500

BioGRID (473): YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), YBX3 (Affinity Capture-MS), ABCB7 (Co-fractionation), ATP6V0D1 (Co-fractionation), COX5A (Co-fractionation)

ESM2 similar proteins: A1L1K8, B5DE31, D5MCN2, O94432, O95817, P14199, P16989, P21573, P21574, P25567, P41073, P41824, P45441, P45978, P46553, P62960, P62961, P67808, P67809, Q00436, Q06066, Q09801, Q10193, Q10422, Q10475, Q21351, Q24629, Q28618, Q3TLH4, Q57UZ7, Q5JVS0, Q5UR41, Q5XJD3, Q62764, Q69Z08, Q6CVS3, Q6NRY1, Q6NYG6, Q6PB22, Q75A59

Diamond homologs: B5DE31, E0J1Q3, E0J500, E1WGN1, O30875, O54310, O65639, O67327, P0A355, P0A356, P0A357, P0A358, P0A361, P0A362, P0A363, P0A972, P0A973, P0A974, P0A975, P0A978, P0A979, P0A980, P0A981, P0A986, P0A987, P0A9X9, P0A9Y0, P0A9Y1, P0A9Y2, P0A9Y3, P0A9Y4, P0A9Y5, P0A9Y6, P0A9Y7, P0A9Y8, P0A9Y9, P0A9Z0, P0C0F1, P0CL01, P0DA48

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 224 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
Transport of Mature Transcript to Cytoplasm	7	18.5×	2e-06
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	18	14.7×	1e-13
Eukaryotic Translation Termination	16	13.4×	6e-12
Peptide chain elongation	15	13.2×	3e-11
Viral mRNA Translation	15	13.2×	3e-11
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	15	13.1×	3e-11
Nonsense-Mediated Decay (NMD)	8	12.9×	5e-06
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	19	12.9×	1e-13

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	18	17.1×	1e-14
negative regulation of translation	12	12.1×	1e-07
ribosomal small subunit biogenesis	10	11.7×	3e-06
translation	22	11.6×	1e-14
regulation of alternative mRNA splicing, via spliceosome	8	10.0×	2e-04
mRNA export from nucleus	6	9.1×	4e-03
mitochondrial translation	10	8.9×	4e-05
RNA processing	7	7.9×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	73
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1784 predictions. Top by Δscore:

Variant	Effect	Δscore
12:10699653:ACC:A	acceptor_loss	1.0000
12:10701249:CTTA:C	donor_loss	1.0000
12:10701250:TTAC:T	donor_loss	1.0000
12:10701251:TACCT:T	donor_loss	1.0000
12:10701252:A:AC	donor_gain	1.0000
12:10701252:ACCTG:A	donor_gain	1.0000
12:10701253:C:CA	donor_loss	1.0000
12:10701253:C:CC	donor_gain	1.0000
12:10701253:CCTG:C	donor_gain	1.0000
12:10701253:CCTGC:C	donor_gain	1.0000
12:10701349:TTGGC:T	acceptor_gain	1.0000
12:10701350:TGGC:T	acceptor_gain	1.0000
12:10701350:TGGCC:T	acceptor_gain	1.0000
12:10701351:GGC:G	acceptor_gain	1.0000
12:10701351:GGCCT:G	acceptor_gain	1.0000
12:10701352:GC:G	acceptor_gain	1.0000
12:10701352:GCC:G	acceptor_gain	1.0000
12:10701353:CC:C	acceptor_gain	1.0000
12:10701353:CCT:C	acceptor_gain	1.0000
12:10701354:C:A	acceptor_gain	1.0000
12:10701354:C:CC	acceptor_gain	1.0000
12:10701354:C:G	acceptor_loss	1.0000
12:10701354:C:T	acceptor_gain	1.0000
12:10701359:A:AC	acceptor_gain	1.0000
12:10701359:A:C	acceptor_gain	1.0000
12:10701957:TACCT:T	donor_loss	1.0000
12:10701958:A:AC	donor_gain	1.0000
12:10701959:C:CA	donor_loss	1.0000
12:10701959:C:CC	donor_gain	1.0000
12:10701959:CCT:C	donor_gain	1.0000

AlphaMissense

2374 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:10713272:G:T	A171D	1.000
12:10713275:T:C	Y170C	1.000
12:10713276:A:C	Y170D	1.000
12:10713276:A:G	Y170H	1.000
12:10713280:A:C	S168R	1.000
12:10713280:A:T	S168R	1.000
12:10713281:C:A	S168I	1.000
12:10713282:T:G	S168R	1.000
12:10713284:C:A	G167V	1.000
12:10713284:C:G	G167A	1.000
12:10713284:C:T	G167E	1.000
12:10713285:C:A	G167W	1.000
12:10713285:C:G	G167R	1.000
12:10713285:C:T	G167R	1.000
12:10713290:A:T	V165E	1.000
12:10713291:C:T	V165M	1.000
12:10713299:C:A	G162V	1.000
12:10713299:C:T	G162E	1.000
12:10713308:C:A	G159V	1.000
12:10713308:C:T	G159D	1.000
12:10713309:C:A	G159C	1.000
12:10713309:C:G	G159R	1.000
12:10713311:G:A	T158I	1.000
12:10713314:A:C	V157G	1.000
12:10713314:A:G	V157A	1.000
12:10713314:A:T	V157E	1.000
12:10713315:C:A	V157L	1.000
12:10713315:C:G	V157L	1.000
12:10713315:C:T	V157M	1.000
12:10713321:C:G	A155P	1.000

dbSNP variants (sampled 300 via entrez): RS1000007588 (12:10706360 C>T), RS1000115625 (12:10706434 C>G), RS1000386084 (12:10718398 A>C,G), RS1000564134 (12:10712528 C>A), RS1000858380 (12:10713336 G>A,T), RS1000873700 (12:10717886 T>C), RS1000912028 (12:10713844 T>C), RS1001004792 (12:10707866 T>C), RS1001069257 (12:10707439 C>G,T), RS1001202021 (12:10699226 T>A), RS1001247558 (12:10721729 T>C), RS1001263038 (12:10719560 A>G), RS1001275794 (12:10699576 G>A), RS1001565629 (12:10710788 T>C), RS1001678990 (12:10721974 C>T)

Disease associations

OMIM: gene MIM:603437 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST010002_208	Refractive error	5.000000e-09
GCST010866_91	Coronary artery disease	5.000000e-09
GCST010867_4	Coronary artery disease	7.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4295720 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, increases expression, affects cotreatment	6
methylmercuric chloride	increases expression, affects cotreatment	3
sodium arsenite	decreases expression, increases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	2
Air Pollutants	increases abundance, increases expression, affects cotreatment, decreases expression	2
Cisplatin	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Cyclosporine	increases expression	2
Aflatoxin B1	affects expression, increases expression	2
Cadmium Chloride	decreases expression	2
FR900359	decreases phosphorylation	1
dicrotophos	increases expression	1
beauvericin	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
deoxynivalenol	increases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression, decreases expression	1
beta-lapachone	increases expression	1
arsenite	affects expression	1
cobaltous chloride	increases expression	1
4-hydroxy-2-nonenal	decreases expression	1
periodate-oxidized adenosine	affects expression	1
coumarin	decreases phosphorylation	1
nivalenol	increases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
chloropicrin	decreases expression	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases expression, affects cotreatment	1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4118551	Binding	Binding affinity to YBX3 in human NCI-H23 cells at 1 uM by mass spectrometry based pull down assay	Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. — Bioorg Med Chem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3LF	Abcam HEK293T YBX3 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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