SERBP1

Summary

SERBP1 (SERPINE1 mRNA binding protein 1, HGNC:17860) is a protein-coding gene on chromosome 1p31.3, encoding SERPINE1 mRNA-binding protein 1 (Q8NC51). Ribosome-binding protein that promotes ribosome hibernation, a process during which ribosomes are stabilized in an inactive state and preserved from proteasomal degradation. It is a selective cancer dependency (DepMap: 68.1% of cell lines).

Enables several functions, including SUMO binding activity; mRNA 3’-UTR binding activity; and ribosome binding activity. Involved in PML body organization and ribosome hibernation. Located in cytosol and nucleus.

Source: NCBI Gene 26135 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 68 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 68.1% of screened cell lines
• MANE Select transcript: NM_001018069

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17860
Approved symbol	SERBP1
Name	SERPINE1 mRNA binding protein 1
Location	1p31.3
Locus type	gene with protein product
Status	Approved
Aliases	CGI-55, CHD3IP, HABP4L, Hero45, PAIRBP1, PAI-RBP1, DKFZP564M2423
Ensembl gene	ENSG00000142864
Ensembl biotype	protein_coding
OMIM	607378
Entrez	26135

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 13 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000361219, ENST00000370990, ENST00000370994, ENST00000370995, ENST00000462814, ENST00000484880, ENST00000490406, ENST00000493607, ENST00000864512, ENST00000864513, ENST00000864514, ENST00000864515, ENST00000864516, ENST00000864517, ENST00000912597, ENST00000912598, ENST00000963867

RefSeq mRNA: 4 — MANE Select: NM_001018069 NM_001018067, NM_001018068, NM_001018069, NM_015640

CCDS: CCDS30746, CCDS30747, CCDS30748, CCDS639

Canonical transcript exons

ENST00000361219 — 8 exons

Exon	Start	End
ENSE00001454078	67407810	67413263
ENSE00001814983	67429988	67430402
ENSE00003538495	67420009	67420186
ENSE00003554001	67415166	67415339
ENSE00003563657	67424888	67424977
ENSE00003596922	67424200	67424277
ENSE00003605347	67425083	67425223
ENSE00003652656	67426135	67426285

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 78.0910 / max 997.1908, expressed in 1821 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12747	62.4854	1816
12748	13.6133	1788
12746	1.9830	958
12745	0.0092	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	99.54	gold quality
calcaneal tendon	UBERON:0003701	99.52	gold quality
biceps brachii	UBERON:0001507	99.51	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	99.38	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.36	gold quality
upper leg skin	UBERON:0004262	99.28	gold quality
trabecular bone tissue	UBERON:0002483	99.23	gold quality
parietal pleura	UBERON:0002400	99.17	gold quality
mammalian vulva	UBERON:0000997	99.13	gold quality
esophagus squamous epithelium	UBERON:0006920	99.12	gold quality
colonic mucosa	UBERON:0000317	99.10	gold quality
pleura	UBERON:0000977	99.09	gold quality
triceps brachii	UBERON:0001509	99.07	gold quality
ventricular zone	UBERON:0003053	99.07	gold quality
gingiva	UBERON:0001828	99.05	gold quality
gluteal muscle	UBERON:0002000	99.05	gold quality
skin of hip	UBERON:0001554	99.04	gold quality
gingival epithelium	UBERON:0001949	99.03	gold quality
oral cavity	UBERON:0000167	99.02	gold quality
tibia	UBERON:0000979	99.01	gold quality
visceral pleura	UBERON:0002401	99.00	gold quality
embryo	UBERON:0000922	98.99	gold quality
cortical plate	UBERON:0005343	98.99	gold quality
squamous epithelium	UBERON:0006914	98.96	gold quality
heart right ventricle	UBERON:0002080	98.94	gold quality
corpus epididymis	UBERON:0004359	98.91	gold quality
cartilage tissue	UBERON:0002418	98.86	gold quality
caput epididymis	UBERON:0004358	98.84	gold quality
sperm	CL:0000019	98.83	gold quality
cauda epididymis	UBERON:0004360	98.83	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-MTAB-9067	yes	20.33
E-CURD-46	yes	19.89
E-CURD-122	yes	19.44
E-MTAB-10042	yes	14.24
E-MTAB-10596	no	1075.39
E-MTAB-8271	no	823.10
E-MTAB-8911	no	272.47
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): F3, SOX17, SRY, USF1

miRNA regulators (miRDB)

225 targeting SERBP1, 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-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AJ-3P	99.96	73.38	5345

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 68.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 29)

• This gene encodes a protein, PAI-RBP1, that binds to an RNA sequence (cyclic nucleotide responsive sequence, CRS) in the plasminogen activator-inhibitor (PAI-1) mRNA that confers cAMP regulation of mRNA stability. (PMID:11001948)
• The 4G allele of the 4G/5G polymorphism in the PAI-1 gene may be a risk factor for IgE-mediated asthma and allergic diseases. (PMID:11972486)
• Polymorphism of the PAI-1 gene promoter does not influence the development of AAA. However, the effect of PAI-1 genotype (5G5G) appears protective on survival following open aneurysm repair. (PMID:12027469)
• interacts with the C-terminal region of the human chromatin-remodeling factor CHD-3 (PMID:12505151)
• We observed that CGI-55 localizes to the nucleolus and co-localizes with p80-coilin positive nuclear-coiled bodies. (PMID:16679534)
• Has two conserved Gly/Arg-rich motif clusters (RGG/RXR box, where X is any amino acid) that may be substrates for arginine-methylation by protein arginine-methyltransferase-1 (PRMT1). (PMID:16879614)
• The presence of the genotype risk factors alone does not seem to be associated with the development of preeclampsia even in the severe presentation form. PAI-1 gene polymorphisms on the development of the preeclampsia was indicated. (PMID:16963292)
• In ovarian cancer, PAI-RBP1 is significantly overexpressed in tumor epithelial cells, suggesting a biological role in tumor invasion and metastasis. Its expression is higher in advanced disease. (PMID:17698176)
• The aim of this study was to assess the expression, localization and hormonal regulation of two novel P(4) receptor candidates, P(4) receptor membrane component (PGRMC) 1 and PGRMC2, as well as the PGRMC1 partner Serpine 1 mRNA binding protein (SERBP1). (PMID:18440126)
• PAI-RBP1 expression level is higher in non-small lung cancer tissues than in normal tissues. (PMID:22373659)
• The RG-rich and RGG box of SERBP1 is asymmetrically dimethylated by PRMT1 and the modification affects protein interaction and intracellular localization of the protein. (PMID:22442049)
• The RNA-binding protein SERBP1 is abundantly expressed in human breast cancer and may represent a novel breast tumour marker with prognostic significance (PMID:23236990)
• Pseudomyogenic haemangioendothelioma consistently displays a SERPINE1-FOSB fusion gene, resulting from a translocation between chromosomes 7 and 19. (PMID:24374978)
• SERBP1 is a component of the LRH-1 transcriptional complex. (PMID:26398198)
• The effects of progesterone treatment on the expression levels of progesterone receptor membrane component 1 (PGRMC1), plasminogen activator inhibitor 1 RNA-binding protein (PAIRBP1), and progestin and adipoQ receptor 7 (PAQR7) on both mRNA and protein levels were investigated in spheroids derived from human glioma cell lines U-87 MG and LN-229. (PMID:27340667)
• Data indicate that serpine1 messenger RNA (mRNA) binding protein 1 (SERBP1) was identified as a downstream target of microRNA miR-26a-5p. (PMID:27449037)
• STMN1,COF1 and PAIRBP1 thus represent proteins associated with proliferative and aggressive tumors of high grades, while TSP2 and POSTN were connected to low grade tumors with better prognosis (PMID:28216224)
• Analysis of deletion constructs of SERBP1 showed that the C-terminal third of the SERBP1 protein, which contains one of its two substrate sites for protein arginine N-methyltransferase 1 (PRMT1), is necessary and sufficient for it to interact with RACK1 (PMID:28267599)
• All these results suggested that miR-218/SERBP1 signal pathway could inhibit the malignant phenotype formation and that targeting this pathway may be a potential novel way for HCC therapeutics. (PMID:28369267)
• we revealed that PVT1 functions as an endogenous “sponge” by competing for miR-448 binding to regulate the miRNA target SERBP1 and, therefore, promotes the proliferation and migration of PC cells. (PMID:28657147)
• Report a dynamic pattern of PGRMC1 and SERBP1 expression in human endometrium throughout the menstrual cycle and highlight a putative novel implication of PGRMC1 in the human decidualization process. (PMID:28911927)
• The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation. (PMID:32762776)
• miR-362-3p acts as a tumor suppressor by targeting SERBP1 in ovarian cancer. (PMID:33526047)
• CircRNA circBACH1 (hsa_circ_0061395) serves as a miR-656-3p sponge to facilitate hepatocellular carcinoma progression through increasing SERBP1 expression. (PMID:33831787)
• G-Quadruplex-Induced Liquid-Liquid Phase Separation in Biomimetic Protocells. (PMID:34270902)
• Circ_0046600 promotes hepatocellular carcinoma progression via up-regulating SERBP1 through sequestering miR-1258. (PMID:34784519)
• A genetically-encoded crosslinker screen identifies SERBP1 as a PKCepsilon substrate influencing translation and cell division. (PMID:34836941)
• YY1-induced long non-coding RNA small nucleolar RNA host gene 8 promotes the tumorigenesis of melanoma via the microRNA-656-3p/SERPINE1 mRNA binding protein 1 axis. (PMID:35156513)
• SERPINE1 mRNA Binding Protein 1 Is Associated with Ischemic Stroke Risk: A Comprehensive Molecular-Genetic and Bioinformatics Analysis of SERBP1 SNPs. (PMID:37240062)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	serbp1a	ENSDARG00000074242
danio_rerio	serbp1b	ENSDARG00000087421
mus_musculus	Serbp1	ENSMUSG00000036371
rattus_norvegicus	Serbp1	ENSRNOG00000005890
drosophila_melanogaster	vig	FBGN0024183
drosophila_melanogaster	PPYR1	FBGN0030623
drosophila_melanogaster	vig2	FBGN0046214

Paralogs (1): HABP4 (ENSG00000130956)

Protein

Protein identifiers

SERPINE1 mRNA-binding protein 1 — Q8NC51 (reviewed: Q8NC51)

Alternative names: PAI1 RNA-binding protein 1, Plasminogen activator inhibitor 1 RNA-binding protein

All UniProt accessions (2): Q8NC51, Q5VU21

UniProt curated annotations — full annotation on UniProt →

Function. Ribosome-binding protein that promotes ribosome hibernation, a process during which ribosomes are stabilized in an inactive state and preserved from proteasomal degradation. Acts via its association with EEF2/eEF2 factor, sequestering EEF2/eEF2 at the A-site of the ribosome and promoting ribosome stabilization and storage in an inactive state. May also play a role in the regulation of mRNA stability: binds to the 3’-most 134 nt of the SERPINE1/PAI1 mRNA, a region which confers cyclic nucleotide regulation of message decay. Seems to play a role in PML-nuclear bodies formation.

Subunit / interactions. Associates with mature 80S ribosomes. Interacts with EEF2/eEF2; interaction sequesters EEF2/eEF2 at the A-site of the ribosome, thereby blocking the interaction sites of the mRNA-tRNA complex, promoting ribosome stabilization and hibernation. Interacts with SPIN1. Interacts with CHD3 and TDRD3. Interacts with ZDHHC17 (via ANK repeats).

Subcellular location. Cytoplasm. Nucleus. Perinuclear region.

Tissue specificity. Expressed at high level in the heart, skeletal muscle and kidney, and at low levels in placenta, liver and brain.

Post-translational modifications. Phosphorylation by MTOR inhibits SERBP1 and relieves ribosome hibernation.

Miscellaneous. May be due to a competing acceptor splice site. May be due to a competing acceptor splice site.

Similarity. Belongs to the SERBP1-HABP4 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8NC51-1	1	yes
Q8NC51-2	2
Q8NC51-3	3
Q8NC51-4	4

RefSeq proteins (4): NP_001018077, NP_001018078, NP_001018079, NP_056455 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006861	HABP4_PAIRBP1-bd	Domain
IPR032381	IHABP4_N	Domain
IPR039764	HABP4/SERBP1-like	Family

Pfam: PF04774, PF16174

UniProt features (62 total): modified residue 28, compositionally biased region 11, cross-link 10, sequence conflict 4, mutagenesis site 3, region of interest 2, splice variant 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

29 structures.

PDB	Method	Resolution (Å)
9PBE	ELECTRON MICROSCOPY	2.19
8K2C	ELECTRON MICROSCOPY	2.4
8XSX	ELECTRON MICROSCOPY	2.4
9P7D	ELECTRON MICROSCOPY	2.57
9P7E	ELECTRON MICROSCOPY	2.59
9PA7	ELECTRON MICROSCOPY	2.67
9P7C	ELECTRON MICROSCOPY	2.78
9P7A	ELECTRON MICROSCOPY	2.81
9B0P	ELECTRON MICROSCOPY	2.82
9FQZ	ELECTRON MICROSCOPY	2.85
6Z6N	ELECTRON MICROSCOPY	2.9
9P78	ELECTRON MICROSCOPY	2.9
9RSX	ELECTRON MICROSCOPY	2.91
9I2E	ELECTRON MICROSCOPY	2.95
8XSY	ELECTRON MICROSCOPY	3
8UKB	ELECTRON MICROSCOPY	3.05
6Z6M	ELECTRON MICROSCOPY	3.1
9P79	ELECTRON MICROSCOPY	3.1
9P8C	ELECTRON MICROSCOPY	3.11
8XSZ	ELECTRON MICROSCOPY	3.2
8Y0X	ELECTRON MICROSCOPY	3.3
8Y0W	ELECTRON MICROSCOPY	3.4
4V6X	ELECTRON MICROSCOPY	5
9AZC
9AZM
9B0F
9B0G
9B0H
9B0R

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NC51-F1	54.57	0.00

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 (38): 25, 52, 68, 122, 140, 165, 188, 197, 199, 203, 205, 208, 211, 216, 221, 226, 234, 329, 330, 364 …

Mutagenesis-validated functional residues (3):

Position	Phenotype
102	not sumoylated; when associated with r-228 and r-281.
228	not sumoylated; when associated with r-102 and r-281.
281	not sumoylated; when associated with r-102 and r-228.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 321 (showing top): MODULE_52, E2F_Q4_01, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GNF2_MSH2, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, BASSO_B_LYMPHOCYTE_NETWORK, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, YANG_BREAST_CANCER_ESR1_LASER_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, MORF_HDAC2, MODULE_16, GNF2_MCM5, USF_C

GO Biological Process (5): negative regulation of translation (GO:0017148), PML body organization (GO:0030578), regulation of mRNA stability (GO:0043488), ribosome hibernation (GO:0141014), regulation of translation (GO:0006417)

GO Molecular Function (8): RNA binding (GO:0003723), mRNA 3’-UTR binding (GO:0003730), translation repressor activity (GO:0030371), SUMO binding (GO:0032183), ribosome binding (GO:0043022), cadherin binding (GO:0045296), translation elongation factor binding (GO:0061770), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
translation	2
negative regulation of translation	2
cytoplasm	2
regulation of translation	1
negative regulation of gene expression	1
negative regulation of protein metabolic process	1
nuclear body organization	1
regulation of RNA stability	1
regulation of mRNA catabolic process	1
post-transcriptional regulation of gene expression	1
regulation of protein metabolic process	1
nucleic acid binding	1
mRNA binding	1
translation regulator activity	1
ubiquitin-like protein binding	1
ribonucleoprotein complex binding	1
cell adhesion molecule binding	1
protein binding	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
extracellular vesicle	1

Protein interactions and networks

STRING

3096 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SERBP1	PGRMC1	O00264	901
SERBP1	DAXX	Q9UER7	810
SERBP1	SERPINE1	P05121	797
SERBP1	RACK1	P25388	587
SERBP1	PAQR8	Q8TEZ7	574
SERBP1	PAQR7	Q86WK9	572
SERBP1	PGR	P06401	552
SERBP1	HNRNPU	Q00839	546
SERBP1	AGO2	Q9UKV8	543
SERBP1	FMR1	Q06787	528
SERBP1	PGRMC2	O15173	523
SERBP1	G3BP1	Q13283	517
SERBP1	PABPC1	P11940	515
SERBP1	IFRD2	Q12894	510
SERBP1	HNRNPC	P07910	507

IntAct

314 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
IGF2BP1	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
SERBP1	CHD3	psi-mi:“MI:0915”(physical association)	0.580
CHD3	SERBP1	psi-mi:“MI:0915”(physical association)	0.580
SERBP1	PICK1	psi-mi:“MI:0915”(physical association)	0.560
SERBP1	SERPINH1	psi-mi:“MI:0915”(physical association)	0.560
SERBP1	PECAM1	psi-mi:“MI:0915”(physical association)	0.560
SERBP1	TGFBR2	psi-mi:“MI:0915”(physical association)	0.560
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
ST6GALNAC6	SERBP1	psi-mi:“MI:0915”(physical association)	0.400
CLIP1	SERBP1	psi-mi:“MI:0915”(physical association)	0.400
RAG1	SERBP1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1745): SERBP1 (Affinity Capture-MS), SERBP1 (Affinity Capture-MS), SERBP1 (Two-hybrid), SERBP1 (Reconstituted Complex), SERBP1 (Affinity Capture-MS), BASP1 (Co-fractionation), FAU (Co-fractionation), OTUB1 (Co-fractionation), RPL37A (Co-fractionation), SERBP1 (Co-fractionation), SERBP1 (Co-fractionation), SERBP1 (Co-fractionation), SERBP1 (Co-fractionation), SERBP1 (Co-fractionation), WDR5 (Co-fractionation)

ESM2 similar proteins: A0A1D8PK71, A0A385XIL0, A1L1K8, A5DI69, A6RVU0, A6ZPB3, A7TQ21, A8XXB0, G0S636, G0S8I1, G1SW77, J9VI89, O13802, O14369, O16053, O23593, O42914, P15891, P25441, P36049, P39015, P39935, P39936, P42846, P45978, P87128, Q05775, Q09252, Q54JD4, Q5ACM9, Q5AQ12, Q5JVS0, Q5XJA5, Q6AXS5, Q6BJ82, Q6C7G8, Q6CMJ8, Q6CQI2, Q6CWY0, Q6FY89

Diamond homologs: A1L1K8, A6NCW0, A6NCW7, A8MUK1, C9J2P7, C9JJH3, C9JLJ4, C9JPN9, C9JVI0, D6R901, D6R9N7, D6RA61, D6RBQ6, D6RCP7, D6RJB6, G1SW77, P0C7H9, P0C7I0, Q0WX57, Q5JVS0, Q5XJA5, Q6AXS5, Q6NRY1, Q6PB22, Q6R6M4, Q7RTZ2, Q8NC51, Q9CY58, Q9I9R0, Q9JKS5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 178 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
Nonsense-Mediated Decay (NMD)	8	13.3×	6e-06
Eukaryotic Translation Initiation	6	13.2×	2e-04
Cap-dependent Translation Initiation	6	13.2×	2e-04
SARS-CoV-1 modulates host translation machinery	6	13.2×	2e-04
Formation of the ternary complex, and subsequently, the 43S complex	8	12.3×	1e-05
Eukaryotic Translation Elongation	6	11.9×	3e-04
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	14	11.8×	3e-09
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	6	11.7×	3e-04

GO biological processes:

GO term	Partners	Fold	FDR
stress granule assembly	6	23.0×	5e-05
cytoplasmic translation	13	15.3×	3e-09
autophagosome maturation	6	13.4×	8e-04
mitophagy	6	12.2×	1e-03
translational initiation	5	11.4×	5e-03
negative regulation of translation	9	11.2×	4e-05
positive regulation of translation	7	10.2×	8e-04
autophagosome assembly	7	10.0×	8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1361 predictions. Top by Δscore:

Variant	Effect	Δscore
1:67413259:CTTGA:C	acceptor_gain	1.0000
1:67413264:C:CC	acceptor_gain	1.0000
1:67415162:TTA:T	donor_loss	1.0000
1:67415163:TAC:T	donor_loss	1.0000
1:67415164:A:AC	donor_gain	1.0000
1:67415164:AC:A	donor_gain	1.0000
1:67415164:ACCTT:A	donor_loss	1.0000
1:67415165:C:A	donor_loss	1.0000
1:67415165:C:CA	donor_gain	1.0000
1:67415165:CC:C	donor_gain	1.0000
1:67415335:TGAGC:T	acceptor_gain	1.0000
1:67415336:GAGC:G	acceptor_gain	1.0000
1:67415337:AGC:A	acceptor_gain	1.0000
1:67415338:GC:G	acceptor_gain	1.0000
1:67415339:CC:C	acceptor_gain	1.0000
1:67415340:C:CC	acceptor_gain	1.0000
1:67415340:C:T	acceptor_gain	1.0000
1:67415341:T:G	acceptor_loss	1.0000
1:67415346:A:AC	acceptor_gain	1.0000
1:67415346:A:C	acceptor_gain	1.0000
1:67415348:A:C	acceptor_gain	1.0000
1:67416427:A:AC	donor_gain	1.0000
1:67416428:C:CC	donor_gain	1.0000
1:67420008:CCTCT:C	donor_gain	1.0000
1:67420183:CTCC:C	acceptor_gain	1.0000
1:67420185:CC:C	acceptor_gain	1.0000
1:67420186:CC:C	acceptor_gain	1.0000
1:67420187:C:CC	acceptor_gain	1.0000
1:67424196:TTA:T	donor_loss	1.0000
1:67424197:TA:T	donor_loss	1.0000

AlphaMissense

2564 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:67413214:A:G	L407P	1.000
1:67413214:A:T	L407Q	1.000
1:67413222:G:C	F404L	1.000
1:67413222:G:T	F404L	1.000
1:67413223:A:C	F404C	1.000
1:67413223:A:G	F404S	1.000
1:67413224:A:G	F404L	1.000
1:67415257:C:T	G360E	1.000
1:67415259:A:C	F359L	1.000
1:67415259:A:T	F359L	1.000
1:67415260:A:C	F359C	1.000
1:67415260:A:G	F359S	1.000
1:67415261:A:C	F359V	1.000
1:67415261:A:G	F359L	1.000
1:67415266:A:C	I357S	1.000
1:67415266:A:G	I357T	1.000
1:67415266:A:T	I357N	1.000
1:67415272:A:G	L355P	1.000
1:67415284:A:T	I351K	1.000
1:67415287:T:A	D350V	1.000
1:67415288:C:G	D350H	1.000
1:67420031:A:G	L325P	1.000
1:67420031:A:T	L325H	1.000
1:67420040:C:T	G322E	1.000
1:67420041:C:G	G322R	1.000
1:67420041:C:T	G322R	1.000
1:67420048:C:A	W319C	1.000
1:67420048:C:G	W319C	1.000
1:67420050:A:G	W319R	1.000
1:67420050:A:T	W319R	1.000

dbSNP variants (sampled 300 via entrez): RS1000050897 (1:67430470 G>A,C), RS1000096209 (1:67430487 C>T), RS1000116282 (1:67414700 C>A), RS1000185212 (1:67409425 A>C), RS1000254052 (1:67414335 T>C), RS1000436092 (1:67408807 GCTAC>G), RS1000508500 (1:67408284 T>A,C), RS1000546040 (1:67429688 C>A,G,T), RS1000587520 (1:67431671 T>G), RS1000702007 (1:67420719 T>C,G), RS1000830177 (1:67423931 C>T), RS1000883920 (1:67423706 C>A,G), RS1000937083 (1:67417839 A>G), RS1001619199 (1:67409048 T>A,C), RS1001868566 (1:67427234 AT>A)

Disease associations

OMIM: gene MIM:607378 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST001438_1	Crohn’s disease	1.000000e-18
GCST003129_26	Primary biliary cholangitis	7.000000e-28
GCST004131_16	Inflammatory bowel disease	5.000000e-111
GCST004132_7	Crohn’s disease	6.000000e-93
GCST004133_2	Ulcerative colitis	4.000000e-41
GCST004162_25	Carotid plaque burden	2.000000e-06
GCST006444_18	Bone mineral density (hip)	7.000000e-06
GCST90093091_2	DHEAS levels	3.000000e-07

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006501	carotid plaque build
EFO:0007702	hip bone mineral density
EFO:0007001	dehydroepiandrosterone sulphate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066419 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 4 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.56	Kd	27.43	nM	CHEMBL3752910
7.56	ED50	27.43	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149377: Binding affinity to human SERBP1 incubated for 45 mins by Kinobead based pull down assay	kd	0.0274	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression	3
sodium arsenite	affects binding, decreases reaction, decreases expression	2
cobaltous chloride	decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	2
Acetaminophen	decreases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Caffeine	decreases expression, decreases phosphorylation	2
Dinitrochlorobenzene	affects binding, decreases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
bisphenol F	increases expression	1
TAK-243	affects sumoylation	1
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
uranyl acetate	affects expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression, affects localization, increases expression	1
arsenite	affects binding, increases reaction	1
methylparaben	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
4-hydroxy-2-nonenal	affects binding	1
nickel sulfate	decreases expression	1
coumarin	affects phosphorylation	1
epigallocatechin gallate	decreases expression	1
pinosylvin	decreases expression	1
tamibarotene	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol B	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652419	Binding	Binding affinity to human SERBP1 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

2 cell lines: 2 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3GT	Abcam HEK293T SERBP1 KO	Transformed cell line	Female
CVCL_D7HG	Ubigene HEK293T SERBP1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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