UBXN11

Summary

UBXN11 (UBX domain protein 11, HGNC:30600) is a protein-coding gene on chromosome 1p36.11, encoding UBX domain-containing protein 11 (Q5T124). May be involved in the reorganization of actin cytoskeleton mediated by RND1, RND2 and RND3.

This gene encodes a protein with a divergent C-terminal UBX domain. The homologous protein in the rat interacts with members of the Rnd subfamily of Rho GTPases at the cell periphery through its C-terminal region. It also interacts with several heterotrimeric G proteins through their G-alpha subunits and promotes Rho GTPase activation. It is proposed to serve a bidirectional role in the promotion and inhibition of Rho activity through upstream signaling pathways. The 3’ coding sequence of this gene contains a polymoprhic region of 24 nt tandem repeats. Several transcripts containing between 1.5 and five repeat units have been reported. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 91544 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 110 total
• Druggable target: yes
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• MANE Select transcript: NM_001389556

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30600
Approved symbol	UBXN11
Name	UBX domain protein 11
Location	1p36.11
Locus type	gene with protein product
Status	Approved
Aliases	SOC, SOCI
Ensembl gene	ENSG00000158062
Ensembl biotype	protein_coding
OMIM	609151
Entrez	91544

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 16 protein_coding, 4 retained_intron

ENST00000314675, ENST00000357089, ENST00000374215, ENST00000374217, ENST00000374221, ENST00000374222, ENST00000374223, ENST00000421827, ENST00000423664, ENST00000442942, ENST00000450041, ENST00000452980, ENST00000472155, ENST00000475591, ENST00000494942, ENST00000496466, ENST00000888431, ENST00000888432, ENST00000945655, ENST00000945656

RefSeq mRNA: 5 — MANE Select: NM_001389556 NM_001077262, NM_001389556, NM_001389559, NM_145345, NM_183008

CCDS: CCDS41286, CCDS41287, CCDS41288

Canonical transcript exons

ENST00000374222 — 15 exons

Exon	Start	End
ENSE00001654394	26306592	26306636
ENSE00001744319	26284362	26284482
ENSE00001768456	26285464	26285541
ENSE00003462243	26282649	26282789
ENSE00003491136	26285823	26286037
ENSE00003501805	26301694	26301722
ENSE00003517212	26282864	26282937
ENSE00003539182	26297962	26298062
ENSE00003541689	26284142	26284245
ENSE00003570400	26297427	26297481
ENSE00003595364	26300926	26301024
ENSE00003629767	26302813	26302918
ENSE00003631443	26282282	26282569
ENSE00003691419	26296919	26296995
ENSE00003787866	26294205	26294331

Expression profiles

Bgee: expression breadth ubiquitous, 219 present calls, max score 99.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.2149 / max 274.0797, expressed in 1790 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11161	13.0389	1785
11163	0.7594	199
11166	0.6552	139
11162	0.5337	169
11165	0.1751	63
11164	0.0525	38

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.11	gold quality
monocyte	CL:0000576	98.01	gold quality
granulocyte	CL:0000094	97.85	gold quality
leukocyte	CL:0000738	97.44	gold quality
right lobe of thyroid gland	UBERON:0001119	95.76	gold quality
left lobe of thyroid gland	UBERON:0001120	95.53	gold quality
adenohypophysis	UBERON:0002196	95.49	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	95.02	gold quality
pituitary gland	UBERON:0000007	94.65	gold quality
left testis	UBERON:0004533	94.61	gold quality
thyroid gland	UBERON:0002046	94.53	gold quality
right testis	UBERON:0004534	94.50	gold quality
spleen	UBERON:0002106	93.32	gold quality
nucleus accumbens	UBERON:0001882	92.93	gold quality
metanephros cortex	UBERON:0010533	92.76	gold quality
right lung	UBERON:0002167	92.43	gold quality
testis	UBERON:0000473	92.17	gold quality
anterior cingulate cortex	UBERON:0009835	91.90	gold quality
caudate nucleus	UBERON:0001873	91.55	gold quality
putamen	UBERON:0001874	91.28	gold quality
oocyte	CL:0000023	91.25	gold quality
left uterine tube	UBERON:0001303	91.21	gold quality
upper lobe of left lung	UBERON:0008952	91.19	gold quality
vermiform appendix	UBERON:0001154	90.83	gold quality
right frontal lobe	UBERON:0002810	90.71	gold quality
upper lobe of lung	UBERON:0008948	90.65	gold quality
hypothalamus	UBERON:0001898	90.44	gold quality
amygdala	UBERON:0001876	90.11	gold quality
right ovary	UBERON:0002118	89.88	gold quality
prefrontal cortex	UBERON:0000451	89.82	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-GEOD-111727	yes	252.69
E-MTAB-6678	yes	22.52
E-ANND-3	yes	13.95
E-CURD-112	yes	13.62
E-CURD-114	yes	10.72
E-MTAB-5061	yes	4.37
E-GEOD-86618	no	150.78
E-GEOD-100618	no	120.73

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 4)

• Socius is a novel Rnd GTPase-interacting protein involved in disassembly of actin stress fibers (PMID:11940653)
• The rat homolog of UBXD5 promotes RhoA activation through G12/13 heterotrimeric G proteins (PMID:16202387)
• Both CD4+ and CD8+ T-cell responses against COA-1 can occur in colorectal cancer patients with metastatic disease (PMID:18974390)
• UBXN11 Predicts as a Poor Index for Colorectal Cancer and Contributes to the Tumorigenesis by Activating NF-kappaB Signaling. (PMID:38622461)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ubxn11	ENSDARG00000053828
mus_musculus	Ubxn11	ENSMUSG00000012126
rattus_norvegicus	Ubxn11	ENSRNOG00000015476

Paralogs (3): NSFL1C (ENSG00000088833), UBXN2A (ENSG00000173960), UBXN2B (ENSG00000215114)

Protein

Protein identifiers

UBX domain-containing protein 11 — Q5T124 (reviewed: Q5T124)

Alternative names: Colorectal tumor-associated antigen COA-1, Socius, UBX domain-containing protein 5

All UniProt accessions (8): Q5T118, Q5T124, Q5T130, X6R8K8, X6R8M6, X6RDK7, X6RDY0, X6RIY5

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the reorganization of actin cytoskeleton mediated by RND1, RND2 and RND3. Promotes RHOA activation mediated by GNA12 and GNA13.

Subunit / interactions. Interacts with GNA12, GNA13, RND1, RND2 and RND3.

Subcellular location. Cytoplasm. Cytoskeleton.

Polymorphism. The number of repeats is polymorphic and varies from 1 to 4.

Isoforms (8)

UniProt ID	Names	Canonical?
Q5T124-1	1	yes
Q5T124-2	2
Q5T124-3	3
Q5T124-4	4
Q5T124-5	5
Q5T124-6	6
Q5T124-7	7
Q5T124-8	8

RefSeq proteins (5): NP_001070730, NP_001376485, NP_001376488, NP_663320, NP_892120 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001012	UBX_dom	Domain
IPR012989	SEP_domain	Domain
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR036241	NSFL1C_SEP_dom_sf	Homologous_superfamily

Pfam: PF00789, PF08059

UniProt features (31 total): splice variant 7, sequence variant 7, sequence conflict 6, repeat 3, region of interest 3, domain 2, chain 1, compositionally biased region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T124-F1	72.42	0.31

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-9696264	RND3 GTPase cycle
R-HSA-9696270	RND2 GTPase cycle
R-HSA-9696273	RND1 GTPase cycle

MSigDB gene sets: 127 (showing top): CCAWYNNGAAR_UNKNOWN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, YY1_Q6, YY1_02, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_24HR, GOBP_PROTEIN_CATABOLIC_PROCESS, GATGKMRGCG_UNKNOWN, GCCATNTTG_YY1_Q6, GOBP_PROTEOLYSIS, GOMF_UBIQUITIN_LIKE_PROTEIN_BINDING, AAGWWRNYGGC_UNKNOWN, GSE13887_HEALTHY_VS_LUPUS_RESTING_CD4_TCELL_UP, chr1p36, WHITFIELD_CELL_CYCLE_G2

GO Biological Process (1): proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (2): ubiquitin binding (GO:0043130), protein binding (GO:0005515)

GO Cellular Component (3): cytosol (GO:0005829), cytoskeleton (GO:0005856), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RHO GTPase cycle	3

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
ubiquitin-dependent protein catabolic process	1
proteasomal protein catabolic process	1
ubiquitin-like protein binding	1
binding	1
cytoplasm	1
intracellular membraneless organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

798 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBXN11	RND1	Q92730	897
UBXN11	RND3	P52199	883
UBXN11	NSFL1C	Q9UNZ2	699
UBXN11	UBXN2A	P68543	646
UBXN11	UBXN10	Q96LJ8	643
UBXN11	UBXN7	O94888	604
UBXN11	UBXN8	O00124	574
UBXN11	MRPL10	Q7Z7H8	573
UBXN11	UBXN1	Q04323	567
UBXN11	UBXN6	Q9BZV1	559
UBXN11	UBXN2B	Q14CS0	541
UBXN11	ANKRD27	Q96NW4	527
UBXN11	UBXN4	Q92575	526
UBXN11	CCDC60	Q8IWA6	507
UBXN11	BGLAP	P02818	506

IntAct

53 interactions, top by confidence:

A	B	Type	Score
UBXN11	TRAF2	psi-mi:“MI:0915”(physical association)	0.740
TRAF2	UBXN11	psi-mi:“MI:0915”(physical association)	0.740
RHOBTB3	UBXN11	psi-mi:“MI:0915”(physical association)	0.670
UBXN11	CFAP206	psi-mi:“MI:0915”(physical association)	0.670
UBXN11	SCNM1	psi-mi:“MI:0915”(physical association)	0.670
CFAP206	UBXN11	psi-mi:“MI:0915”(physical association)	0.670
SCNM1	UBXN11	psi-mi:“MI:0915”(physical association)	0.670
UBXN11	RHOBTB3	psi-mi:“MI:0915”(physical association)	0.670
PRKAB2	UBXN11	psi-mi:“MI:0915”(physical association)	0.560
UBXN11	EIF4E2	psi-mi:“MI:0915”(physical association)	0.560
EIF4E	UBXN11	psi-mi:“MI:0915”(physical association)	0.560
UBXN11	PSMA1	psi-mi:“MI:0915”(physical association)	0.560
UBXN11	TLE5	psi-mi:“MI:0915”(physical association)	0.560
UBXN11	PRKAA1	psi-mi:“MI:0915”(physical association)	0.560
RNF213	UBXN11	psi-mi:“MI:0915”(physical association)	0.560
UBXN11	USHBP1	psi-mi:“MI:0915”(physical association)	0.560
UBXN11	ENKD1	psi-mi:“MI:0915”(physical association)	0.560
UBXN11	SH2D4A	psi-mi:“MI:0915”(physical association)	0.560
EIF4E2	UBXN11	psi-mi:“MI:0915”(physical association)	0.560
UBXN11	EIF4E	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (99): UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), UBXN11 (Two-hybrid), C6orf165 (Two-hybrid), NCKAP1 (Affinity Capture-MS)

ESM2 similar proteins: A0MLS4, A2BD09, A2D4U1, A2D670, A2T6K4, O14669, P01257, P01286, P02818, P02820, P02822, P27916, P41547, P51693, P63292, P70160, P84348, P84349, P84350, Q03157, Q0VCT2, Q2NL23, Q3KNT9, Q3TYX2, Q5HZE8, Q5T124, Q60549, Q64375, Q6AYE5, Q6BEG6, Q6BEG7, Q71SY6, Q76IQ4, Q7M742, Q7TNI2, Q86UD1, Q8JFY4, Q8K2B0, Q8QZR4, Q8R182

Diamond homologs: Q5T124, Q8R512, Q9D572

SIGNOR signaling

0 interactions.

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — GBM.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	77
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2738 predictions. Top by Δscore:

Variant	Effect	Δscore
1:26282676:T:TA	donor_gain	1.0000
1:26282677:C:A	donor_gain	1.0000
1:26282789:CCTG:C	acceptor_loss	1.0000
1:26282790:C:CA	acceptor_loss	1.0000
1:26282950:A:T	acceptor_gain	1.0000
1:26284357:CTCA:C	donor_loss	1.0000
1:26284358:TCAC:T	donor_loss	1.0000
1:26284359:CACCT:C	donor_loss	1.0000
1:26284361:C:CT	donor_loss	1.0000
1:26284478:CTCAC:C	acceptor_gain	1.0000
1:26284479:TCAC:T	acceptor_gain	1.0000
1:26284480:CAC:C	acceptor_gain	1.0000
1:26284480:CACC:C	acceptor_gain	1.0000
1:26284481:AC:A	acceptor_gain	1.0000
1:26284481:ACC:A	acceptor_loss	1.0000
1:26284482:CC:C	acceptor_gain	1.0000
1:26284482:CCT:C	acceptor_loss	1.0000
1:26285537:CAGCG:C	acceptor_gain	1.0000
1:26285540:CG:C	acceptor_gain	1.0000
1:26285542:C:CC	acceptor_gain	1.0000
1:26285819:CTACC:C	donor_loss	1.0000
1:26285820:TA:T	donor_loss	1.0000
1:26285821:A:AC	donor_gain	1.0000
1:26285822:C:CC	donor_gain	1.0000
1:26286034:TCCC:T	acceptor_gain	1.0000
1:26286035:CCC:C	acceptor_gain	1.0000
1:26286035:CCCC:C	acceptor_gain	1.0000
1:26286036:CC:C	acceptor_gain	1.0000
1:26286036:CCC:C	acceptor_gain	1.0000
1:26286037:CC:C	acceptor_gain	1.0000

AlphaMissense

3381 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:26294326:G:C	F146L	0.983
1:26294326:G:T	F146L	0.983
1:26294328:A:G	F146L	0.983
1:26294304:A:G	W154R	0.974
1:26294304:A:T	W154R	0.974
1:26294309:A:G	L152P	0.971
1:26285468:A:G	F283S	0.967
1:26294302:C:A	W154C	0.963
1:26294302:C:G	W154C	0.963
1:26285512:G:C	F268L	0.961
1:26285512:G:T	F268L	0.961
1:26285514:A:G	F268L	0.961
1:26282543:A:G	I440T	0.960
1:26285875:C:T	G241D	0.959
1:26282711:G:C	F410L	0.958
1:26282711:G:T	F410L	0.958
1:26282713:A:G	F410L	0.958
1:26282739:A:G	I401T	0.958
1:26282670:C:G	R424P	0.955
1:26282739:A:T	I401N	0.952
1:26282548:A:C	F438L	0.950
1:26282548:A:T	F438L	0.950
1:26282550:A:G	F438L	0.950
1:26285875:C:A	G241V	0.948
1:26282530:G:C	F444L	0.947
1:26282530:G:T	F444L	0.947
1:26282532:A:G	F444L	0.947
1:26282712:A:G	F410S	0.947
1:26282739:A:C	I401S	0.946
1:26285885:A:C	Y238D	0.946

dbSNP variants (sampled 300 via entrez): RS1000016449 (1:26301969 T>C), RS1000055212 (1:26304491 A>G), RS1000162128 (1:26308410 G>A), RS1000217951 (1:26285662 C>G,T), RS1000347906 (1:26301960 A>G,T), RS1000351945 (1:26285359 G>T), RS1000423029 (1:26291066 C>T), RS1000438141 (1:26314632 G>A), RS1000464453 (1:26306562 A>AG), RS1000495480 (1:26306719 G>A), RS1000495557 (1:26309857 A>G), RS1000654375 (1:26303111 A>G), RS1000672334 (1:26313201 C>CCATTCTAT), RS1000761910 (1:26303614 G>A,C,T), RS1000826323 (1:26302299 G>T)

Disease associations

OMIM: gene MIM:609151 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001762_596	Obesity-related traits	7.000000e-06
GCST001762_647	Obesity-related traits	4.000000e-06
GCST90002394_130	Monocyte percentage of white cells	4.000000e-42
GCST90002402_535	Platelet count	1.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004501	HOMA-IR
EFO:0007989	monocyte percentage of leukocytes
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5291603 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases abundance, increases expression	3
bisphenol A	decreases methylation, decreases expression, affects cotreatment	2
sodium arsenite	increases abundance, increases expression	2
Arsenic	affects methylation, increases abundance, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
Valproic Acid	affects cotreatment, increases expression, increases methylation	2
Aflatoxin B1	decreases methylation, increases methylation	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
jinfukang	increases expression	1
(+)-JQ1 compound	decreases expression	1
Fulvestrant	decreases methylation, affects cotreatment	1
Acetaminophen	decreases expression	1
Amiodarone	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Cisplatin	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Okadaic Acid	increases expression	1
Acrylamide	decreases 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
CHEMBL5225344	Binding	Inhibition of SOC (unknown origin) at 300 nM relative to control	The Emerging Landscape of Small-Molecule Therapeutics for the Treatment of Huntington’s Disease. — J Med Chem

Clinical trials (associated diseases)

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