VIM

Summary

VIM (vimentin, HGNC:12692) is a protein-coding gene on chromosome 10p13, encoding Vimentin (P08670). Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells.

This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients.

Source: NCBI Gene 7431 — RefSeq curated summary.

At a glance

• Gene–disease (curated): cataract (Definitive, GenCC) — +2 more curated relationships
• GWAS associations: 6
• Clinical variants (ClinVar): 138 total — 1 likely-pathogenic
• GTEx eGene: eQTL in 23 tissues, sQTL in 10 (q < 0.05)
• Phenotypes (HPO): 5
• Drug target: yes — 1 curated mechanism-of-action drug
• Constraint (gnomAD): pLI 0.86 (intermediate), LOEUF 0.54 (moderately constrained)
• MANE Select transcript: NM_003380
• Interaction hub: 4,691 STRING partners (top 1% of genes corpus-wide)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12692
Approved symbol	VIM
Name	vimentin
Location	10p13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000026025
Ensembl biotype	protein_coding
OMIM	193060
Entrez	7431

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 15 protein_coding, 7 nonsense_mediated_decay, 2 retained_intron, 2 protein_coding_CDS_not_defined

MANE Select: ENST00000544301

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 7, TSL 5: 1

ENST00000544301, ENST00000224237, ENST00000421459, ENST00000469543, ENST00000478746, ENST00000485947, ENST00000487938, ENST00000495528, ENST00000497849, ENST00000637053, ENST00000881961, ENST00000881962, ENST00000881963, ENST00000946784, ENST00000946785, ENST00000946786, ENST00000946787, ENST00000978705, ENST00001031270, ENST00001031271, ENST00001031276, ENST00001031281, ENST00001031282, ENST00001124066, ENST00001124067, ENST00001141527

RefSeq mRNA: 1 — MANE Select: NM_003380 NM_003380

CCDS: CCDS7120

Canonical transcript exons

ENST00000544301 — 10 exons

Exon	Start	End
ENSE00000692805	17233587	17233682
ENSE00000692812	17234693	17234818
ENSE00000815998	17236294	17236379
ENSE00001121153	17235846	17235889
ENSE00001270949	17235169	17235389
ENSE00001270958	17230650	17230710
ENSE00001942703	17228241	17228524
ENSE00002284410	17229276	17229985
ENSE00003614198	17233770	17233931
ENSE00003647967	17237230	17237593

Expression profiles

Bgee: expression breadth ubiquitous, 307 present calls, max score 99.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2467.6537 / max 125601.9960, expressed in 1738 samples.

Highest expression (Bgee): ventricular zone, descending thoracic aorta, coronary artery, blood vessel layer, layer of synovial tissue.

Genetic regulation across tissues (GTEx eQTL / sQTL)

VIM is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 23 tissues and its splicing (sQTL) in 10 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 33 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Artery Tibial	eqtl	3.5e-14	+0.16	10:17229401:G:C
Brain Nucleus accumbens basal ganglia	eqtl	1.2e-11	+0.28	10:16975670:C:T
Nerve Tibial	eqtl	2.4e-11	+0.20	10:17222487:T:C
Adipose Subcutaneous	eqtl	2.5e-09	+0.19	10:17229401:G:C
Brain Cortex	eqtl	5.6e-09	+0.23	10:16975670:C:T
Thyroid	eqtl	2.9e-06	+0.12	10:17160866:T:C
Artery Coronary	sqtl	3.4e-06	+2.06	10:17829375:G:A
Brain Frontal Cortex BA9	eqtl	5.5e-06	+0.17	10:16983379:G:A
Artery Aorta	eqtl	6.1e-06	+0.16	10:17166919:G:A
Skin Not Sun Exposed Suprapubic	eqtl	3.2e-05	-0.11	10:16897319:T:TG
Testis	sqtl	2.4e-04	+0.82	10:17228075:T:G
Cells Cultured fibroblasts	eqtl	4.2e-04	+0.09	10:16956057:T:G
Spleen	eqtl	2.0e-03	-0.18	10:16975567:G:A
Skin Sun Exposed Lower leg	eqtl	2.3e-03	+0.08	10:17229401:G:C
Kidney Cortex	eqtl	2.6e-03	+1.10	10:17307997:A:AATT
Artery Coronary	eqtl	2.8e-03	+0.18	10:17260737:A:G
Brain Anterior cingulate cortex BA24	eqtl	4.4e-03	+0.18	10:16963755:C:T
Breast Mammary Tissue	eqtl	1.1e-02	+0.09	10:17234067:C:T
Thyroid	sqtl	1.3e-02	+0.98	10:17940204:A:G
Adipose Visceral Omentum	eqtl	1.4e-02	+0.13	10:17229111:G:C

FANTOM5 promoters

showing 10 of 13 alternative TSS:

Promoter ID	TPM avg	Samples expressed
104054	2442.2995	1693
104057	7.6571	1454
104050	6.6265	1417
104073	5.2122	1240
104053	1.6280	818
104046	1.4872	412
104052	0.9798	522
104051	0.7548	191
205739	0.4312	189
104055	0.1770	84

Top tissues by expression

showing 100 of 312 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	99.99	gold quality
descending thoracic aorta	UBERON:0002345	99.97	gold quality
right coronary artery	UBERON:0001625	99.96	gold quality
blood vessel layer	UBERON:0004797	99.96	gold quality
layer of synovial tissue	UBERON:0007616	99.96	gold quality
dorsal root ganglion	UBERON:0000044	99.95	gold quality
urethra	UBERON:0000057	99.95	gold quality
aorta	UBERON:0000947	99.95	gold quality
nerve	UBERON:0001021	99.95	gold quality
tibial nerve	UBERON:0001323	99.95	gold quality
ascending aorta	UBERON:0001496	99.95	gold quality
thoracic aorta	UBERON:0001515	99.95	gold quality
artery	UBERON:0001637	99.95	gold quality
trigeminal ganglion	UBERON:0001675	99.95	gold quality
popliteal artery	UBERON:0002250	99.95	gold quality
decidua	UBERON:0002450	99.95	gold quality
tibial artery	UBERON:0007610	99.95	gold quality
synovial joint	UBERON:0002217	99.94	gold quality
olfactory bulb	UBERON:0002264	99.94	gold quality
calcaneal tendon	UBERON:0003701	99.94	gold quality
coronary artery	UBERON:0001621	99.93	gold quality
left coronary artery	UBERON:0001626	99.93	gold quality
lower lobe of lung	UBERON:0008949	99.91	gold quality
stromal cell of endometrium	CL:0002255	99.90	gold quality
parietal pleura	UBERON:0002400	99.90	gold quality
tendon of biceps brachii	UBERON:0008188	99.90	gold quality
right ovary	UBERON:0002118	99.89	gold quality
left ovary	UBERON:0002119	99.89	gold quality
peritoneum	UBERON:0002358	99.89	gold quality
cartilage tissue	UBERON:0002418	99.89	gold quality
adipose tissue of abdominal region	UBERON:0007808	99.89	gold quality
omental fat pad	UBERON:0010414	99.89	gold quality
tendon	UBERON:0000043	99.88	gold quality
skin of hip	UBERON:0001554	99.88	gold quality
endocervix	UBERON:0000458	99.86	gold quality
superficial temporal artery	UBERON:0001614	99.86	gold quality
cauda epididymis	UBERON:0004360	99.86	gold quality
saphenous vein	UBERON:0007318	99.86	gold quality
pleura	UBERON:0000977	99.85	gold quality
nipple	UBERON:0002030	99.85	gold quality
vena cava	UBERON:0004087	99.85	gold quality
smooth muscle tissue	UBERON:0001135	99.84	gold quality
mammary duct	UBERON:0001765	99.84	gold quality
left lobe of thyroid gland	UBERON:0001120	99.82	gold quality
mucosa of stomach	UBERON:0001199	99.82	gold quality
adult organism	UBERON:0007023	99.82	gold quality
gall bladder	UBERON:0002110	99.81	gold quality
mammalian vulva	UBERON:0000997	99.80	gold quality
pericardium	UBERON:0002407	99.80	gold quality
cardiac muscle of right atrium	UBERON:0003379	99.80	gold quality
visceral pleura	UBERON:0002401	99.79	gold quality
adipose tissue	UBERON:0001013	99.78	gold quality
right lobe of thyroid gland	UBERON:0001119	99.78	gold quality
myometrium	UBERON:0001296	99.78	gold quality
thyroid gland	UBERON:0002046	99.78	gold quality
lung	UBERON:0002048	99.78	gold quality
connective tissue	UBERON:0002384	99.78	gold quality
periodontal ligament	UBERON:0008266	99.78	gold quality
left uterine tube	UBERON:0001303	99.77	gold quality
upper arm skin	UBERON:0004263	99.77	gold quality
body of uterus	UBERON:0009853	99.77	gold quality
penis	UBERON:0000989	99.76	gold quality
upper lobe of lung	UBERON:0008948	99.76	gold quality
monocyte	CL:0000576	99.75	gold quality
mononuclear cell	CL:0000842	99.75	gold quality
ganglionic eminence	UBERON:0004023	99.75	gold quality
upper lobe of left lung	UBERON:0008952	99.75	gold quality
leukocyte	CL:0000738	99.74	gold quality
embryo	UBERON:0000922	99.74	gold quality
seminal vesicle	UBERON:0000998	99.74	gold quality
upper leg skin	UBERON:0004262	99.74	gold quality
tibia	UBERON:0000979	99.73	gold quality
trachea	UBERON:0003126	99.73	gold quality
right uterine tube	UBERON:0001302	99.72	gold quality
cardiac atrium	UBERON:0002081	99.72	gold quality
right atrium auricular region	UBERON:0006631	99.71	gold quality
placenta	UBERON:0001987	99.70	gold quality
right lung	UBERON:0002167	99.70	gold quality
trabecular bone tissue	UBERON:0002483	99.70	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	99.70	gold quality
ovary	UBERON:0000992	99.69	gold quality
ectocervix	UBERON:0012249	99.68	gold quality
lymph node	UBERON:0000029	99.67	gold quality
bone element	UBERON:0001474	99.67	gold quality
caecum	UBERON:0001153	99.66	gold quality
bone marrow	UBERON:0002371	99.66	gold quality
granulocyte	CL:0000094	99.65	gold quality
skin of abdomen	UBERON:0001416	99.65	gold quality
skin of leg	UBERON:0001511	99.65	gold quality
caput epididymis	UBERON:0004358	99.65	gold quality
lower esophagus muscularis layer	UBERON:0035833	99.65	gold quality
blood	UBERON:0000178	99.64	gold quality
lower esophagus	UBERON:0013473	99.64	gold quality
vermiform appendix	UBERON:0001154	99.63	gold quality
bone marrow cell	CL:0002092	99.62	gold quality
urinary bladder	UBERON:0001255	99.61	gold quality
spleen	UBERON:0002106	99.61	gold quality
subcutaneous adipose tissue	UBERON:0002190	99.61	gold quality
thymus	UBERON:0002370	99.61	gold quality
muscle layer of sigmoid colon	UBERON:0035805	99.61	gold quality

Single-cell (SCXA)

Detected in 90 experiment(s), a significant marker in 62.

Experiment	Marker?	Max mean expression
E-HCAD-36	yes	17123.00
E-MTAB-7407	yes	16811.04
E-GEOD-137537	yes	14012.52
E-MTAB-8142	yes	13936.54
E-GEOD-135922	yes	12559.53
E-CURD-79	yes	10585.91
E-MTAB-9154	yes	8573.37
E-MTAB-8205	yes	8235.09
E-GEOD-134144	yes	8030.79
E-MTAB-9841	yes	7971.21
E-MTAB-10596	yes	7907.32
E-MTAB-10855	yes	7727.88
E-GEOD-124263	yes	7715.33
E-CURD-112	yes	7675.41
E-MTAB-9906	yes	7616.13

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Ovary	tissue	3491.8	high
Adipose tissue	tissue	2075.9	high
Cervix	tissue	1395.2	medium
Bone marrow	tissue	1374.3	high
Vagina	tissue	1280.4	low
Smooth muscle	tissue	1036.0	not detected
Thyroid gland	tissue	1032.1	high
Endometrium 1	tissue	1008.3	medium
Lung	tissue	982.2	high
Placenta	tissue	968.0	high
Gallbladder	tissue	899.4	not detected
Fallopian tube	tissue	884.0	high
Breast	tissue	835.5	high
Spinal cord	tissue	811.7
Urinary bladder	tissue	806.3	not detected
Spleen	tissue	772.8	high
Lymph node	tissue	755.1	high
Choroid plexus	tissue	705.7
Tonsil	tissue	698.1	high
Retina	tissue	677.7	high
Superior colliculi	tissue	668.4
Appendix	tissue	576.4	high
Skin 1	tissue	565.1	high
Pituitary gland	tissue	549.0
Heart muscle	tissue	536.1	not detected
Seminal vesicle	tissue	519.3	high
Tongue	tissue	519.0
Esophagus	tissue	424.1	not detected
Thymus	tissue	384.5
Colon	tissue	382.0	low
Epididymis	tissue	377.7	high
Rectum	tissue	376.4	low
Adrenal gland	tissue	350.8	low
Pancreas	tissue	349.0	medium
Hippocampal formation	tissue	303.9
Substantia nigra	tissue	299.2
Prostate	tissue	267.0	not detected
Stomach 1	tissue	263.1	not detected
Salivary gland	tissue	261.5	not detected
Small intestine	tissue	251.9	not detected
Testis	tissue	235.4	high
Septum	tissue	227.2
Entorhinal cortex	tissue	226.8
Nucleus accumbens	tissue	226.1
Parathyroid gland	tissue	211.3	not detected
Hippocampus	tissue	208.4	low
Duodenum	tissue	205.5	not detected
Kidney	tissue	199.2	high
Basal ganglia	tissue	191.2	medium
Periaqueductal gray	tissue	184.3
Amygdala	tissue	183.9
Liver	tissue	180.2	low
Cerebral cortex	tissue	179.0	low
Temporal cortex	tissue	179.0
Skeletal muscle	tissue	178.7	not detected
Motor cortex	tissue	178.7
Hypothalamus	tissue	176.9
Medulla oblongata	tissue	172.4
Prefrontal cortex	tissue	155.7
Pons	tissue	153.3

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Blood vessel (5524.1), Area postrema (927.2), Dorsal spinal cord (811.7), Nucleus raphe pallidus (669.3), Anterior thalamic nucleus, ventral (537.6).

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets:

Target	Regulation
PLVAP	Activation

Upstream regulators (CollecTRI, top): AP1, AR, ATF4, CDK9, CTNNB1, CUX1, CXXC1, ERG, ESR1, ETV4, EZH2, FOS, FOXC1, GLI1, HDGF, HEXIM1, HIF1A, HIPK2, HMGA2, HNF4A, HOXA5, HOXA7, HSF4, IRF6, JDP2, JUN, KLF4, KLF8, LEF1, MARK1, MTA1, MYB, NFKB1, NFKB, OVOL2, PARP1, PAWR, PBX1, POLR2A, RBMS3

miRNA regulators (miRDB)

Targeting VIM by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 50 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
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-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
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-548A-3P	99.76	70.58	3524
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-1287-3P	99.63	66.93	492
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-7844-5P	99.55	68.56	1428

Functional genomics

gnomAD constraint: pLI 0.86, LOEUF 0.542, missense Z 0.856 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000544301 splits into 3 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
10:17,229,423–17,229,678	134 / 126.4	1.06	no
10:17,229,679–17,229,787	23 / 50.9	0.45	no
10:17,229,788–17,237,268	394 / 437.5	0.90	no

Literature-anchored findings (GeneRIF, showing 40)

• These findings suggest that platelet vimentin may regulate fibrinolysis in plasma and thrombi by binding platelet-derived Vn.PAI-1 complexes. (PMID:11744725)
• association with MICAL, a novel CasL interacting molecule (PMID:11827972)
• Vimentin expression correlates with the cytoplasmic localization of wild-type p53 in human primary glioblastoma. (PMID:12084347)
• Menin’s interaction with glial fibrillary acidic protein and vimentin suggests a role for the intermediate filament network in regulating menin activity. (PMID:12169273)
• Results describe the asymmetric distribution of vimentin in the human sperm head. (PMID:12194205)
• expression correlated with motility of prostate carcinoma cells, poor cell differentiation, and presence of bone metastasis (PMID:12210485)
• specific interaction of the periplakin linker domain with keratin 8 and vimentin (PMID:12366696)
• The 3’ untranslated region of human vimentin mRNA binds protein complexes containing eEF-1gamma and HAX-1. (PMID:12466525)
• It is secreted by activated monocyte-derived macrophages (PMID:12483219)
• vimentin expression contributes to the invasive phenotype in androgen-independent prostate cancer but cannot confer it alone. (PMID:12727854)
• The vimentin promoter is a target of the beta-catenin/TCF pathway and strongly suggest an implication of this regulation in epithelial cell migration/invasion in breast cancer. (PMID:12750294)
• role of mitogen-activated protein kinase-activated protein kinase-2 phosphorylation in retaining assembly capacity (PMID:12761892)
• vimentin, in conjunction with low molecular weight heparan sulfate proteoglycans, contributes to the enhanced binding of human group IIA PLA2 to apoptotic T cells (PMID:12829607)
• High MW vimentin was formed after the digestion of vimentin by caspase-3 but not caspase-8. It acted as an autoantigen to form anti-vimentin autoantibody in vivo. (PMID:12906105)
• findings implicate reduced vimentin in the conversion of these tumorigenic prostate epithelial cells into slow growing, less aggressive cells (PMID:14595690)
• study of human vimentin rod 1 structure and the sequencing of assembly steps in intermediate filament formation (PMID:15231822)
• It is unlikely that ependymal vimentin is directly involved in the pathogenesis of Chiari II malformation, but may reflect a secondary upregulation due to defective expression of another gene. (PMID:15255035)
• Data suggest that the PAL-E antibody defines secretion of vimentin as a molecular distinction among endothelial cells and exposes a novel, extracellular role for vimentin in the blood vasculature. (PMID:15456890)
• examination of mutation the LNDR to LNDS motif in vimentin to examine role in epidermolysis bullosa simplex (PMID:15556930)
• Interacts with alpha2beta1-enriched focal adhesions and this association is lost after prolonged adhesion of endothelial cells to collagen. (PMID:15777792)
• Results indicate that protein kinase C epsilon-mediated phosphorylation of vimentin is a key process in integrin traffic through the cell. (PMID:16270034)
• Kidney recipients from non-heart-beating donors showed higher levels of anti-vimentin antibodies than heart-beating donors. (PMID:16298568)
• Apoptotic neutrophils express vimentin on their surface; these cells may participate in the development of autoantibodies directed against cytoskeletal proteins, a condition frequently reported in several inflammatory diseases. (PMID:16365157)
• All polyps were immunohistochemically positive for vimentin. (PMID:16487365)
• regulation of vimentin is controlled by SIP1 in breast neoplasms (PMID:16568083)
• isolated & identified vimentin as the major skeletal-muscle group A streptococcus (GAS)-binding protein; vimentin expression was up-regulated on injured skeletal-muscle cells in vitro and was expressed in muscle tissues from a patient with GAS myonecrosis (PMID:16703512)
• actin and vimentin filaments can interact directly through the tail domain of vimentin (PMID:16901892)
• Data show that the architecture of the vimentin cytoskeleton is modified by perturbation of the GTPase ARF1. (PMID:16912072)
• Increased vimentin expression was found in pseudomyxoma peritonei. (PMID:17031402)
• unit-length filaments appears to be a dynamic and a relatively loosely packed structure with a roughly even mass distribution over its cross-section (PMID:17050693)
• Vimentin is involved in binding of NKp46 to M. tuberculosis H37Ra-infected mononuclear phagocytes. (PMID:17056548)
• The regulatory protease factor Xa is able to cleave IbeA between R297 and K298 residues, and this cleavage abolishes the IbeA-vimentin interaction. (PMID:17083913)
• Vimentin filaments in cross-section exhibit predominantly a four-stranded protofibrilar organization with a right-handed supertwist with a helical pitch of about 96 nm. (PMID:17289402)
• a kinetic model for the in vitro assembly of intermediate filaments from tetrameric vimentin (PMID:17403663)
• Vimentin is a major arterial substrate for transglutaminases.Transglutaminase-mediated vimentin dimerization produces a novel unifying pathway by which vasodilatory and remodeling responses may be regulated. (PMID:17476115)
• In conclusion, ablation of vimentin expression inhibits migration and invasion of colon and breast cancer cell lines. (PMID:17585878)
• The nestin(-) vimentin(+) fibroblasts may represent a novel type of multipotent adult stem cells in human dermis. (PMID:17652163)
• ZBP-89 functions as a repressor by recruiting HDAC1 to the vimentin promoter. (PMID:17663720)
• study of vimentin protein filament structure and assembly by electron paramagnetic resonance spectroscopy of site-directed spin labels. Review. (PMID:17703067)
• The suppression of vimentin expression by ras, and the relief of this suppression by TGFbeta, occurs in a promoter-independent fashion, possibly through sequences in the first or second intron. (PMID:17719575)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	vim	ENSDARG00000010008
danio_rerio	viml	ENSDARG00000044501
mus_musculus	Vim	ENSMUSG00000026728
rattus_norvegicus	Vim	ENSRNOG00000018087

Paralogs (68): KRT33A (ENSG00000006059), KRT31 (ENSG00000094796), NEFM (ENSG00000104722), KRT23 (ENSG00000108244), KRT37 (ENSG00000108417), KRT32 (ENSG00000108759), KRT18 (ENSG00000111057), LMNB1 (ENSG00000113368), KRT36 (ENSG00000126337), KRT17 (ENSG00000128422), GFAP (ENSG00000131095), KRT34 (ENSG00000131737), KRT33B (ENSG00000131738), NES (ENSG00000132688), PRPH (ENSG00000135406), KRT85 (ENSG00000135443), KRT7 (ENSG00000135480), KRT71 (ENSG00000139648), INA (ENSG00000148798), LMNTD1 (ENSG00000152936), LMNA (ENSG00000160789), KRT84 (ENSG00000161849), KRT82 (ENSG00000161850), KRT80 (ENSG00000167767), KRT1 (ENSG00000167768), KRT24 (ENSG00000167916), KRT8 (ENSG00000170421), KRT78 (ENSG00000170423), KRT86 (ENSG00000170442), KRT75 (ENSG00000170454), KRT6C (ENSG00000170465), KRT4 (ENSG00000170477), KRT74 (ENSG00000170484), KRT72 (ENSG00000170486), KRT83 (ENSG00000170523), BFSP2 (ENSG00000170819), KRT19 (ENSG00000171345), KRT15 (ENSG00000171346), KRT38 (ENSG00000171360), KRT13 (ENSG00000171401), KRT9 (ENSG00000171403), KRT20 (ENSG00000171431), KRT27 (ENSG00000171446), KRT2 (ENSG00000172867), KRT28 (ENSG00000173908), DES (ENSG00000175084), LMNB2 (ENSG00000176619), SYNM (ENSG00000182253), KRT76 (ENSG00000185069), KRT6B (ENSG00000185479), KRT79 (ENSG00000185640), KRT73 (ENSG00000186049), KRT5 (ENSG00000186081), KRT26 (ENSG00000186393), KRT10 (ENSG00000186395), KRT3 (ENSG00000186442), KRT16 (ENSG00000186832), KRT14 (ENSG00000186847), KRT12 (ENSG00000187242), KRT77 (ENSG00000189182)

+8 more (showing top 60).

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:98932) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 31 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal cell morphology	2
abnormal astrocyte morphology	2
abnormal vasoconstriction	1
abnormal angiogenesis	1
abnormal cerebellum morphology	1
abnormal cerebellar Purkinje cell layer	1
Purkinje cell degeneration	1
abnormal Purkinje cell morphology	1
decreased Purkinje cell number	1
cataract	1
increased anxiety-related response	1
abnormal locomotor behavior	1
hyperactivity	1
impaired coordination	1
impaired balance	1
abnormal vasodilation	1
abnormal blood vessel morphology	1
disorganized secondary lens fibers	1
abnormal motor learning	1
abnormal lens fiber morphology	1
abnormal cell migration	1
abnormal leukocyte migration	1
abnormal leukocyte tethering or rolling	1
abnormal leukocyte adhesion	1
decreased mean systemic arterial blood pressure	1

+6 more (showing top 25).

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Chlorocebus aethiops	P84198	100.0%	Diamond
Macaca fascicularis	Q4R4X4	100.0%	Diamond
Pongo abelii	Q5R408	100.0%	Diamond
Bos taurus	P48616	99.4%	Diamond
Ovis aries	Q9MZA9	99.4%	Diamond
Mesocricetus auratus	P02544	99.3%	Diamond
Cricetulus griseus	P48670	99.3%	Diamond
Pan troglodytes	A5A6N0	98.3%	Diamond
Sus scrofa	P02547	98.2%	Diamond
Canis lupus familiaris	A0A8C0N8E3	97.4%	Diamond
Carassius auratus	P48677	95.6%	Diamond
Felis catus	E1AB55	95.2%	Diamond
Acanthocheilonema viteae	Q17107	93.4%	Diamond
Xenopus laevis	P24789	92.4%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
VIM-AS1	ncRNA	100507347
TRDMT1	protein-coding	1787
ST8SIA6	protein-coding	338596
ST8SIA6-AS1	ncRNA	100128098
CUBN	protein-coding	8029
RSU1	protein-coding	6251

Protein

Protein identifiers

Vimentin — P08670 (reviewed: P08670)

All UniProt accessions (6): A0A1B0GTT5, A0A1B0GVG8, B0YJC4, B0YJC5, P08670, V9HWE1

UniProt curated annotations — full annotation on UniProt →

Function. Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. Plays a role in cell directional movement, orientation, cell sheet organization and Golgi complex polarization at the cell migration front. Protects SCRIB from proteasomal degradation and facilitates its localization to intermediate filaments in a cell contact-mediated manner. May promote axon outgrowth and motor fiber repair via DSP-mediated recruitment to outgrowth tips. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.

Subunit / interactions. Homomer assembled from elementary dimers. Identified in complexes that contain VIM, EZR, AHNAK, BFSP1, BFSP2, ANK2, PLEC, PRX and spectrin. Identified in a complex containing at least DSP, JUP, VIM and CDH2; the complex is more abundant following crush injury in regenerating motor neurons and may promote axon outgrowth and motor fiber repair. Interacts with BCAS3. Interacts with LGSN. Interacts with SYNM. Interacts (via rod region) with PLEC (via CH 1 domain). Interacts with PLEC isoform 1C. Interacts with STK33. Interacts with LARP6. Interacts with RAB8B. Interacts with TOR1A; the interaction associates TOR1A with the cytoskeleton. Interacts with TOR1AIP1. Interacts with DIAPH1. Interacts with EPPK1; interaction is dependent of higher-order structure of intermediate filament. Interacts with the non-receptor tyrosine kinase SRMS; the interaction leads to phosphorylation of VIM. Interacts with NOD2. Interacts (via head region) with CORO1C. Interacts with HDGF (isoform 2). Interacts with PRKCE (via phorbol-ester/DAG-type 2 domain). Interacts with BFSP2. Interacts with PPL. Interacts (via rod domain) with PKP1. Interacts with PKP2. Interacts with SCRIB (via PDZ domains); the interaction protects SCRIB from proteasomal degradation and facilitates SCRIB localization to intermediate filaments, the interaction is reduced by cell contact inhibition. (Microbial infection) Interacts with HCV core protein. (Microbial infection) Interacts with Chandipura virus glycoprotein; this interaction might facilitate the binding of the virus to the cells.

Subcellular location. Cytoplasm. Cytoskeleton. Nucleus matrix. Cell membrane. Cell projection. Axon.

Tissue specificity. Highly expressed in fibroblasts, some expression in T- and B-lymphocytes, and little or no expression in Burkitt’s lymphoma cell lines. Expressed in many hormone-independent mammary carcinoma cell lines.

Post-translational modifications. Filament disassembly during mitosis is promoted by phosphorylation at Ser-55 as well as by nestin. One of the most prominent phosphoproteins in various cells of mesenchymal origin. Phosphorylation is enhanced during cell division, at which time vimentin filaments are significantly reorganized. Phosphorylation by PKN1 inhibits the formation of filaments. Phosphorylated at Ser-56 by CDK5 during neutrophil secretion in the cytoplasm. Phosphorylated by STK33. Phosphorylated on tyrosine residues by SRMS. O-glycosylated during cytokinesis at sites identical or close to phosphorylation sites, this interferes with the phosphorylation status. S-nitrosylation is induced by interferon-gamma and oxidatively-modified low-densitity lipoprotein (LDL(ox)) possibly implicating the iNOS-S100A8/9 transnitrosylase complex.

Disease relevance. Cataract 30, multiple types (CTRCT30) [MIM:116300] An opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The central alpha-helical coiled-coil IF rod domain mediates elementary homodimerization. The [IL]-x-C-x-x-[DE] motif is a proposed target motif for cysteine S-nitrosylation mediated by the iNOS-S100A8/A9 transnitrosylase complex.

Induction. Up-regulated by muramyl-dipeptide and lipopolysaccharide.

Similarity. Belongs to the intermediate filament family.

RefSeq proteins (1): NP_003371* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006821	Intermed_filament_DNA-bd	Domain
IPR018039	IF_conserved	Conserved_site
IPR039008	IF_rod_dom	Domain
IPR050405	Intermediate_filament	Family

Pfam: PF00038, PF04732

UniProt features (110 total): modified residue 56, cross-link 12, sequence conflict 9, region of interest 8, helix 8, coiled-coil region 3, glycosylation site 3, compositionally biased region 2, sequence variant 2, initiator methionine 1, chain 1, strand 1, turn 1, short sequence motif 1, site 1, domain 1

Structure

Experimental structures (PDB)

26 structures by resolution:

PDB	Title	Method	Resolution (Å)
1GK7	HUMAN VIMENTIN COIL 1A FRAGMENT (1A)	X-RAY DIFFRACTION	1.4
4YPC	Trimeric crystal structure of vimentin coil1B fragment	X-RAY DIFFRACTION	1.44
4MD5	Immune Receptor	X-RAY DIFFRACTION	1.65
3SWK	Crystal structure of vimentin coil1B fragment	X-RAY DIFFRACTION	1.7
4MDJ	Immune Receptor	X-RAY DIFFRACTION	1.7
3G1E	X-ray crystal structure of coil 1A of human vimentin	X-RAY DIFFRACTION	1.83
1GK6	Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B)	X-RAY DIFFRACTION	1.9
6ATF	HLA-DRB1*1402 in complex with Vimentin59-71	X-RAY DIFFRACTION	1.9
6ATI	HLA-DRB1*1402 in complex with Vimentin-64Cit59-71	X-RAY DIFFRACTION	1.98
4MDI	Immune Receptor	X-RAY DIFFRACTION	2
4YV3	Trimeric crystal structure of vimentin coil1B fragment	X-RAY DIFFRACTION	2
6YXK	Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74	X-RAY DIFFRACTION	2
4MD0	Immune Receptor	X-RAY DIFFRACTION	2.19
5WHF	Crystal structure of vimentin coil 1B packed in a high-order filamentous form	X-RAY DIFFRACTION	2.25
1GK4	HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2)	X-RAY DIFFRACTION	2.3
3TRT	Crystal structure of stabilised vimentin coil2 fragment	X-RAY DIFFRACTION	2.3
4MCY	Immune Receptor	X-RAY DIFFRACTION	2.3
6BIR	HLA-DRB1 in complex with citrullinated Vimentin peptide	X-RAY DIFFRACTION	2.3
4MCZ	Immune Receptor	X-RAY DIFFRACTION	2.41
3S4R	Crystal structure of vimentin coil1A/1B fragment with a stabilizing mutation	X-RAY DIFFRACTION	2.45
3SSU	Crystal structure of vimentin coil1A/1B fragment	X-RAY DIFFRACTION	2.6
8TRR	T cell recognition of citrullinated vimentin peptide presented by HLA-DR4	X-RAY DIFFRACTION	2.65
3KLT	Crystal structure of a vimentin fragment	X-RAY DIFFRACTION	2.7
8TRQ	T cell recognition of citrullinated vimentin peptide presented by HLA-DR4	X-RAY DIFFRACTION	2.75
3UF1	Crystal Structure of Vimentin (fragment 144-251) from Homo sapiens, Northeast Structural …	X-RAY DIFFRACTION	2.81
8RVE	Vimentin intermediate filament	ELECTRON MICROSCOPY	7.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P08670-F1	78.05	0.52

Antibody-complex structures (SAbDab)

1 antibodies co-crystallized with this protein: 6YXK

Human Protein Atlas

Protein class: Predicted intracellular proteins, Plasma proteins, Disease related genes, Human disease related genes, Eye disease

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): intermediate filaments

Antibody reliability (HPA): IH enhanced · IF supported

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1)

Position	Role
351	stutter

Post-translational modifications (68)

Type	Positions
N-acetylserine	2
Phosphoserine	5, 7, 8, 9, 10, 25, 26, 34, 39, 42, 47, 49, 51, 55, 56, 66, 72, 73, 83, 87, 144, 214, 226, 299, 325, 409, 412, 419, 420, 430, 438, 459
Phosphothreonine	20, 426, 436, 446, 458
Phosphotyrosine	53, 61, 117
N6-acetyllysine	120, 129, 139, 168, 188, 223, 235, 294, 373, 445
N6-succinyllysine	120, 129, 188, 294, 445
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)	104, 120, 129, 139, 223, 262, 294, 313, 373, 439, 445
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo1)	445

Glycosylation sites (3)

Type	Positions
O-linked (glcnac) serine	7, 34
O-linked (glcnac) threonine	33

Function

Pathways and Gene Ontology

Reactome pathways

8 curated (TAS) of 30; 2 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

30 pathways:

ID	Pathway	Evidence
R-HSA-9918487	Dengue Virus Genome Translation and Replication ⚕	curated
R-HSA-9918481	Dengue Virus-Host Interactions ⚕	curated
R-HSA-9646399	Aggrephagy	curated
R-HSA-264870	Caspase-mediated cleavage of cytoskeletal proteins	curated
R-HSA-9927432	Developmental Lineage of Mammary Gland Myoepithelial Cells	curated
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	curated
R-HSA-9013422	RHOBTB1 GTPase cycle	curated
R-HSA-390522	Striated Muscle Contraction	curated
R-HSA-109581	Apoptosis	—
R-HSA-111465	Apoptotic cleavage of cellular proteins	—
R-HSA-75153	Apoptotic execution phase	—
R-HSA-9612973	Autophagy	—
R-HSA-9613829	Chaperone Mediated Autophagy	electronic
R-HSA-1280215	Cytokine Signaling in Immune system	—
R-HSA-1266738	Developmental Biology	—
R-HSA-9734767	Developmental Cell Lineages	—
R-HSA-9734779	Developmental Cell Lineages of the Integumentary System	—
R-HSA-9924644	Developmental Lineages of the Mammary Gland	—
R-HSA-168256	Immune System	—
R-HSA-9615710	Late endosomal microautophagy	electronic
R-HSA-1632852	Macroautophagy	—
R-HSA-397014	Muscle contraction	—
R-HSA-5357801	Programmed Cell Death	—
R-HSA-9012999	RHO GTPase cycle	—
R-HSA-9706574	RHOBTB GTPase Cycle	—
R-HSA-9663891	Selective autophagy	—
R-HSA-162582	Signal Transduction	—
R-HSA-449147	Signaling by Interleukins	—
R-HSA-194315	Signaling by Rho GTPases	—
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3	—

MSigDB gene sets: 564 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, TSUNODA_CISPLATIN_RESISTANCE_UP, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_LENS_FIBER_CELL_DIFFERENTIATION, GOBP_EPITHELIUM_DEVELOPMENT, IIZUKA_LIVER_CANCER_EARLY_RECURRENCE, GOBP_INTERMEDIATE_FILAMENT_BASED_PROCESS, DORSAM_HOXA9_TARGETS_UP, YAGI_AML_WITH_INV_16_TRANSLOCATION, HARRIS_HYPOXIA, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_INTERMEDIATE_FILAMENT_ORGANIZATION, GOBP_RESPONSE_TO_PEPTIDE, GOBP_CELLULAR_RESPONSE_TO_LIPID

GO Biological Process (8): positive regulation of gene expression (GO:0010628), positive regulation of collagen biosynthetic process (GO:0032967), regulation of mRNA stability (GO:0043488), intermediate filament organization (GO:0045109), cellular response to lipopolysaccharide (GO:0071222), cellular response to muramyl dipeptide (GO:0071225), positive regulation of axon extension (GO:0045773), positive regulation of protein localization (GO:1903829)

GO Molecular Function (10): double-stranded RNA binding (GO:0003725), structural constituent of cytoskeleton (GO:0005200), structural constituent of eye lens (GO:0005212), protein domain specific binding (GO:0019904), identical protein binding (GO:0042802), molecular adaptor activity (GO:0060090), scaffold protein binding (GO:0097110), keratin filament binding (GO:1990254), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (15): cytoplasm (GO:0005737), peroxisome (GO:0005777), microtubule organizing center (GO:0005815), cytosol (GO:0005829), cytoskeleton (GO:0005856), intermediate filament (GO:0005882), plasma membrane (GO:0005886), focal adhesion (GO:0005925), nuclear matrix (GO:0016363), axon (GO:0030424), cell leading edge (GO:0031252), intermediate filament cytoskeleton (GO:0045111), phagocytic vesicle (GO:0045335), extracellular exosome (GO:0070062), neuron projection (GO:0043005)

Reactome top-level categories

13 top-level categories:

Category	Pathways
Autophagy	3
Dengue Virus Infection	2
Apoptotic cleavage of cellular proteins	1
Muscle contraction	1
Signaling by Interleukins	1
RHOBTB GTPase Cycle	1
Selective autophagy	1
Developmental Lineages of the Mammary Gland	1
Programmed Cell Death	1
Apoptotic execution phase	1
Immune System	1
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Cytokine Signaling in Immune system	1

GO top-level categories

50 GO namespaces:

Category	Terms
cellular anatomical structure	5
protein binding	3
cellular response to oxygen-containing compound	2
structural molecule activity	2
cytoskeleton	2
binding	2
gene expression	1
regulation of gene expression	1
positive regulation of macromolecule biosynthetic process	1
positive regulation of biosynthetic process	1
positive regulation of collagen metabolic process	1
collagen biosynthetic process	1
regulation of collagen biosynthetic process	1
regulation of RNA stability	1
regulation of mRNA catabolic process	1
intermediate filament cytoskeleton organization	1
supramolecular fiber organization	1
response to lipopolysaccharide	1
cellular response to molecule of bacterial origin	1
cellular response to lipid	1
response to muramyl dipeptide	1
cellular response to nitrogen compound	1
positive regulation of cell growth	1
regulation of axon extension	1
positive regulation of developmental growth	1
axon extension	1
positive regulation of axonogenesis	1
intracellular protein localization	1
regulation of protein localization	1
positive regulation of biological process	1
RNA binding	1
cytoskeleton organization	1
molecular_function	1
intermediate filament binding	1
nucleic acid binding	1
intracellular anatomical structure	1
microbody	1
microtubule cytoskeleton	1
cytoplasm	1
intracellular membraneless organelle	1
intermediate filament cytoskeleton	1
polymeric cytoskeletal fiber	1
membrane	1
cell periphery	1
cell-substrate junction	1
nuclear lumen	1
neuron projection	1
endocytic vesicle	1
extracellular vesicle	1
plasma membrane bounded cell projection	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 19 of 33 annotations. The rest are phylogenetic / computational / electronic (IEA).

19 experimentally-supported GO terms:

GO term	NS	Evidence
cellular response to lipopolysaccharide	BP	mutant phenotype
cellular response to muramyl dipeptide	BP	mutant phenotype
positive regulation of collagen biosynthetic process	BP	mutant phenotype
regulation of mRNA stability	BP	mutant phenotype
cytoplasm	CC	direct assay
cytoskeleton	CC	direct assay
cytosol	CC	direct assay
extracellular exosome	CC	high-throughput assay
focal adhesion	CC	high-throughput assay
intermediate filament	CC	direct assay
intermediate filament cytoskeleton	CC	direct assay
peroxisome	CC	direct assay
double-stranded RNA binding	MF	direct assay
identical protein binding	MF	physical interaction
keratin filament binding	MF	physical interaction
molecular adaptor activity	MF	experiment
protein domain specific binding	MF	physical interaction
scaffold protein binding	MF	physical interaction
structural constituent of cytoskeleton	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 4,691 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VIM	CDH1	P12830	887
VIM	ZEB1	P37275	879
VIM	UBAC1	Q9BSL1	877
VIM	ZEB2	O60315	862
VIM	SNAI2	O43623	845
VIM	SNAI1	O95863	830
VIM	CDH2	P19022	770
VIM	TWIST1	Q15672	717
VIM	FN1	P02751	702
VIM	GAN	Q9H2C0	700
VIM	COL1A1	P02452	696
VIM	PLEC	Q15149	689
VIM	IGDCC3	Q8IVU1	662
VIM	EPCAM	P16422	653
VIM	LGALS1	P09382	643

IntAct

Human interaction partners of VIM in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 269 partners by confidence:

Partner	Interaction type	MIscore	Records
NEFM	physical association	0.910	4
NOD2	physical association	0.850	12
NEFL	association	0.840	9
GFAP	physical association	0.830	8
KRT20	physical association	0.830	8
DES	physical association	0.820	5
NES	physical association	0.800	1
KAT7	physical association	0.750	4
SYNC	physical association	0.740	3
PNMA5	physical association	0.720	6
TXLNB	physical association	0.720	6
AKT1	physical association	0.710	28
KIAA0408	physical association	0.670	4
PRPH	physical association	0.670	4
SMARCB1	physical association	0.670	4
HTT	physical association	0.670	3
YWHAZ	physical association	0.670	1
YWHAG	physical association	0.650	1
CRMP1	physical association	0.630	3
NCR1	physical association	0.610	3
CFTR	association	0.610	1
HTRA3	association	0.600	12
LOXL2	physical association	0.600	5
ACE2	colocalization	0.600	4
PKP1	physical association	0.590	3
ADAL	physical association	0.560	3
AGGF1	physical association	0.560	3
AK2	physical association	0.560	3
ARMC7	physical association	0.560	3
ASCL4	physical association	0.560	3

BioGRID (1,110 interactions; top human partners by supporting records in a sample of 600 records): GAN (Affinity Capture-MS; 7 records), NEFM (Affinity Capture-MS; 7 records), GFAP (Two-hybrid; 6 records), NEFL (Affinity Capture-MS; 6 records), DES (Affinity Capture-MS; 5 records), NES (Affinity Capture-MS; 5 records), CPEB4 (Affinity Capture-MS; 4 records), EPPK1 (Affinity Capture-MS; 4 records), INA (Affinity Capture-MS; 4 records), SYNC (Affinity Capture-MS; 4 records), DSP (Proximity Label-MS; 3 records), KRT20 (Two-hybrid; 3 records), MICAL1 (Affinity Capture-Western; 3 records), PKN1 (Two-hybrid; 3 records), PLA2G2A (Affinity Capture-MS; 3 records)

SIGNOR signaling

showing 32 of 49 signaling interactions:

A	Effect	B	Mechanism
PAK1	unknown	VIM	phosphorylation
PLK1	up-regulates	VIM	phosphorylation
AKT	“up-regulates quantity by stabilization”	VIM	phosphorylation
AKT1	“up-regulates quantity by stabilization”	VIM	phosphorylation
ERG	“up-regulates quantity by expression”	VIM	“transcriptional regulation”
ETV4	“up-regulates quantity by expression”	VIM	“transcriptional regulation”
TOR1AIP1	“up-regulates activity”	VIM	binding
RNF208	“down-regulates quantity by destabilization”	VIM	ubiquitination
PRKCZ	“up-regulates activity”	VIM	phosphorylation
PRKCI	“up-regulates activity”	VIM	phosphorylation
VIM	“up-regulates activity”	LARP6	binding
hsa-mir-494-3p	“down-regulates quantity by repression”	VIM	“post transcriptional regulation”
hsa-miR-30a-3p	“down-regulates quantity by repression”	VIM	“post transcriptional regulation”
hsa-miR-148a-3p	“down-regulates quantity by repression”	VIM	“post transcriptional regulation”
CDK5	“up-regulates activity”	VIM	phosphorylation
PRKCB	“up-regulates quantity”	VIM	phosphorylation
TWIST1	“up-regulates quantity by expression”	VIM	“transcriptional regulation”
VIM	up-regulates	Epithelial-mesenchymal_transition
ZEB1	“up-regulates quantity by expression”	VIM	“transcriptional regulation”
SNAI1	“up-regulates quantity by expression”	VIM	“transcriptional regulation”
SNAI2	“up-regulates quantity by expression”	VIM	“transcriptional regulation”
LEF1	“up-regulates quantity by expression”	VIM	“transcriptional regulation”
TCF7	“up-regulates quantity by expression”	VIM	“transcriptional regulation”
CDK1	down-regulates	VIM	phosphorylation
AURKB	down-regulates	VIM	phosphorylation
PRKCA	“down-regulates quantity by destabilization”	VIM	phosphorylation
PRKCA	“down-regulates activity”	VIM	phosphorylation
ROCK1	“down-regulates activity”	VIM	phosphorylation
PRKACA	“down-regulates activity”	VIM	phosphorylation
PAK2	“down-regulates activity”	VIM	phosphorylation
CAMK2D	unknown	VIM	phosphorylation
PAK	“down-regulates activity”	VIM	phosphorylation

Protein complexes (CORUM) (2)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

2 complexes by size:

Complex	Subunits	Members
★ CD4 receptor complex	9	PTPRCAP, TFRC, TUBA1C, TUBB, VIM, CD4, LCK, MYH9, PTPRC
pERK-vimentin-KPNA2 complex	3	KPNA2, MAPK3, VIM

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 269 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
Activation of BAD and translocation to mitochondria	5	21.3×	5e-04
JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1	5	14.5×	2e-03
Activation of BH3-only proteins	5	13.9×	2e-03
activated TAK1 mediates p38 MAPK activation	5	13.9×	2e-03
Regulation of TP53 Activity through Acetylation	5	12.8×	2e-03
Constitutive Signaling by AKT1 E17K in Cancer	5	11.8×	3e-03
TAK1-dependent IKK and NF-kappa-B activation	7	11.8×	5e-04
Intrinsic Pathway for Apoptosis	7	11.4×	5e-04

Disease & clinical

Genetic variants

Variant evidence for VIM: 138 ClinVar records (1 pathogenic / likely pathogenic); 6 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	68
Likely benign	30
Benign	23

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
692107	NM_003380.5(VIM):c.1160T>C (p.Leu387Pro)	Likely pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore VIM’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 25 predictions of 524):

Position(s)	Effect	Δscore	Sites
10:17233575	acceptor_gain	1.0000
10:17233581	acceptor_gain	1.0000
10:17233585–17233586	acceptor_loss	1.0000	6
10:17233683–17233684	donor_loss	1.0000	5
10:17233765	acceptor_gain	1.0000
10:17233768–17233769	acceptor_loss	1.0000	2
10:17233769	acceptor_gain	1.0000
10:17233932–17233933	donor_loss	1.0000	3
10:17234690	acceptor_gain	1.0000
10:17234691–17234692	acceptor_loss	1.0000	4

AlphaMissense

1,474 missense substitutions predicted likely pathogenic (of 3,061 scored), across 365 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M376	9	0.984	0.999
M391	9	0.940	0.999
N111	8	0.999	1.000
D394	8	0.999	1.000
F114	8	0.997	1.000
N128	8	0.996	0.999
D211	8	0.981	0.995
D112	8	0.970	0.994
F233	8	0.969	0.999
N283	8	0.948	0.992
H379	8	0.943	0.997
D209	8	0.942	0.982
F86	8	0.930	0.993
D297	8	0.923	0.971
D264	8	0.918	0.982
D85	8	0.909	0.981
H238	8	0.887	0.993
D176	8	0.879	0.970
D181	8	0.863	0.973
D219	8	0.842	0.916

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Disease associations

OMIM: gene MIM:193060 | disease phenotypes:

GenCC curated gene-disease

3 curated gene-disease records:

Disease	Classification	Inheritance	Records
cataract	Definitive	Autosomal dominant
cataract 30	Strong	Autosomal dominant	2
pulverulent cataract	Supportive	Autosomal dominant

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (1 panels, 1 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

1 panels:

Panel	Rating
Bilateral congenital or childhood onset cataracts	green

Mondo (3): cataract 30 (MONDO:0007286), pulverulent cataract (MONDO:0011430), cataract (MONDO:0005129)

HPO phenotypes

5 phenotypes (HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0001115	Posterior polar cataract
HP:0003577	Congenital onset
HP:0007657	Diffuse nuclear cataract
HP:0010693	Pulverulent cataract

GWAS associations

6 associations:

Study	Trait	p-value
GCST90011899_182	Aspartate aminotransferase levels	3e-21
GCST90002397_760	Mean spheric corpuscular volume	8e-14
GCST002221_72	Cholesterol, total	3e-11
GCST004235_63	Total cholesterol levels	5e-11
GCST010242_319	HDL cholesterol levels	6e-11
GCST010244_26	Triglyceride levels	2e-8

EFO canonical traits (from GWAS)

4 canonical traits:

EFO ID	Trait name
EFO:0004574	total cholesterol measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004530	triglyceride measurement
EFO:0004736	aspartate aminotransferase measurement

MeSH disease descriptors

3 disease descriptors:

Descriptor	Name	Tree numbers
D002386	Cataract	C11.510.245
C565133	Cataract, Coppock-Like *(supp.)*
C566157	Cataract, Nuclear Diffuse Nonprogressive *(supp.)*

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3712854 (SINGLE PROTEIN)

Drugs by curated mechanism of action (ChEMBL)

Drugs whose curated ChEMBL mechanism of action targets the VIM protein itself — single-protein targets only (drugs acting on a protein family or complex that merely includes it are excluded). Includes antibodies and oligonucleotides that bioactivity screening does not capture.

1 curated-mechanism drugs:

Drug	Modality	Max phase
PRITUMUMAB	Antibody	2

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

2 measured of 2 human assays (3 total across all organisms); most potent 2 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
CHEMBL5412999	KD	1000 nM
CHEMBL5653589	KD	1440 nM

ChEMBL bioactivities

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

pChembl	Type	Value	Unit	Molecule
6.19	Kd	640.2	nM	CHEMBL3752910
6.00	Kd	1000	nM	CHEMBL5412999
6.00	Kd	1005	nM	CHEMBL5653589
5.99	ED50	1033	nM	CHEMBL3752910
5.79	ED50	1622	nM	CHEMBL5653589

PubChem BioAssay actives

3 with measured affinity, of 30 total; 3 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	2149765: Binding affinity to human VIM incubated for 45 mins by Kinobead based pull down assay	kd	0.6402	uM
(2R)-6-amino-N-[(2R)-1-[[6-amino-5-[[(2R)-2-[[(2R)-6-amino-2-[[2-[[2-[[2-[[2-[4-aminobutyl-[2-[4-aminobutyl-[2-[[2-(4-benzoylanilino)acetyl]-(2-methylpropyl)amino]acetyl]amino]acetyl]amino]acetyl]-(2-methylpropyl)amino]acetyl]-(1,3-benzodioxol-5-ylmethyl)amino]acetyl]-(2-methoxyethyl)amino]acetyl]amino]hexanoyl]amino]-4-methylsulfanylbutanoyl]amino]-6-oxohexyl]amino]-4-methylsulfanyl-1-oxobutan-2-yl]-2-[[2-[[2-[[2-[[2-[4-aminobutyl-[2-[4-aminobutyl-[2-[[2-(4-benzoylanilino)acetyl]-(2-methylpropyl)amino]acetyl]amino]acetyl]amino]acetyl]-(2-methylpropyl)amino]acetyl]-(1,3-benzodioxol-5-ylmethyl)amino]acetyl]-(2-methoxyethyl)amino]acetyl]amino]hexanamide	2005096: Binding affinity to his-tagged recombinant Vimentin (unknown origin) assessed as dissociation constant by ELISA analysis	kd	1.0000	uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149765: Binding affinity to human VIM incubated for 45 mins by Kinobead based pull down assay	kd	1.0047	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression, increases reaction, affects cotreatment, affects reaction (+3 more)	30
bisphenol A	increases expression, increases reaction, affects reaction, decreases reaction, affects cotreatment (+1 more)	15
Cadmium Chloride	increases expression, decreases expression, increases localization, increases metabolic processing, affects reaction (+9 more)	14
Particulate Matter	decreases reaction, affects reaction, affects expression, decreases expression, increases abundance (+1 more)	13
Tretinoin	decreases expression, increases reaction, affects cotreatment, increases expression	12
Resveratrol	affects cotreatment, decreases expression, affects secretion, decreases reaction, increases expression	9
Arsenic	increases reaction, decreases reaction, affects cotreatment, increases abundance, decreases expression (+4 more)	9
Benzo(a)pyrene	affects cotreatment, decreases expression, increases methylation, affects reaction, decreases reaction (+2 more)	8
Estradiol	affects cotreatment, decreases expression, increases reaction, affects binding, decreases reaction (+1 more)	8
2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one	increases abundance, increases expression, decreases reaction, increases reaction, decreases expression (+4 more)	7
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases reaction, increases abundance, increases expression	7
bisphenol S	affects cotreatment, decreases methylation, increases expression, decreases expression, affects reaction	7
Arsenic Trioxide	increases expression, affects reaction, decreases reaction, decreases expression, increases reaction	7
Cadmium	decreases reaction, increases abundance, increases palmitoylation, increases expression, decreases expression	7
Silicon Dioxide	decreases reaction, increases expression, increases reaction, affects secretion, increases secretion (+1 more)	7
arsenite	decreases reaction, increases expression, increases abundance, increases reaction, decreases expression (+3 more)	5
Fulvestrant	decreases methylation, affects cotreatment, decreases reaction, increases expression	5
Acetylcysteine	decreases reaction, increases expression, increases abundance, decreases expression	5
Cisplatin	decreases expression, increases reaction, increases expression, decreases reaction	5
Endosulfan	decreases reaction, increases expression	5
Niclosamide	decreases reaction, increases expression, decreases response to substance, increases phosphorylation, decreases expression	5
Tobacco Smoke Pollution	decreases reaction, increases expression, increases reaction, affects expression, decreases expression	5
Valproic Acid	decreases expression, increases expression	5
cobaltous chloride	decreases reaction, increases expression, increases reaction	4
SB 203580	decreases reaction, increases expression, increases phosphorylation, increases abundance	4
U 0126	decreases reaction, increases expression, increases abundance, increases reaction, increases phosphorylation	4
Air Pollutants	affects expression, decreases expression, increases abundance, increases expression	4
Copper	affects cotreatment, decreases expression, affects binding, increases cleavage	4
Doxorubicin	decreases phosphorylation, increases expression, increases response to substance, affects expression, affects cotreatment (+1 more)	4
Glucose	affects cotreatment, increases expression, increases secretion, increases reaction	4

ChEMBL screening assays

18 unique, capped per target: 18 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4270856	Binding	Binding affinity to vimentin in human Hela cells lysates assessed as protein enrichment by measuring normalized heavy/light ratio at by nano-LC-ESIMS/MS analysis	Determination of Gymnemic Acid I as a Protein Biosynthesis Inhibitor Using Chemical Proteomics. — *J Nat Prod*

Cellosaurus cell lines

7 cell lines: 7 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2L2	Abcam HeLa VIM KO	Cancer cell line	Female
CVCL_B8RP	Abcam HCT 116 VIM KO	Cancer cell line	Male
CVCL_B9U4	Abcam A-549 VIM KO	Cancer cell line	Male
CVCL_D1UW	Abcam U-87MG VIM KO	Cancer cell line	Male
CVCL_E0SW	Ubigene HeLa VIM KO	Cancer cell line	Female
CVCL_TX43	HAP1 VIM (-) 1	Cancer cell line	Male
CVCL_TX44	HAP1 VIM (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for VIM across ~30M SureChEMBL compounds — explore on Sugi Predict.