VIM

vimentin, the group of Intermediate filaments Type III

Basic information

Region (hg38): 10:17228240-17237593

Links

ENSG00000026025 ∙ NCBI:7431 ∙ OMIM:193060 ∙ HGNC:12692 ∙ Uniprot:P08670 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pulverulent cataract (Supportive), mode of inheritance: AD
• cataract 30 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 30, multiple types	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	19126778

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VIM gene.

• Cataract 30 (37 variants)
• not provided (34 variants)
• Inborn genetic diseases (16 variants)
• VIM-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VIM gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				9	4	13
missense			32	2		34
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	1	5
non coding				10	19	29
Total	0	0	33	21	23

Variants in VIM

This is a list of pathogenic ClinVar variants found in the VIM region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-17228992-C-T			Likely benign (Feb 05, 2020)
10-17229111-G-C			Benign (Jun 28, 2018)
10-17229207-G-C			Likely benign (Apr 29, 2019)
10-17229396-C-T			Benign (May 25, 2021)
10-17229401-G-C		Cataract 30	Benign (Dec 05, 2021)
10-17229435-TC-T		Developmental cataract • Cataract 30	Pathogenic/Likely pathogenic (Dec 23, 2015)
10-17229445-C-T			Uncertain significance (Dec 01, 2018)
10-17229468-G-A		Cataract 30	Uncertain significance (Feb 02, 2022)
10-17229477-G-A		not specified	Uncertain significance (Jun 27, 2023)
10-17229504-C-G		Cataract 30	Uncertain significance (Dec 08, 2022)
10-17229511-A-G		not specified	Uncertain significance (Jul 26, 2022)
10-17229513-G-C		not specified	Uncertain significance (Dec 16, 2022)
10-17229521-G-T		Cataract 30 • VIM-related disorder	Benign/Likely benign (Nov 11, 2020)
10-17229556-G-A		Cataract 30	Uncertain significance (Aug 23, 2022)
10-17229589-C-A		Cataract 30	Uncertain significance (Aug 30, 2021)
10-17229631-T-C		not specified	Uncertain significance (Feb 21, 2024)
10-17229638-C-G		not specified	Uncertain significance (Feb 13, 2024)
10-17229651-G-A		not specified	Uncertain significance (Jun 07, 2023)
10-17229698-C-G		not specified	Uncertain significance (Oct 05, 2023)
10-17229704-C-T		Cataract 30	Benign (Dec 31, 2019)
10-17229708-T-C		not specified	Uncertain significance (Nov 07, 2022)
10-17229806-T-C		Cataract 30	Likely benign (Dec 08, 2021)
10-17229845-A-G		Cataract 30	Likely benign (Dec 08, 2021)
10-17229872-CGAG-C		Cataract 30	Uncertain significance (Dec 08, 2022)
10-17229873-G-A		Cataract 30	Pathogenic (Mar 15, 2009)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VIM	protein_coding	protein_coding	ENST00000544301	9	9335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.713	0.287	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	213	269	0.792	0.0000153	3020
Missense in Polyphen		76	103.52	0.73416		1118
Synonymous	0.647	103	112	0.922	0.00000602	915
Loss of Function	3.51	4	21.6	0.185	0.00000104	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000205	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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. {ECO:0000269|PubMed:21746880}.
• Disease: DISEASE: 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. {ECO:0000269|PubMed:19126778, ECO:0000269|PubMed:26694549, ECO:0000269|PubMed:28450710}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: MicroRNAs in cancer - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Allograft Rejection;Spinal Cord Injury;Primary Focal Segmental Glomerulosclerosis FSGS;Apoptosis-related network due to altered Notch3 in ovarian cancer;Striated Muscle Contraction;TGF-B Signaling in Thyroid Cells for Epithelial-Mesenchymal Transition;Interleukin-4 and 13 signaling;T-Cell antigen Receptor (TCR) Signaling Pathway;Alpha6Beta4Integrin;Caspase-mediated cleavage of cytoskeletal proteins;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Striated Muscle Contraction;Muscle contraction;EGFR1;Caspase Cascade in Apoptosis;Aurora B signaling (Consensus)

Recessive Scores

• pRec: 0.958

Intolerance Scores

• loftool: 0.0455
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.718
• hipred: Y
• hipred_score: 0.858
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vim
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Zebrafish Information Network

• Gene name: vim
• Affected structure: regenerating fin
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: negative regulation of neuron projection development;astrocyte development;viral process;cytokine-mediated signaling pathway;muscle filament sliding;positive regulation of collagen biosynthetic process;regulation of mRNA stability;intermediate filament organization;positive regulation of translation;Bergmann glial cell differentiation;SMAD protein signal transduction;lens fiber cell development;cellular response to lipopolysaccharide;cellular response to muramyl dipeptide;cellular response to interferon-gamma
• Cellular component: cytoplasm;peroxisome;cytosol;polysome;cytoskeleton;intermediate filament;plasma membrane;focal adhesion;nuclear matrix;cell leading edge;neuron projection;phagocytic vesicle;extracellular exosome;ribonucleoprotein complex
• Molecular function: double-stranded RNA binding;structural constituent of cytoskeleton;structural constituent of eye lens;protein binding;protein C-terminus binding;protein domain specific binding;identical protein binding;scaffold protein binding;keratin filament binding