VIM
vimentin, the group of Intermediate filaments Type III
Basic information
Region (hg38): 10:17228241-17237593
Links
Phenotypes
GenCC
Source:
- pulverulent cataract (Supportive), mode of inheritance: AD
- cataract 30 (Strong), mode of inheritance: AD
- cataract (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| 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
- Cataract_30 (49 variants)
- not_specified (44 variants)
- not_provided (26 variants)
- VIM-related_disorder (6 variants)
- Developmental_cataract (1 variants)
- syndrome_with_premature-aging (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. These statistics are base on transcript: NM_000003380.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | 14 | ||||
| missense | 62 | 68 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 1 | 2 | 64 | 13 | 5 |
Highest pathogenic variant AF is 0.000011177209
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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
- essential_gene_gene_trap
- 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