Cataract 30

Summary

Cataract 30 (MONDO:0007286) is a disease caused by VIM (GenCC Strong), with 2 cohort genes.

At a glance

• Causal gene: VIM (GenCC Strong)
• Cohort genes: 2
• ClinVar variants: 59

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	cataract 30
Mondo ID	MONDO:0007286
MeSH	C566157
OMIM	116300
DOID	DOID:0110248
UMLS	C3805411
MedGen	811741
GARD	0024545
Is cancer (heuristic)	no

Also known as: cataract 30 · cataract type 30 · CTRCT30

Data availability: 59 ClinVar variants · 2 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › disorder of orbital region › eye disorder › lens disorder › cataract › early-onset non-syndromic cataract › early-onset partial cataract › cataract 30

Related subtypes (4): early-onset posterior subcapsular cataract, early-onset anterior polar cataract, cerulean cataract, early-onset zonular cataract

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

59 retrieved; paginated sample, class counts are floors:

24 uncertain significance, 21 likely benign, 10 benign, 2 benign/likely benign, 1 pathogenic, 1 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
12199	NM_003380.5(VIM):c.451G>A (p.Glu151Lys)	VIM-AS1	Pathogenic	no assertion criteria provided
217338	NM_003380.5(VIM):c.15del (p.Val6fs)	VIM-AS1	Pathogenic/Likely pathogenic	no assertion criteria provided
4808532	NM_003380.5(VIM):c.227G>T (p.Gly76Val)	LOC130003452	Uncertain significance	criteria provided, single submitter
541104	NM_003380.5(VIM):c.167C>A (p.Ser56Tyr)	LOC130003452	Uncertain significance	criteria provided, single submitter
1051392	NM_003380.5(VIM):c.911G>A (p.Arg304Gln)	VIM	Uncertain significance	criteria provided, single submitter
1353044	NM_003380.5(VIM):c.134G>A (p.Arg45His)	VIM	Uncertain significance	criteria provided, multiple submitters, no conflicts
1486484	NM_003380.5(VIM):c.598G>C (p.Glu200Gln)	VIM	Uncertain significance	criteria provided, single submitter
1699008	NM_003380.5(VIM):c.46G>A (p.Gly16Ser)	VIM	Uncertain significance	criteria provided, single submitter
2012232	NM_003380.5(VIM):c.626A>G (p.Asp209Gly)	VIM	Uncertain significance	criteria provided, single submitter
2015068	NM_003380.5(VIM):c.1024C>G (p.Arg342Gly)	VIM	Uncertain significance	criteria provided, single submitter
2084511	NM_003380.5(VIM):c.814G>A (p.Val272Ile)	VIM	Uncertain significance	criteria provided, multiple submitters, no conflicts
2345133	NM_003380.5(VIM):c.1372A>G (p.Thr458Ala)	VIM	Uncertain significance	criteria provided, multiple submitters, no conflicts
2368041	NM_003380.5(VIM):c.1080C>G (p.Asp360Glu)	VIM	Uncertain significance	criteria provided, multiple submitters, no conflicts
2872982	NM_003380.5(VIM):c.82C>G (p.Arg28Gly)	VIM	Uncertain significance	criteria provided, single submitter
2872983	NM_003380.5(VIM):c.451GAG[2] (p.Glu153del)	VIM	Uncertain significance	criteria provided, single submitter
3047409	NM_003380.5(VIM):c.646G>A (p.Ala216Thr)	VIM	Uncertain significance	criteria provided, single submitter
3892842	NM_003380.5(VIM):c.1032G>A (p.Met344Ile)	VIM	Uncertain significance	criteria provided, single submitter
4198802	NM_003380.5(VIM):c.490C>G (p.Leu164Val)	VIM	Uncertain significance	criteria provided, multiple submitters, no conflicts
425575	NM_003380.5(VIM):c.623A>G (p.Gln208Arg)	VIM	Uncertain significance	criteria provided, single submitter
4279621	NM_003380.5(VIM):c.1008+1G>A	VIM	Uncertain significance	criteria provided, single submitter
4745556	NM_003380.5(VIM):c.1115T>C (p.Met372Thr)	VIM	Uncertain significance	criteria provided, single submitter
4807145	NM_003380.5(VIM):c.538G>A (p.Glu180Lys)	VIM	Uncertain significance	criteria provided, single submitter
930366	NM_003380.5(VIM):c.1141C>T (p.Arg381Cys)	VIM	Uncertain significance	criteria provided, single submitter
949490	NM_003380.5(VIM):c.468G>C (p.Glu156Asp)	VIM	Uncertain significance	criteria provided, single submitter
959458	NM_003380.5(VIM):c.758A>G (p.His253Arg)	VIM	Uncertain significance	criteria provided, single submitter
962651	NM_003380.5(VIM):c.1374_1375dup (p.Ser459fs)	VIM	Uncertain significance	criteria provided, single submitter
2893287	NM_003380.5(VIM):c.563+15A>C	LOC130003453	Likely benign	criteria provided, single submitter
1110631	NM_003380.5(VIM):c.624+7A>C	VIM	Likely benign	criteria provided, single submitter
1127193	NM_003380.5(VIM):c.1009-8C>A	VIM	Likely benign	criteria provided, single submitter
1165657	NM_003380.5(VIM):c.807G>T (p.Leu269=)	VIM	Benign	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · Orphanet: 2 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
VIM	Definitive	Autosomal dominant	cataract	4

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
VIM	Orphanet:675396	Epithelioid hemangioma
VIM	Orphanet:98984	Pulverulent cataract

Cohort genes → proteins

2 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
VIM	HGNC:12692	ENSG00000026025	P08670	Vimentin	gencc,clinvar
VIM-AS1	HGNC:44879	ENSG00000229124		VIM antisense RNA 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
VIM	Vimentin	Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 2 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Other/Unknown	2	1.8×	0.312

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
VIM	Other/Unknown	no		Intermed_filament_DNA-bd, IF_conserved, IF_rod_dom
VIM-AS1	Other/Unknown	no

Expression context

Cohort genes with no expression data: 0.

2 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
descending thoracic aorta	1
right coronary artery	1
ventricular zone	1
leukocyte	1
male germ line stem cell (sensu Vertebrata) in testis	1
monocyte	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
VIM	307	ubiquitous	marker	ventricular zone, descending thoracic aorta, right coronary artery
VIM-AS1	135	ubiquitous	marker	monocyte, leukocyte, male germ line stem cell (sensu Vertebrata) in testis

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
VIM	6,814
VIM-AS1	0

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 1

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
VIM	P08670	26

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 10. Enrichment computed across 2 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Caspase-mediated cleavage of cytoskeletal proteins	1	951.7×	0.005	VIM
Developmental Lineage of Mammary Gland Myoepithelial Cells	1	543.8×	0.005	VIM
Chaperone Mediated Autophagy	1	496.5×	0.005	VIM
RHOBTB1 GTPase cycle	1	475.8×	0.005	VIM
Late endosomal microautophagy	1	326.3×	0.005	VIM
Dengue Virus Genome Translation and Replication	1	317.2×	0.005	VIM
Striated Muscle Contraction	1	308.6×	0.005	VIM
Aggrephagy	1	248.3×	0.005	VIM
Interleukin-4 and Interleukin-13 signaling	1	102.9×	0.011	VIM
Dengue Virus-Host Interactions	1	45.7×	0.022	VIM

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
lens fiber cell development	1	2106.5×	0.003	VIM
cellular response to muramyl dipeptide	1	1685.2×	0.003	VIM
Bergmann glial cell differentiation	1	1532.0×	0.003	VIM
astrocyte development	1	1123.5×	0.003	VIM
positive regulation of collagen biosynthetic process	1	648.1×	0.004	VIM
regulation of mRNA stability	1	421.3×	0.005	VIM
intermediate filament organization	1	240.7×	0.006	VIM
negative regulation of neuron projection development	1	237.3×	0.006	VIM
cellular response to type II interferon	1	208.1×	0.006	VIM
neuron projection development	1	122.1×	0.010	VIM
cellular response to lipopolysaccharide	1	98.0×	0.011	VIM
positive regulation of gene expression	1	38.7×	0.026	VIM

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 1 of 2 evidence-associated genes (50%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
VIM	0	0
VIM-AS1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
VIM	18	Binding:18

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	2	VIM, VIM-AS1

Undrugged target profiles

2 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
VIM	18	—
VIM-AS1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.