VIM p.Val330=
c.990G>C · rs2493191415 · VCV2080210
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
cataract 30
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.7 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 19.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- VIM
- Protein
- p.Val330=
- Coding
- c.990G>C
- MANE Select
- NM_003380
- dbSNP
- rs2493191415
- Type
- single nucleotide variant
- Location
- chr10:17234800 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 78.05 · 26 PDB
- Residue 330
- an α-helix; the if rod domain; the 'coil 2' region
Similar variants
- VIM p.Arg45His Uncertain significance ★★ ⚠ same condition
- VIM p.Asp360Glu Uncertain significance ★★ ⚠ same condition
- VIM p.Leu164Val Uncertain significance ★★ ⚠ same condition
- VIM p.Thr458Ala Uncertain significance ★★ ⚠ same condition
- VIM p.Val272Ile Uncertain significance ★★ ⚠ same condition
- VIM c.1008+18A>G Benign/Likely benign ★★ same condition
- VIM c.1009-10C>T Benign ★★ same condition
- VIM c.1360-18G>T Likely benign ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/vim-p-val330 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown