VIM p.Glu374=
c.1122G>A · rs749331181 · VCV2028925
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, amr)
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 0.69 | GERP -4, phastCons 0.93 |
| Overall | ||
| CADD | 7.388 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
Admixed American · 8/60,006 alleles
Filtering AF
0.00661%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00482%
Overall
0.00347%
56/1,614,076 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0133% | 7,501 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| European (non-Finnish) | 0.00356% | 28,096 |
| African / African-American | 0.00267% | 37,463 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- VIM
- Protein
- p.Glu374=
- Coding
- c.1122G>A
- MANE Select
- NM_003380
- dbSNP
- rs749331181
- Type
- single nucleotide variant
- Location
- chr10:17235282 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 78.05 · 26 PDB
- Residue 374
- 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-glu374 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown