Is VIM p.Thr94= (c.282C>T) pathogenic?

VIM p.Thr94= (c.282C>T) is classified Benign in VIM (ClinVar, Single submitter, 2 submitters; last evaluated 2019-12-31). Rare (popmax 0.368%, afr); Associated with cataract 30.

What condition is associated with VIM p.Thr94= (c.282C>T)?

VIM p.Thr94= (c.282C>T) is associated with cataract 30 (ClinVar).

How common is VIM p.Thr94= (c.282C>T) in the general population?

VIM p.Thr94= (c.282C>T) is rare (popmax 0.368%, afr) (gnomAD).

VIM p.Thr94=

c.282C>T · rs144539901 · VCV779851

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.368%, afr)

Conditions

cataract 30

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.21	GERP -1.4, phastCons 0.35
Overall
CADD	17.63	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.368% African / African-American · 273/74,100 alleles

Filtering AF 0.332% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.318%

Overall 0.0197% 309/1,571,736 alleles · rare exomes 159/1,419,428 · genomes 150/152,308 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.368%	271
Remaining individualsnot grpmax-eligible	0.0328%	3,049
Admixed American	0.03%	3,334

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.Thr94=
Coding: c.282C>T
MANE Select: NM_003380
dbSNP: rs144539901
Type: single nucleotide variant
Location: chr10:17229704 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.86 (gnomAD)
Structure: AlphaFold pLDDT 78.05 · 26 PDB
Residue 94: the 'head' region

Full VIM gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cataract 30 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

VIM p.Thr94Ile Uncertain significance ★ same residue
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

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-thr94 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown