Is VIM p.Thr458Ala (c.1372A>G) pathogenic?

VIM p.Thr458Ala (c.1372A>G) is classified Uncertain significance in VIM (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-11). AlphaMissense: likely benign (0.1636); Ultra-rare (popmax 0.0107%, nfe); Associated with cataract 30.

What condition is associated with VIM p.Thr458Ala (c.1372A>G)?

VIM p.Thr458Ala (c.1372A>G) is associated with cataract 30 (ClinVar).

How common is VIM p.Thr458Ala (c.1372A>G) in the general population?

VIM p.Thr458Ala (c.1372A>G) is ultra-rare (popmax 0.0107%, nfe) (gnomAD).

What do computational predictors say about VIM p.Thr458Ala (c.1372A>G)?

AlphaMissense predicts likely benign (score 0.1636) — an in-silico prediction, not a clinical call.

VIM p.Thr458Ala

c.1372A>G · rs747701399 · VCV2345133

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1636 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

cataract 30

Computational evidence

Protein change
AlphaMissense	0.1636	likely benign
REVEL	0.293	indeterminate
SaProt	LLR -9.90	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 7,480 bp · p 0.038 · regional, not allelic
Overall
CADD	23.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% European (non-Finnish) · 126/1,175,032 alleles

Filtering AF 0.00915% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00859%

Overall 0.00822% 132/1,605,622 alleles · ultra-rare exomes 127/1,453,494 · genomes 5/152,128 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0107%	9,326
Remaining individualsnot grpmax-eligible	0.00483%	20,696
African / African-American	0.00401%	24,945

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.Thr458Ala
Coding: c.1372A>G
MANE Select: NM_003380
dbSNP: rs747701399
Type: single nucleotide variant
Location: chr10:17237242 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.86 (gnomAD)
Structure: AlphaFold pLDDT 78.05 · 26 PDB
Residue 458: the 'tail' region; a modified residue (phosphothreonine)

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.Arg45His Uncertain significance ★★ ⚠ same condition
VIM p.Asp360Glu Uncertain significance ★★ ⚠ same condition
VIM p.Leu164Val 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
VIM c.720+18C>T Benign/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-thr458ala (accessed [today's date]).

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