Is VIM p.Leu40Arg (c.119T>G) pathogenic?

VIM p.Leu40Arg (c.119T>G) is classified Uncertain significance in VIM (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-03). AlphaMissense: ambiguous (0.3512); No allele count reported in gnomAD v4.1 (AN 1,608,100).

How common is VIM p.Leu40Arg (c.119T>G) in the general population?

VIM p.Leu40Arg (c.119T>G) is no allele count reported in gnomAD v4.1 (AN 1,608,100) (gnomAD).

What do computational predictors say about VIM p.Leu40Arg (c.119T>G)?

AlphaMissense predicts ambiguous (score 0.3512) — an in-silico prediction, not a clinical call.

VIM p.Leu40Arg

c.119T>G · VCV3814990

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3512 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,608,100)

Computational evidence

Protein change
AlphaMissense	0.3512	ambiguous
REVEL	0.537	indeterminate
SaProt	LLR -5.51	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP -0.39, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 255 bp · p 0.5 · regional, not allelic
Overall
CADD	22.7	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,608,100). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: VIM
Protein: p.Leu40Arg
Coding: c.119T>G
MANE Select: NM_003380
Type: single nucleotide variant
Location: chr10:17229541 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.86 (gnomAD)
Structure: AlphaFold pLDDT 78.05 · 26 PDB
Residue 40: the 'head' region

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

Similar variants

VIM p.Arg45His Uncertain significance ★★ ⚠ same type
VIM p.Asp360Glu Uncertain significance ★★ ⚠ same type
VIM p.Leu164Val Uncertain significance ★★ ⚠ same type
VIM p.Thr458Ala Uncertain significance ★★ ⚠ same type
VIM p.Val272Ile Uncertain significance ★★ ⚠ same type
VIM c.1008+18A>G Benign/Likely benign ★★ same type
VIM c.1008+99G>A Benign ★★ same type
VIM c.1009-10C>T Benign ★★ same type

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-leu40arg (accessed [today's date]).

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