Is VIM p.Asp271= (c.813C>T) pathogenic?

VIM p.Asp271= (c.813C>T) is classified Benign in VIM (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-21). Common (popmax 17.1%, afr) — too common for a highly-penetrant pathogenic allele; Associated with cataract 30.

What condition is associated with VIM p.Asp271= (c.813C>T)?

VIM p.Asp271= (c.813C>T) is associated with cataract 30 (ClinVar).

VIM p.Asp271=

Q: How common is VIM p.Asp271= (c.813C>T) in the general population?

VIM p.Asp271= (c.813C>T) is common (popmax 17.1%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.813C>T · rs4903 · VCV474044

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 17.1%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

cataract 30

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.59 · evaluated, not missing
Constraint at this position
Conservation	phyloP -9.5	GERP -4
Overall
CADD	5.897	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 17.1% African / African-American · 12,834/74,964 alleles

Filtering AF 16.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 16.8%

Overall 0.974% 15,721/1,614,042 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	17.1%	6
Middle Eastern	1.34%	75
Remaining individualsnot grpmax-eligible	1.25%	80
Admixed American	1.12%	89
South Asian	0.726%	138
East Asian	0.285%	350
European (non-Finnish)	0.0469%	2,134
Ashkenazi Jewishnot grpmax-eligible	0.0372%	2,692

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.Asp271=
Coding: c.813C>T
MANE Select: NM_003380
dbSNP: rs4903
Type: single nucleotide variant
Location: chr10:17233862 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.86 (gnomAD)
Structure: AlphaFold pLDDT 78.05 · 26 PDB
Residue 271: an α-helix; the if rod domain; the 'coil 2' 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.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-asp271 (accessed [today's date]).

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