Is VCL p.Ala482Asp (c.1445C>A) pathogenic?

VCL p.Ala482Asp (c.1445C>A) is classified Uncertain significance in VCL (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-13). AlphaMissense: likely pathogenic (0.8286); Very rare (popmax 0.000169%, nfe); Associated with hypertrophic cardiomyopathy 15.

What condition is associated with VCL p.Ala482Asp (c.1445C>A)?

VCL p.Ala482Asp (c.1445C>A) is associated with hypertrophic cardiomyopathy 15, dilated cardiomyopathy 1W (ClinVar).

How common is VCL p.Ala482Asp (c.1445C>A) in the general population?

VCL p.Ala482Asp (c.1445C>A) is very rare (popmax 0.000169%, nfe) (gnomAD).

What do computational predictors say about VCL p.Ala482Asp (c.1445C>A)?

AlphaMissense predicts likely pathogenic (score 0.8286) — an in-silico prediction, not a clinical call.

VCL p.Ala482Asp

c.1445C>A · rs531596507 · VCV1772783

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.8286 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

hypertrophic cardiomyopathy 15

Computational evidence

Protein change
AlphaMissense	0.8286	likely pathogenic
REVEL	0.348	indeterminate
SaProt	LLR -4.73	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.7, phastCons 1
Regional constraint	o/e 0.82	unconstrained · MANE · 38 kb · p 3e-08 · regional, not allelic
Overall
CADD	27.1	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

Grpmax group 0.000169% European (non-Finnish) · 2/1,180,042 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000124% 2/1,614,032 alleles · very rare exomes 1/1,461,876 · genomes 1/152,156 · joint denominator

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: VCL
Protein: p.Ala482Asp
Coding: c.1445C>A
MANE Select: NM_014000
dbSNP: rs531596507
Type: single nucleotide variant
Location: chr10:74094363 (GRCh38)
Gene constraint: LOEUF 0.461 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 86.69 · 37 PDB
Residue 482: the 'n-terminal globular head' region; the '3 x 112 aa tandem repeats' region; an α-helix

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

Disease context

hypertrophic cardiomyopathy 15 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy 1W

Similar variants

VCL p.Ala482Gly Uncertain significance ★ ⚠ same residue
VCL c.1176+4G>C Uncertain significance ★★ same condition
VCL c.1352+5G>A Uncertain significance ★★ same condition
VCL c.1543+1G>T Uncertain significance ★★ same condition
VCL c.1543+4A>G Uncertain significance ★★ same condition
VCL c.1743+6A>G Uncertain significance ★★ same condition
VCL c.1744-1G>T Uncertain significance ★★ same condition
VCL c.2022+5G>T Uncertain significance ★★ 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/vcl-p-ala482asp (accessed [today's date]).

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