Is VCAN p.Ala798= (c.2394C>G) pathogenic?

VCAN p.Ala798= (c.2394C>G) is classified Likely benign in VCAN (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-07). Absent from gnomAD v4.1.

How common is VCAN p.Ala798= (c.2394C>G) in the general population?

VCAN p.Ala798= (c.2394C>G) is absent from gnomAD v4.1 (gnomAD).

VCAN p.Ala798=

c.2394C>G · rs2479052318 · VCV2135100

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.84	GERP -1.3, phastCons 1
Overall
CADD	2.411	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: VCAN
Protein: p.Ala798=
Coding: c.2394C>G
MANE Select: NM_004385
dbSNP: rs2479052318
Type: single nucleotide variant
Location: chr5:83520700 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Residue 798: the 'gag-alpha (glucosaminoglycan attachment domain)' region

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

Similar variants

VCAN p.Ala798Thr Uncertain significance ★★ ⚠ same residue
VCAN p.Ala798Val Conflicting classifications of pathogenicity ★ ⚠ same residue
VCAN c.4004-1G>A Pathogenic ★★ same type
VCAN c.4004-2A>C Pathogenic ★★ same type
VCAN c.4004-2A>G Pathogenic ★★ same type
VCAN c.4004-5T>C Pathogenic ★★ same type
VCAN c.9265+1G>C Pathogenic ★★ same type
VCAN c.9266-5G>A Uncertain significance ★★ 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/vcan-p-ala798 (accessed [today's date]).

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