Is ACAN p.Ser802fs (c.2403dup) pathogenic?

ACAN p.Ser802fs (c.2403dup) is classified Likely pathogenic in ACAN (ClinVar, Single submitter, 1 submitter; last evaluated 2018-12-03). Absent from gnomAD; Associated with ACAN-related disorder.

What condition is associated with ACAN p.Ser802fs (c.2403dup)?

ACAN p.Ser802fs (c.2403dup) is associated with ACAN-related disorder (ClinVar).

How common is ACAN p.Ser802fs (c.2403dup) in the general population?

ACAN p.Ser802fs (c.2403dup) is absent from gnomAD (gnomAD).

ACAN p.Ser802fs

c.2403dup · rs2141602321 · VCV1224397

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ACAN-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 12 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.33	GERP 1, phastCons 0.002
Region caveats
Repeat context	tandem	CCTCAGAGGAGCCATTCC simple repeat · ambiguous alignment · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: ACAN
Protein: p.Ser802fs
Coding: c.2403dup
MANE Select: NM_001369268
dbSNP: rs2141602321
Type: Duplication
Location: chr15:88854983 (GRCh38)
Gene constraint: LOEUF 0.377 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 53.32 · 4 PDB
Residue 802: the 'ks' region; the 'disordered' region; the '12 x 6 aa approximate tandem repeats of e-[gve]-p-[sfy]-[apt]-[tsp]' region

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

Disease context

ACAN-related disorder

Similar variants

ACAN p.Ile398fs Likely pathogenic ★ same condition
ACAN p.Ala2280fs Likely pathogenic same condition
ACAN c.630-13G>A Pathogenic ★★ same condition
ACAN p.Arg236Ter Pathogenic ★★ same condition
ACAN p.Arg386Ter Pathogenic/Likely pathogenic ★★ same condition
ACAN p.Arg394Ter Pathogenic ★★ same condition
ACAN p.Asn108fs Pathogenic/Likely pathogenic ★★ same condition
ACAN p.Cys2304Ter Pathogenic/Likely pathogenic ★★ 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/acan-p-ser802fs (accessed [today's date]).

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