Is ACAN p.Arg93fs (c.273del) pathogenic?

ACAN p.Arg93fs (c.273del) is classified Pathogenic in ACAN (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-09-28). Absent from gnomAD; Associated with Short stature and advanced bone age.

What condition is associated with ACAN p.Arg93fs (c.273del)?

ACAN p.Arg93fs (c.273del) is associated with Short stature and advanced bone age (ClinVar).

How common is ACAN p.Arg93fs (c.273del) in the general population?

ACAN p.Arg93fs (c.273del) is absent from gnomAD (gnomAD).

ACAN p.Arg93fs

c.273del · rs1555453708 · VCV440744

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Short stature and advanced bone age

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 3 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1

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.Arg93fs
Coding: c.273del
MANE Select: NM_001369268
dbSNP: rs1555453708
Type: Deletion
Location: chr15:88838864 (GRCh38)
Gene constraint: LOEUF 0.377 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 53.32 · 4 PDB
Residue 93: a disulfide bond; an α-helix; the ig-like v-type domain; the 'g1-a' region

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

Disease context

Short stature and advanced bone age — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACAN p.Arg93Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
ACAN p.Arg93His Uncertain significance ★ ⚠ same residue
ACAN p.Arg93= Likely benign ★ same residue
ACAN p.Gln1798fs Pathogenic same condition
ACAN p.Phe582fs Pathogenic same condition
ACAN c.2026+1G>A Pathogenic same condition
ACAN p.Asn108fs Pathogenic/Likely pathogenic ★★ same type
ACAN p.Glu518fs Pathogenic ★★ 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/acan-p-arg93fs (accessed [today's date]).

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