Is ACAN p.Arg315fs (c.944_948del) pathogenic?

ACAN p.Arg315fs (c.944948del) is classified Pathogenic in ACAN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-24). Absent from gnomAD.

How common is ACAN p.Arg315fs (c.944_948del) in the general population?

ACAN p.Arg315fs (c.944_948del) is absent from gnomAD (gnomAD).

ACAN p.Arg315fs

c.944_948del · rs2505251328 · VCV2772792

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 6 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP -2.2, 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.Arg315fs
Coding: c.944_948del
MANE Select: NM_001369268
dbSNP: rs2505251328
Type: Microsatellite
Location: chr15:88843536 (GRCh38)
Gene constraint: LOEUF 0.377 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 53.32 · 4 PDB
Residue 315: a disulfide bond; a β-strand; the link 2 domain; the 'g1-b'' region

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

Similar variants

ACAN p.Arg315Trp Uncertain significance ★★ ⚠ same residue
ACAN p.Asp206delinsGlyTer Likely pathogenic ★ same type
ACAN p.Gln2065fs Likely pathogenic ★ same type
ACAN p.Glu2297fs Pathogenic ★ same type
ACAN p.Leu11fs Pathogenic ★ same type
ACAN p.Lys2462fs Pathogenic ★ same type
ACAN p.Glu687del Uncertain significance ★ same type
ACAN p.Lys2501del 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/acan-p-arg315fs (accessed [today's date]).

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