Is CAPN3 p.Ile502fs (c.1504_1505del) pathogenic?

CAPN3 p.Ile502fs (c.15041505del) is classified Pathogenic in CAPN3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-01). Absent from gnomAD.

How common is CAPN3 p.Ile502fs (c.1504_1505del) in the general population?

CAPN3 p.Ile502fs (c.1504_1505del) is absent from gnomAD (gnomAD).

CAPN3 p.Ile502fs

c.1504_1505del · rs2141199913 · VCV1694740

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
NMD	predicted	premature termination codon in exon 11 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -0.2, 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: CAPN3
Protein: p.Ile502fs
Coding: c.1504_1505del
MANE Select: NM_000070
dbSNP: rs2141199913
Type: Deletion
Location: chr15:42401790 (GRCh38)
Gene constraint: LOEUF 0.896 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 79.18 · 5 PDB
Residue 502: the 'domain iii' region; a UniProt-annotated variant site (in lgmdr1)

Full CAPN3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAPN3 p.Ile502Thr Likely pathogenic ★★★ same residue
CAPN3 p.Ile502Val Uncertain significance ★★ ⚠ same residue
CAPN3 p.Ile502Phe Uncertain significance ⚠ same residue
CAPN3 c.1194-2del Pathogenic ★★★ same type
CAPN3 p.Asp764fs Pathogenic ★★★ same type
CAPN3 p.Gln660_Ile661insTer Pathogenic ★★★ same type
CAPN3 p.Glu582fs Pathogenic ★★★ same type
CAPN3 p.Gly441fs 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/capn3-p-ile502fs (accessed [today's date]).

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