Is CAPRIN1 p.Arg297fs (c.891_894del) pathogenic?

CAPRIN1 p.Arg297fs (c.891894del) is classified Pathogenic in CAPRIN1 (ClinVar, Single submitter, 1 submitter). No gnomAD frequency available for this variant; Associated with juvenile myoclonic epilepsy.

What condition is associated with CAPRIN1 p.Arg297fs (c.891_894del)?

CAPRIN1 p.Arg297fs (c.891_894del) is associated with juvenile myoclonic epilepsy (ClinVar).

How common is CAPRIN1 p.Arg297fs (c.891_894del) in the general population?

CAPRIN1 p.Arg297fs (c.891_894del) is no gnomAD frequency available for this variant (gnomAD).

How is Juvenile myoclonic epilepsy inherited?

Typically Multigenic/multifactorial (Orphanet). A genetic counselor can assess individual risk for a family.

CAPRIN1 p.Arg297fs

c.891_894del · rs2496067951 · VCV2580936

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

Conditions

juvenile myoclonic epilepsy

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 9 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.4	GERP -0.31, 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: CAPRIN1
Protein: p.Arg297fs
Coding: c.891_894del
MANE Select: NM_005898
dbSNP: rs2496067951
Type: Deletion
Location: chr11:34082964 (GRCh38)
Gene constraint: LOEUF 0.372 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 58.64 · 6 PDB

Full CAPRIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

juvenile myoclonic epilepsy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Juvenile myoclonic epilepsy (Orphanet):

Inheritance: Multigenic/multifactorial
Onset: Adolescent, Childhood

Similar variants

CAPRIN1 p.Arg297Thr Uncertain significance ★ ⚠ same residue
CAPRIN1 p.Ala280fs Pathogenic ★ same type
CAPRIN1 p.Asp578fs Likely pathogenic ★ same type
CAPRIN1 p.Gln332fs Pathogenic ★ same type
CAPRIN1 p.Ile127fs Likely pathogenic ★ same type
CAPRIN1 p.Lys72fs Pathogenic ★ same type
CAPRIN1 p.Ser498fs Pathogenic ★ same type
CAPRIN1 p.Thr534_Leu535insTer 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/caprin1-p-arg297fs (accessed [today's date]).

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