Is CAPRIN1 p.Ser550fs (c.1648del) pathogenic?

CAPRIN1 p.Ser550fs (c.1648del) is classified Likely pathogenic in CAPRIN1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-05-07). Associated with CAPRIN1-related disorder.

What condition is associated with CAPRIN1 p.Ser550fs (c.1648del)?

CAPRIN1 p.Ser550fs (c.1648del) is associated with CAPRIN1-related disorder (ClinVar).

CAPRIN1 p.Ser550fs

c.1648del · VCV3345374

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

CAPRIN1-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 15 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -0.23, phastCons 1

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

Variant & gene context

Gene: CAPRIN1
Protein: p.Ser550fs
Coding: c.1648del
MANE Select: NM_005898
Type: Deletion
Location: chr11:34091996 (GRCh38)
Gene constraint: LOEUF 0.372 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 58.64 · 6 PDB
Residue 550: a UniProt-annotated variant site (in nedlaad; likely pathogenic); a UniProt-annotated variant site (in nedlaad; likely pathogenic; 50% decrease of transcript and protein levels in patient-derived cells compared to controls); the 'disordered' region

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

Disease context

CAPRIN1-related disorder

Similar variants

CAPRIN1 p.Ser498fs Pathogenic ★ same condition
CAPRIN1 p.Gln419fs Likely pathogenic ★ same condition
CAPRIN1 p.Glu293fs Likely pathogenic ★ same condition
CAPRIN1 p.Ser264Ter Likely pathogenic ★ same condition
CAPRIN1 p.Thr478Ala Uncertain significance ★ ⚠ same condition
CAPRIN1 p.Tyr605Ter Uncertain significance ★ same condition
CAPRIN1 p.Val175Leu Uncertain significance ⚠ same condition
CAPRIN1 p.Ala280fs 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-ser550fs (accessed [today's date]).

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