Is CAPRIN1 p.Glu293= (c.879G>A) pathogenic?

CAPRIN1 p.Glu293= (c.879G>A) is classified Pathogenic in CAPRIN1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-04-11). Absent from gnomAD v4.1; Associated with neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder.

How common is CAPRIN1 p.Glu293= (c.879G>A) in the general population?

CAPRIN1 p.Glu293= (c.879G>A) is absent from gnomAD v4.1 (gnomAD).

CAPRIN1 p.Glu293=

Q: What condition is associated with CAPRIN1 p.Glu293= (c.879G>A)?

CAPRIN1 p.Glu293= (c.879G>A) is associated with neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder (ClinVar).

c.879G>A · rs2496067678 · VCV3069139

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,696)

Conditions

neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.39	donor loss · deltas
Pangolin	Δ0.72	loss · gain 0.01 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Overall
CADD	22.7	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,696). 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.Glu293=
Coding: c.879G>A
MANE Select: NM_005898
dbSNP: rs2496067678
Type: single nucleotide variant
Location: chr11:34082877 (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

neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAPRIN1 p.Arg458Ter Pathogenic ★★ same condition
CAPRIN1 p.Arg356Ter Pathogenic ★ same condition
CAPRIN1 p.Arg358Ter Pathogenic ★ same condition
CAPRIN1 p.Glu293fs Likely pathogenic ★ same residue
CAPRIN1 p.Gly31Ter Likely pathogenic ★ same condition
CAPRIN1 p.Ser482Ter Likely pathogenic ★ same condition
CAPRIN1 c.826+16A>G Uncertain significance ★ same condition
CAPRIN1 p.Gln298Ter Uncertain significance ★ same condition

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-glu293 (accessed [today's date]).

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