CAPRIN1

Chr 11AD

cell cycle associated protein 1

Also known as: CONDCAC, GPIAP1, GPIP137, GRIP137, M11S1, NEDLAAD, RNG105, p137GPI

NCBI Gene: 4076ENSG00000135387UniProt: Q14444OMIM: 601178

CAPRIN1 encodes an mRNA-binding protein that regulates mRNA transport, translation, and stability through formation of cytoplasmic ribonucleoprotein granules and stress granules, playing essential roles in neurogenesis and synaptic plasticity. Mutations cause autosomal dominant neurodegeneration with childhood-onset cerebellar ataxia and cognitive decline, or neurodevelopmental disorder with language impairment, autism, and ADHD. The gene is highly constrained against loss-of-function mutations (pLI = 0.97), reflecting its critical role in neuronal function.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismADLOEUF 0.312 OMIM phenotypes
Clinical Summary— CAPRIN1
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Gene-Disease Validity (ClinGen)
neurodegeneration, childhood-onset, with cerebellar ataxia and cognitive decline · ADModerate

Moderate evidence — consider for supplementary testing

2 total gene-disease associations curated

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Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.97). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.31LOEUF
pLI 0.972
Z-score 5.22
OE 0.17 (0.10–0.31)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
1.69Z-score
OE missense 0.76 (0.69–0.84)
301 obs / 395.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.17 (0.10–0.31)
0≤0.351.4
Missense OE0.76 (0.69–0.84)
0≤0.61.4
Synonymous OE1.09
0≤1.21.6
LoF obs/exp: 8 / 46.4Missense obs/exp: 301 / 395.7Syn Z: -0.85
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
moderateCAPRIN1-related neurodevelopmental disorderLOFAD
DN
0.2599th %ile
GOF
0.3094th %ile
LOF
0.78top 5%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to loss-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOFprediction above median · LOEUF 0.31
GOF1 literature citation

Literature Evidence

GOFThese findings associate the gain-of-function Pro512Leu mutation to early-onset ataxia and neurodegeneration, unveiling a critical residue of CAPRIN1 and a key role of RNA-protein interactions.PMID:36136249

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CAPRIN1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients