CAPRIN1

cell cycle associated protein 1

Basic information

Region (hg38): 11:34051731-34102610

Previous symbols: [ "M11S1", "GPIAP1" ]

Links

ENSG00000135387 ∙ NCBI:4076 ∙ OMIM:601178 ∙ HGNC:6743 ∙ Uniprot:Q14444 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Childhood-onset neurodegeneration with cerebellar ataxia and cognitive decline; Neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	35979925; 36136249

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAPRIN1 gene.

• CAPRIN1-related neurodevelopmental disorders (1 variants)
• Juvenile myoclonic epilepsy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPRIN1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			28	1		29
nonsense		2	2			4
start loss						0
frameshift	2		1			3
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					1	1
Total	2	2	32	1	1

Variants in CAPRIN1

This is a list of pathogenic ClinVar variants found in the CAPRIN1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-34052532-G-A		not specified	Uncertain significance (Oct 19, 2023)
11-34052533-C-T		not specified	Uncertain significance (May 28, 2024)
11-34052539-A-T		not specified	Uncertain significance (Sep 29, 2022)
11-34052589-A-T		not specified	Uncertain significance (Feb 03, 2023)
11-34071722-A-G			Likely benign (Oct 01, 2024)
11-34071739-A-G			Uncertain significance (Dec 07, 2023)
11-34071750-C-T			Pathogenic (Jan 02, 2024)
11-34071783-C-T		Seizure;Intellectual disability, moderate;Autism;Autistic behavior	Likely pathogenic (Mar 01, 2023)
11-34071920-AG-A			Uncertain significance (Jun 08, 2022)
11-34071946-G-T			Uncertain significance (May 03, 2023)
11-34076263-C-T		not specified	Uncertain significance (Jun 10, 2022)
11-34076392-G-C		CAPRIN1-related disorder	Uncertain significance (Jul 11, 2024)
11-34076404-T-C		not specified	Uncertain significance (Dec 13, 2022)
11-34076423-T-G		not specified	Uncertain significance (May 30, 2024)
11-34076436-C-G			Uncertain significance (Mar 24, 2023)
11-34076456-A-C			Uncertain significance (Feb 18, 2024)
11-34076565-A-G		not specified	Uncertain significance (Jun 26, 2023)
11-34076571-A-G		not specified	Uncertain significance (May 16, 2024)
11-34076613-G-T		not specified	Uncertain significance (Mar 31, 2024)
11-34076628-T-C		not specified	Uncertain significance (Sep 22, 2023)
11-34076647-G-A			Likely pathogenic (Mar 01, 2024)
11-34079630-A-G		Neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder	Uncertain significance (Dec 18, 2024)
11-34079747-G-T			Uncertain significance (Nov 19, 2023)
11-34079750-C-T		Moyamoya angiopathy	Likely pathogenic (-)
11-34082846-A-G		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPRIN1	protein_coding	protein_coding	ENST00000341394	18	49474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.972	0.0275	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	301	396	0.761	0.0000209	4629
Missense in Polyphen		75	133.11	0.56346		1683
Synonymous	-0.852	148	135	1.09	0.00000654	1336
Loss of Function	5.22	8	46.4	0.173	0.00000245	496

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000117	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000117	0.000109
South Asian	0.000103	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the transport and translation of mRNAs of proteins involved in synaptic plasticity in neurons and cell proliferation and migration in multiple cell types. Binds directly and selectively to MYC and CCND2 RNAs. In neuronal cells, directly binds to several mRNAs associated with RNA granules, including BDNF, CAMK2A, CREB1, MAP2, NTRK2 mRNAs, as well as to GRIN1 and KPNB1 mRNAs, but not to rRNAs. {ECO:0000269|PubMed:17210633}.

Recessive Scores

• pRec: 0.0883

Intolerance Scores

• loftool: 0.379
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.467
• hipred: Y
• hipred_score: 0.775
• ghis: 0.702

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Caprin1
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of translation;positive regulation of dendrite morphogenesis;positive regulation of dendritic spine morphogenesis
• Cellular component: P-body;cytosol;cytoplasmic stress granule;membrane;dendrite;synapse
• Molecular function: RNA binding;protein binding