CAPRIN2

caprin family member 2, the group of C1q domain containing

Basic information

Region (hg38): 12:30709552-30823302

Previous symbols: [ "C1QDC1" ]

Links

ENSG00000110888 ∙ NCBI:65981 ∙ OMIM:610375 ∙ HGNC:21259 ∙ Uniprot:Q6IMN6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAPRIN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPRIN2 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				1	3	4
missense			49	1	1	51
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	51	2	5

Variants in CAPRIN2

This is a list of pathogenic ClinVar variants found in the CAPRIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-30709933-G-A		not specified	Uncertain significance (Jun 05, 2023)
12-30710315-G-A		not specified	Uncertain significance (Nov 14, 2023)
12-30710321-C-T		not specified	Uncertain significance (Dec 15, 2023)
12-30710423-C-T		not specified	Uncertain significance (Aug 11, 2022)
12-30711571-G-A		not specified	Uncertain significance (Jul 06, 2021)
12-30711580-C-T		not specified	Uncertain significance (Dec 02, 2022)
12-30711586-C-T		not specified	Uncertain significance (Feb 12, 2024)
12-30711596-T-A		not specified	Uncertain significance (Jun 09, 2022)
12-30711602-C-G		not specified	Uncertain significance (May 02, 2024)
12-30713799-G-A		not specified	Uncertain significance (Sep 22, 2023)
12-30713810-T-C		not specified	Uncertain significance (Jun 09, 2022)
12-30713849-T-C		not specified	Uncertain significance (May 16, 2024)
12-30713872-A-G			Benign (Jun 05, 2018)
12-30715034-G-A		not specified	Uncertain significance (Dec 07, 2023)
12-30715074-C-T			Benign (Apr 16, 2018)
12-30715096-A-G		not specified	Uncertain significance (Oct 06, 2021)
12-30716560-C-A		not specified	Uncertain significance (May 17, 2023)
12-30716588-G-A		not specified	Uncertain significance (Dec 19, 2023)
12-30716594-C-T		not specified	Uncertain significance (Aug 08, 2023)
12-30716610-G-A		not specified	Likely benign (Jun 22, 2024)
12-30716621-G-A		not specified	Uncertain significance (Oct 13, 2023)
12-30716637-G-T		not specified	Uncertain significance (Oct 13, 2023)
12-30719082-C-A		not specified	Uncertain significance (Jan 26, 2022)
12-30719093-G-C		not specified	Uncertain significance (Oct 13, 2023)
12-30719127-A-G			Benign (May 24, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPRIN2	protein_coding	protein_coding	ENST00000298892	17	45400

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.102	0.898	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.613	504	544	0.926	0.0000274	7022
Missense in Polyphen		123	176.69	0.69613		2331
Synonymous	-0.473	210	201	1.04	0.0000107	2065
Loss of Function	5.31	14	57.5	0.244	0.00000292	682

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000403	0.000391
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.000109	0.000109
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000981	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes phosphorylation of the Wnt coreceptor LRP6, leading to increased activity of the canonical Wnt signaling pathway (PubMed:18762581). Faciliates constitutive LRP6 phosphorylation by CDK14/CCNY during G2/M stage of the cell cycle, which may potentiate cells for Wnt signaling (PubMed:27821587). May regulate the transport and translation of mRNAs, modulating for instance the expression of proteins involved in synaptic plasticity in neurons (By similarity). Involved in regulation of growth as erythroblasts shift from a highly proliferative state towards their terminal phase of differentiation (PubMed:14593112). May be involved in apoptosis (PubMed:14593112). {ECO:0000250|UniProtKB:Q05A80, ECO:0000269|PubMed:14593112, ECO:0000269|PubMed:18762581, ECO:0000269|PubMed:27821587}.

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.880
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.91

Haploinsufficiency Scores

• pHI: 0.744
• hipred: N
• hipred_score: 0.371
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.208

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Caprin2
• Phenotype: vision/eye phenotype

Zebrafish Information Network

• Gene name: caprin2
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: negative regulation of translation;negative regulation of cell growth;positive regulation of protein binding;positive regulation of peptidyl-serine phosphorylation;positive regulation of transcription by RNA polymerase II;positive regulation of dendrite morphogenesis;positive regulation of dendritic spine morphogenesis;positive regulation of canonical Wnt signaling pathway
• Cellular component: nucleus;cytoplasm;mitochondrion;centrosome;cytosol;plasma membrane;receptor complex
• Molecular function: RNA binding;signaling receptor binding;protein binding;metal ion binding