CAPRIN2

protein-coding

caprin family member 2, the group of C1q domain containing

Gene summary

The protein encoded by this gene may regulate the transport of mRNA. It may play a role in the differentiation of erythroblasts. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

Previous symbols:

C1QDC1

MANE transcript

NM_001385503.1

Inheritance

—

ClinVar variants

U:135B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr12:30,709,552-30,823,302

External References & Databases

Ensembl (ENSG00000110888)

Transcript & Mutation Effects

hg38 • Region Span ~113.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CAPRIN2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 134

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001385503.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	3 clinvar	5
missense			129 clinvar	4 clinvar	1 clinvar	134
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	135	5	4	144

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 264 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001385503.1	RefSeq	NP_001372432.1	18	MANE Select
ENST00000695402.1	Ensembl	ENSP00000511883.1	18	MANE Select
NM_001002259.3	RefSeq	NP_001002259.1	18	Standard
NM_001206856.3	RefSeq	NP_001193785.1	17	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
caprin2	Danio rerio	Structure: post-vent region Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

caprin2

Danio rerio

Structure: post-vent region

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

RNA binding
signaling receptor binding
protein binding
metal ion binding

Cellular Component

nucleus
cytoplasm
mitochondrion
centrosome
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298892
Coding exons: 17
Length: 45400
Individuals with no LoFs: 125707
Homozygous LoFs: 0
Heterozygous LoFs: 41
Defined: 125748
p: 0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.613	504	544	0.926	0.0000274	7022
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.208

Gene Damage Prediction

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