CLSTN2 calsyntenin 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLSTN2provided by HGNC
Official Full Name: calsyntenin 2provided by HGNC
Primary source: HGNC:HGNC:17448
See related: Ensembl:ENSG00000158258 MIM:611323; AllianceGenome:HGNC:17448
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CS2; CSTN2; CDHR13; ALC-GAMMA; alcagamma
Summary: Predicted to enable calcium ion binding activity. Predicted to be involved in positive regulation of synapse assembly and positive regulation of synaptic transmission. Predicted to be located in several cellular components, including Golgi membrane; endoplasmic reticulum membrane; and postsynaptic density. Predicted to be active in cell surface; glutamatergic synapse; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in ovary (RPKM 37.4), brain (RPKM 15.7) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q23

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (139935185..140577397)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (142682539..143324729)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (139654027..140296239)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

KLKB1 and CLSTN2 are associated with HDL-mediated cholesterol efflux capacity in a genome-wide association study.
Title: KLKB1 and CLSTN2 are associated with HDL-mediated cholesterol efflux capacity in a genome-wide association study.
Calsyntenin-3 interacts with the sodium-dependent vitamin C transporter-2 to regulate vitamin C uptake.
Title: Calsyntenin-3 interacts with the sodium-dependent vitamin C transporter-2 to regulate vitamin C uptake.
Study did not find support for an association of KIBRA either alone or in combination with CLSTN2 with memory performance or hippocampal volume, nor did variation in these genes influence longitudinal memory decline or hippocampal atrophy in older adults
Title: Investigating the influence of KIBRA and CLSTN2 genetic polymorphisms on cross-sectional and longitudinal measures of memory performance and hippocampal volume in older individuals.
The results of this study supports the view that effects of KIBRA and CLSTN2 polymorphisms genetic polymorphisms on cognitive functioning may be most easily disclosed at suboptimal levels of cognitive ability, such as in old-age depression.
Title: Interactive effects of KIBRA and CLSTN2 polymorphisms on episodic memory in old-age unipolar depression.
No increased risk of any type of late development, and cognitive impairment was associated with CLSTN2 (rs6439886)
Title: The role of memory-related gene polymorphisms, KIBRA and CLSTN2, on replicate memory assessment in the elderly.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
This study showed that the KIBRA and CLSTN2 genes interactively modulate episodic memory performance.
Title: KIBRA and CLSTN2 polymorphisms exert interactive effects on human episodic memory.
Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Cognitive flexibility is associated with KIBRA variant and modulated by recent tobacco use.
calsyntenins play an essential role in learning and this role is modulated both by CLSTN2 genotype and, during adolescent development, by exposure to tobacco smoke.
Title: Allelic variation of calsyntenin 2 (CLSTN2) modulates the impact of developmental tobacco smoke exposure on mnemonic processing in adolescents.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population. EBI GWAS Catalog EBI GWAS CatalogPubMed
A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-80030 (e-PCR)
- UniSTS:101644

RH47981 (e-PCR)
- UniSTS:7181

SHGC-24365 (e-PCR)
- UniSTS:25359

G66792 (e-PCR)
- UniSTS:166673

A008B10 (e-PCR)
- UniSTS:28445

RH121819 (e-PCR)
- UniSTS:134968

WI-14298 (e-PCR)
- UniSTS:83519

SHGC-147671 (e-PCR)
- UniSTS:175944

RH122827 (e-PCR)
- UniSTS:135014

D3S3394 (e-PCR)
- UniSTS:41879

D3S3366 (e-PCR)
- UniSTS:62892

SHGC-83921 (e-PCR)
- UniSTS:103604

RH47922 (e-PCR)
- UniSTS:6588

SHGC-154475 (e-PCR)
- UniSTS:178115

RH25530 (e-PCR)
- UniSTS:90580

RH119104 (e-PCR)
- UniSTS:138996

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in associative learning	IEA Inferred from Electronic Annotation more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in inhibitory synapse assembly	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: calsyntenin-2

Names: alcadein gamma; cadherin-related family member 13

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.