CLSTN3 calsyntenin 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLSTN3provided by HGNC
Official Full Name: calsyntenin 3provided by HGNC
Primary source: HGNC:HGNC:18371
See related: Ensembl:ENSG00000139182 MIM:611324; AllianceGenome:HGNC:18371
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: CSTN3; CDHR14; alcbeta
Summary: Enables cell-cell adhesion mediator activity and neurexin family protein binding activity. Involved in L-ascorbic acid metabolic process and regulation of synapse assembly. Predicted to be located in several cellular components, including Golgi membrane; dendrite; and postsynaptic density. Predicted to be part of protein-containing complex. Predicted to be active in several cellular components, including GABA-ergic synapse; lipid droplet; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in brain (RPKM 35.5), kidney (RPKM 13.1) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (7129093..7158945)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (7142174..7172097)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (7282967..7311541)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

CLSTN3beta enforces adipocyte multilocularity to facilitate lipid utilization.
Title: CLSTN3β enforces adipocyte multilocularity to facilitate lipid utilization.
CLSTN3 gene variant associates with obesity risk and contributes to dysfunction in white adipose tissue.
Title: CLSTN3 gene variant associates with obesity risk and contributes to dysfunction in white adipose tissue.
ApoE expression attenuated intracellular trafficking of APP and Alcbeta
Title: Stabilization of intracellular trafficking and metabolism of amyloid β-protein precursor and Alcadein β by apolipoprotein E.
structure of Calsyntenin 3 and its interaction with neurexin 1alpha
Title: Calsyntenin-3 molecular architecture and interaction with neurexin 1α.
The C-terminal fragment but not full-length Cst-3 accumulated in dystrophic neurites surrounding amyloidbeta plaques in Tg2576 mouse and Alzheimer disease brains.
Title: Calsyntenin-3 C-terminal fragment accumulates in dystrophic neurites surrounding aβ plaques in tg2576 mouse and Alzheimer disease brains: its neurotoxic role in mediating dystrophic neurite formation.
Alcadein and amyloid beta-protein precursor regulates FE65-dependent gene transactivation [alcalpha1, alcbeta, alcgamma]
Title: Coordinated metabolism of Alcadein and amyloid beta-protein precursor regulates FE65-dependent gene transactivation.

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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

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

RH103815 (e-PCR)
- UniSTS:98140

D12S931 (e-PCR)
- UniSTS:149932

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables cell-cell adhesion mediator activity	IDA Inferred from Direct Assay more info	PubMed
enables cell-cell adhesion mediator activity	ISS Inferred from Sequence or Structural Similarity more info
enables enzyme inhibitor activity	ISS Inferred from Sequence or Structural Similarity more info
enables neurexin family protein binding	IDA Inferred from Direct Assay more info	PubMed
enables neurexin family protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in L-ascorbic acid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in adaptive thermogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in excitatory synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in inhibitory synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of excitatory synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of lipid droplet fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of lipid storage	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of inhibitory synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of lipid catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein localization to synapse	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
involved_in protein secretion	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell growth	IEA Inferred from Electronic Annotation more info
involved_in regulation of excitatory synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of presynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of synapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in sympathetic neuron projection extension	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse assembly	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, GABAergic	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, glutamatergic	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
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
is_active_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in lipid droplet	IEA Inferred from Electronic Annotation more info
is_active_in lipid droplet	ISS Inferred from Sequence or Structural Similarity more info
is_active_in organelle membrane contact site	ISS Inferred from Sequence or Structural Similarity 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
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: calsyntenin-3

Names: alc-beta; alcadein beta; cadherin-related family member 14

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.