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CLSTN3 calsyntenin 3 [ Homo sapiens (human) ]

Gene ID: 9746, updated on 3-Apr-2024

Summary

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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
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 act upstream of or within several processes, including chemical synaptic transmission; positive regulation of protein localization to synapse; and synapse assembly. Predicted to be located in postsynaptic density. Predicted to be part of protein-containing complex. Predicted to be active in several cellular components, including GABA-ergic synapse; glutamatergic synapse; and postsynaptic membrane. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
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

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See CLSTN3 in Genome Data Viewer
Location:
12p13.31
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7129093..7158945)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7142174..7172097)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7282967..7311541)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:7260830-7262029 Neighboring gene complement C1r subcomponent like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7265863-7266364 Neighboring gene C1RL antisense RNA 1 Neighboring gene RNA, U6 small nuclear 485, pseudogene Neighboring gene retinol binding protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7283265-7283766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4199 Neighboring gene Sharpr-MPRA regulatory region 5519 Neighboring gene uncharacterized LOC124902869 Neighboring gene MPRA-validated peak1553 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7340767-7341268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7341269-7341768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7342139-7342855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7342856-7343571 Neighboring gene peroxisomal biogenesis factor 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Calsyntenin 3β Is Dynamically Regulated by Temperature in Murine Brown Adipose and Marks Human Multilocular Fat. Plucińska K, et al. Front Endocrinol (Lausanne), 2020. PMID 33101212, Free PMC Article
  2. CLSTN3 gene variant associates with obesity risk and contributes to dysfunction in white adipose tissue. Bai N, et al. Mol Metab, 2022 Sep. PMID 35753632, Free PMC Article
  3. Calsyntenin-3 molecular architecture and interaction with neurexin 1α. Lu Z, et al. J Biol Chem, 2014 Dec 12. PMID 25352602, Free PMC Article
  4. 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. Uchida Y, et al. Am J Pathol, 2013 May. PMID 23499467
  5. Stabilization of intracellular trafficking and metabolism of amyloid β-protein precursor and Alcadein β by apolipoprotein E. Kimura A, et al. FEBS Lett, 2015 Aug 19. PMID 26213366

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CLSTN3beta enforces adipocyte multilocularity to facilitate lipid utilization.
    Title: CLSTN3β enforces adipocyte multilocularity to facilitate lipid utilization.
  2. 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.
  3. 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.
  4. structure of Calsyntenin 3 and its interaction with neurexin 1alpha
    Title: Calsyntenin-3 molecular architecture and interaction with neurexin 1α.
  5. 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.
  6. 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.
Submit: New GeneRIF Correction

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0726, MGC131797, MGC138488

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables X11-like protein binding IEA
Inferred from Electronic Annotation
more info
  
enables amyloid-beta binding IEA
Inferred from Electronic Annotation
more info
  
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 kinesin binding IEA
Inferred from Electronic Annotation
more info
  
enables neurexin family protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
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 regulation of cell growth IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of presynapse assembly IEA
Inferred from Electronic Annotation
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
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in lipid droplet 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
  
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.

mRNA and Protein(s)

  1. NM_014718.4 → NP_055533.2  calsyntenin-3 precursor

    See identical proteins and their annotated locations for NP_055533.2

    Status: VALIDATED

    Source sequence(s)
    AA864252, AC018653, AJ277460, DA092023
    Consensus CDS
    CCDS8575.1
    UniProtKB/Swiss-Prot
    A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9
    UniProtKB/TrEMBL
    B4DRB1, B7Z9U4
    Related
    ENSP00000266546.6, ENST00000266546.11
    Conserved Domains (1) summary
    cd11304
    Location:32 → 140
    Cadherin_repeat; Cadherin tandem repeat domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    7129093..7158945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429921.1 → XP_047285877.1  calsyntenin-3 isoform X2

    UniProtKB/Swiss-Prot
    A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9
    Related
    ENST00000537408.1

  2. XM_047429919.1 → XP_047285875.1  calsyntenin-3 isoform X1

  3. XM_047429920.1 → XP_047285876.1  calsyntenin-3 isoform X2

    UniProtKB/Swiss-Prot
    A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160008.1 Reference GRCh38.p14 PATCHES

    Range
    56779..86631
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332547.1 → XP_054188522.1  calsyntenin-3 isoform X2

    UniProtKB/Swiss-Prot
    A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9

  2. XM_054332546.1 → XP_054188521.1  calsyntenin-3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    7142174..7172097
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373906.1 → XP_054229881.1  calsyntenin-3 isoform X2

    UniProtKB/Swiss-Prot
    A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9

  2. XM_054373905.1 → XP_054229880.1  calsyntenin-3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BQT9.1 GenPept UniProtKB/Swiss-Prot:Q9BQT9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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