CLSTN1 calsyntenin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLSTN1provided by HGNC
Official Full Name: calsyntenin 1provided by HGNC
Primary source: HGNC:HGNC:17447
See related: Ensembl:ENSG00000171603 MIM:611321; AllianceGenome:HGNC:17447
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CST-1; CSTN1; CDHR12; PIK3CD; ALC-ALPHA; XB31alpha; alcalpha1; alcalpha2
Summary: This gene is a member of the calsyntenin family, a subset of the cadherin superfamily. The encoded transmembrane protein, also known as alcadein-alpha, is thought to bind to kinesin-1 motors to mediate the axonal anterograde transport of certain types of vesicle. Amyloid precursor protein (APP) is trafficked via these vesicles and so this protein is being investigated to see how it might contribute to the mechanisms underlying Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
Expression: Ubiquitous expression in brain (RPKM 135.7), skin (RPKM 44.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.22

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (9728926..9824526, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (9271709..9367444, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (9788984..9884584, complement)

Chromosome 1 - NC_000001.11 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 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?

Results suggests that APP partially compensates for defective Alcalpha in anterograde transport by providing an alternative cargo receptor for kinesin-1.
Title: Phosphorylation of multiple sites within an acidic region of Alcadein α is required for kinesin-1 association and Golgi exit of Alcadein α cargo.
Calsyntenin-1 contributes to the early stages of the hepatitis C virus replication cycle and the formation of the replication complex.
Title: Calsyntenin-1 mediates hepatitis C virus replication.
Increased plasma p3-Alcalpha35, a major fragment of alcalpha1, may indicate an endophenotype in Alzheimer's disease patients with progressive cognitive impairment.
Title: Increased levels of plasma p3-alcα35, a major fragment of Alcadeinα by γ-secretase cleavage, in Alzheimer's disease.
Increased plasma p3-alcadein (alc) alpha, evident in the early stages of cognitive impairment, suggests that alc metabolites are useful plasma biomarkers of Alzheimer's disease.
Title: Potential utility of soluble p3-alcadein α plasma levels as a biomarker for sporadic Alzheimer's disease.
findings show that calsyntenin-1 is reduced in Alzheimer's disease brains and that the extent of this reduction correlates with increased amyloid-beta
Title: Calsyntenin-1 mediates axonal transport of the amyloid precursor protein and regulates Aβ production.
CLSTN1 is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells.
Title: The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle.
Phosphorylation of KLC1 at serine 460 modulates binding and trafficking of calsyntenin-1.
Title: Phosphorylation of kinesin light chain 1 at serine 460 modulates binding and trafficking of calsyntenin-1.
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

SHGC-16182 (e-PCR)
- UniSTS:45313

RH50479 (e-PCR)
- UniSTS:76863

WI-16324 (e-PCR)
- UniSTS:81471

WI-16255 (e-PCR)
- UniSTS:81472

SHGC-74173 (e-PCR)
- UniSTS:27732

D17S1247 (e-PCR)
- UniSTS:149860

RH11792 (e-PCR)
- UniSTS:8321

D1S1458 (e-PCR)
- UniSTS:149654

NIB2114 (e-PCR)
- UniSTS:41902

RH15907 (e-PCR)
- UniSTS:78774

A006Z42 (e-PCR)
- UniSTS:65230

RH63840 (e-PCR)
- UniSTS:60132

IB3691 (e-PCR)
- UniSTS:47589

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables X11-like protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables amyloid-beta binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables kinesin binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in neurotransmitter receptor transport to postsynaptic membrane	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 synapse maturation	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated transport in synapse	IEA Inferred from Electronic Annotation 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 endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in neuron projection	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in postsynaptic endosome	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-1

Names: alcadein-alpha; alzheimer-related cadherin-like protein; cadherin-related family member 12; non-classical cadherin XB31alpha

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)

NM_001009566.3 → NP_001009566.1 calsyntenin-1 isoform 1 precursor

See identical proteins and their annotated locations for NP_001009566.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AL357140, AL691449

Consensus CDS

CCDS30580.1

UniProtKB/Swiss-Prot

A8K183, O94985, Q5SR52, Q5UE58, Q71MN0, Q8N4K9

Related

ENSP00000366513.4, ENST00000377298.9

Conserved Domains (2) summary

cd11304
Location:168 → 258

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:365 → 477

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
NM_001302883.1 → NP_001289812.1 calsyntenin-1 isoform 3 precursor

See identical proteins and their annotated locations for NP_001289812.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in a shorter isoform (3) that is missing an internal segment compared to isoform 1.

Source sequence(s)

AB020718, AL357140, BI335759

UniProtKB/TrEMBL

B4E3Q1, Q5SR54

Conserved Domains (2) summary

cd11304
Location:168 → 258

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:365 → 525

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
NM_014944.4 → NP_055759.3 calsyntenin-1 isoform 2 precursor

See identical proteins and their annotated locations for NP_055759.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in a shorter isoform (2) that is missing an internal segment compared to isoform 1.

Source sequence(s)

AB020718, AL357140, BI335759

Consensus CDS

CCDS105.1

UniProtKB/TrEMBL

Q5SR54

Related

ENSP00000354997.4, ENST00000361311.4

Conserved Domains (2) summary

cd11304
Location:41 → 149

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:355 → 467

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...