CLSTN2

gene
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Also known as CSTN2CS2FLJ39113CDHR13

Summary

CLSTN2 (calsyntenin 2, HGNC:17448) is a protein-coding gene on chromosome 3q23, encoding Calsyntenin-2 (Q9H4D0). Postsynaptic adhesion molecule that binds to presynaptic neurexins to mediate synapse formation, and which is involved in learning and memory.

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.

Source: NCBI Gene 64084 — RefSeq curated summary.

At a glance

  • GWAS associations: 17
  • Clinical variants (ClinVar): 187 total
  • MANE Select transcript: NM_022131

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17448
Approved symbolCLSTN2
Namecalsyntenin 2
Location3q23
Locus typegene with protein product
StatusApproved
AliasesCSTN2, CS2, FLJ39113, CDHR13
Ensembl geneENSG00000158258
Ensembl biotypeprotein_coding
OMIM611323
Entrez64084

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron

ENST00000458420, ENST00000511524

RefSeq mRNA: 1 — MANE Select: NM_022131 NM_022131

CCDS: CCDS3112

Canonical transcript exons

ENST00000458420 — 17 exons

ExonStartEnd
ENSE00001037980140562811140562956
ENSE00001037981140558640140558857
ENSE00001037982140563080140563203
ENSE00001037986140562138140562308
ENSE00001037995140556513140556661
ENSE00001323069140563961140564145
ENSE00002067943139935185139935483
ENSE00002618362140566053140577397
ENSE00003460827140404558140404766
ENSE00003474379140459521140459769
ENSE00003512187140403629140403824
ENSE00003520080140546515140546681
ENSE00003534288140175951140176073
ENSE00003542073140466610140466731
ENSE00003627637140421125140421274
ENSE00003674166140448519140448704
ENSE00003692488140532324140532486

Expression profiles

Bgee: expression breadth ubiquitous, 223 present calls, max score 94.85.

FANTOM5 (CAGE): breadth broad, TPM avg 11.9081 / max 612.0247, expressed in 795 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
3883311.5170779
388320.3911177

Top tissues by expression

273 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011594.85gold quality
ponsUBERON:000098894.07gold quality
Brodmann (1909) area 23UBERON:001355492.97gold quality
left ovaryUBERON:000211991.94gold quality
middle temporal gyrusUBERON:000277191.49gold quality
postcentral gyrusUBERON:000258190.93gold quality
substantia nigra pars compactaUBERON:000196590.90gold quality
parietal lobeUBERON:000187290.67gold quality
superior frontal gyrusUBERON:000266190.00gold quality
substantia nigra pars reticulataUBERON:000196689.39gold quality
right ovaryUBERON:000211888.72gold quality
entorhinal cortexUBERON:000272888.64gold quality
ovaryUBERON:000099288.22gold quality
cortical plateUBERON:000534386.24gold quality
prefrontal cortexUBERON:000045184.09gold quality
primary visual cortexUBERON:000243684.04gold quality
adipose tissueUBERON:000101383.93gold quality
thoracic mammary glandUBERON:000520083.93gold quality
mammary glandUBERON:000191183.89gold quality
mammary ductUBERON:000176583.79gold quality
occipital lobeUBERON:000202183.76gold quality
subcutaneous adipose tissueUBERON:000219083.63gold quality
buccal mucosa cellCL:000233683.60silver quality
vena cavaUBERON:000408783.36silver quality
cardiac muscle of right atriumUBERON:000337983.24silver quality
connective tissueUBERON:000238482.84gold quality
frontal cortexUBERON:000187082.51gold quality
cerebral cortexUBERON:000095681.60gold quality
Ammon’s hornUBERON:000195481.36gold quality
neocortexUBERON:000195081.30gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-GEOD-180759yes1828.80
E-HCAD-35yes938.86
E-HCAD-30yes805.17
E-HCAD-25yes590.34
E-GEOD-93593yes7.26
E-ANND-3yes6.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting CLSTN2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-3689D100.0066.141181
HSA-MIR-4533100.0069.482758
HSA-MIR-453499.9966.581907
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-211099.9666.681930
HSA-MIR-808299.9567.271170
HSA-MIR-627-3P99.9071.423316
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-612499.8769.783551
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-576-5P99.8470.462582
HSA-MIR-6515-3P99.8268.191933
HSA-MIR-3913-5P99.7867.26968
HSA-MIR-471999.7372.103329
HSA-MIR-494-3P99.7071.452795
HSA-MIR-10394-5P99.6566.831852
HSA-MIR-120599.6566.761826
HSA-MIR-3158-5P99.6567.511763
HSA-MIR-7156-5P99.6468.811369
HSA-MIR-4666B99.6468.691282
HSA-MIR-29899.6367.561916
HSA-MIR-425-5P99.5967.67900

Literature-anchored findings (GeneRIF, showing 8)

  • Alcadein and amyloid beta-protein precursor regulates FE65-dependent gene transactivation [alcalpha1, alcbeta, alcgamma] (PMID:15037614)
  • 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. (PMID:19058786)
  • This study showed that the KIBRA and CLSTN2 genes interactively modulate episodic memory performance. (PMID:19804789)
  • No increased risk of any type of late development, and cognitive impairment was associated with CLSTN2 (rs6439886) (PMID:21643791)
  • 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. (PMID:25080189)
  • 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 (PMID:26415670)
  • Calsyntenin-3 interacts with the sodium-dependent vitamin C transporter-2 to regulate vitamin C uptake. (PMID:34673103)
  • KLKB1 and CLSTN2 are associated with HDL-mediated cholesterol efflux capacity in a genome-wide association study. (PMID:36812656)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioclstn2aENSDARG00000060637
danio_rerioclstn2bENSDARG00000060638
mus_musculusClstn2ENSMUSG00000032452
rattus_norvegicusClstn2ENSRNOG00000043085
drosophila_melanogasterCalsFBGN0039928
caenorhabditis_elegansWBGENE00000403

Paralogs (2): CLSTN3 (ENSG00000139182), CLSTN1 (ENSG00000171603)

Protein

Protein identifiers

Calsyntenin-2Q9H4D0 (reviewed: Q9H4D0)

Alternative names: Alcadein-gamma

All UniProt accessions (1): Q9H4D0

UniProt curated annotations — full annotation on UniProt →

Function. Postsynaptic adhesion molecule that binds to presynaptic neurexins to mediate synapse formation, and which is involved in learning and memory. Promotes synapse development by acting as a cell adhesion molecule at the postsynaptic membrane, which associates with neurexin-alpha at the presynaptic membrane.

Subcellular location. Postsynaptic cell membrane. Endoplasmic reticulum membrane. Golgi apparatus membrane. Cell projection. Dendrite.

Tissue specificity. Restricted to the brain.

Post-translational modifications. Proteolytically processed under normal cellular conditions. A primary zeta-cleavage generates a large extracellular (soluble) N-terminal domain (sAlc) and a short C-terminal transmembrane fragment (CTF1). A secondary cleavage catalyzed by gamma-secretase within the transmembrane domain releases the beta-Alc-gamma chain in the extracellular milieu and produces an intracellular fragment (AlcICD). This processing is strongly suppressed in the tripartite complex formed with APBA2 and APP, which seems to prevent the association with PSEN1.

Domain organisation. Binds synaptic Ca(2+) with its cytoplasmic domain.

Similarity. Belongs to the calsyntenin family.

RefSeq proteins (1): NP_071414* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002126Cadherin-like_domDomain
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR015919Cadherin-like_sfHomologous_superfamily
IPR045588CLSTN_CDomain

Pfam: PF00028, PF19699

UniProt features (23 total): glycosylation site 6, sequence variant 4, compositionally biased region 3, topological domain 2, sequence conflict 2, domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H4D0-F179.460.51

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (6): 56, 98, 342, 374, 716, 729

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 160 (showing top): BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP, BENPORATH_ES_WITH_H3K27ME3, GOBP_COGNITION, GOBP_BEHAVIOR, GOBP_SYNAPSE_ASSEMBLY, GOBP_ASSOCIATIVE_LEARNING, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GOCC_CELL_SURFACE, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, CAGCTG_AP4_Q5, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_CELL_ADHESION

GO Biological Process (6): homophilic cell-cell adhesion (GO:0007156), associative learning (GO:0008306), positive regulation of synaptic transmission (GO:0050806), positive regulation of synapse assembly (GO:0051965), inhibitory synapse assembly (GO:1904862), cell adhesion (GO:0007155)

GO Molecular Function (1): calcium ion binding (GO:0005509)

GO Cellular Component (14): Golgi membrane (GO:0000139), endoplasmic reticulum membrane (GO:0005789), cell surface (GO:0009986), dendrite (GO:0030425), postsynaptic membrane (GO:0045211), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), postsynaptic density (GO:0014069), membrane (GO:0016020), cell projection (GO:0042995), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
synapse assembly2
cytoplasm2
endomembrane system2
intracellular membrane-bounded organelle2
cell-cell adhesion1
learning1
chemical synaptic transmission1
positive regulation of cell communication1
positive regulation of signaling1
modulation of chemical synaptic transmission1
positive regulation of nervous system development1
regulation of synapse assembly1
positive regulation of cell junction assembly1
cellular process1
metal ion binding1
Golgi apparatus1
bounding membrane of organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
neuron projection1
dendritic tree1
synaptic membrane1
postsynapse1
postsynaptic density1
postsynaptic membrane1
postsynaptic specialization membrane1
synapse1
membrane1
cell periphery1
asymmetric synapse1
postsynaptic specialization1
cell junction1

Protein interactions and networks

STRING

1054 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLSTN2A0A2R8YFG2A0A2R8YFG2898
CLSTN2GRIP1Q9Y3R0669
CLSTN2KLC2Q9H0B6599
CLSTN2CDH17Q12864593
CLSTN2KLC4Q9NSK0589
CLSTN2KLC1Q07866575
CLSTN2KLC3Q6P597528
CLSTN2NRXN2Q9P2S2525
CLSTN2SLC12A9Q9BXP2477
CLSTN2ACANP16112447
CLSTN2CCN2P29279445
CLSTN2WWC1Q8IX03445
CLSTN2FHITP49789436
CLSTN2FAM227BQ96M60421
CLSTN2VLDLRP98155407

IntAct

2 interactions, top by confidence:

ABTypeScore
CLSTN2EXOC3psi-mi:“MI:0914”(association)0.350

BioGRID (25): CLSTN2 (Proximity Label-MS), CLSTN2 (Affinity Capture-MS), MYCBP2 (Affinity Capture-MS), SPTB (Affinity Capture-MS), RPL23 (Affinity Capture-MS), CUX1 (Affinity Capture-MS), TYK2 (Affinity Capture-MS), NUP37 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), NUP160 (Affinity Capture-MS), APBA3 (Affinity Capture-MS), BPIFA1 (Affinity Capture-MS), LMAN1 (Affinity Capture-MS), UTP20 (Affinity Capture-MS), NUP43 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IKU3, A0A8M9PFP2, A1A5Y0, A2A863, A2VCU8, A5A6L1, B0S5G3, L7VG99, O00622, O08841, O35118, O42493, O93512, P08163, P08833, P16042, P16144, P17668, P18406, Q07663, Q0VCN6, Q13753, Q501P1, Q53RD9, Q5R9Q9, Q61220, Q61592, Q64632, Q6DDW2, Q7T3Q2, Q7ZV46, Q7ZXL5, Q8R4Y4, Q8R553, Q8VDA1, Q91166, Q91167, Q91713, Q99JH7, Q9BQT9

Diamond homologs: A0A8M9PFP2, B0S5G3, F1R520, O02840, O55111, O88278, O94985, P30944, P33151, P55287, P55288, Q0VCN6, Q14517, Q5DRC8, Q5R9Q9, Q63418, Q6Q0N0, Q6URK6, Q6V1P9, Q86UP0, Q8BNA6, Q8R553, Q8VDA1, Q96JQ0, Q99JH7, Q9BQT9, Q9EPL2, Q9ER65, Q9H4D0, Q9HCU4, Q9NYQ6, Q9R0M0, P55289, Q5DRA8, Q5DRE0, Q6V0I7, Q967F4, Q9UN71, Q9V498, Q9VW71

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

187 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance158
Likely benign9
Benign5

Top pathogenic / likely-pathogenic (0)

SpliceAI

5262 predictions. Top by Δscore:

VariantEffectΔscore
3:140012538:G:Tdonor_gain1.0000
3:140081310:A:Tdonor_gain1.0000
3:140175942:A:AGacceptor_gain1.0000
3:140175943:T:Gacceptor_gain1.0000
3:140175946:TCTA:Tacceptor_loss1.0000
3:140175948:TA:Tacceptor_loss1.0000
3:140175949:A:AGacceptor_gain1.0000
3:140175950:G:Aacceptor_loss1.0000
3:140175950:G:GCacceptor_gain1.0000
3:140175950:GT:Gacceptor_gain1.0000
3:140175950:GTC:Gacceptor_gain1.0000
3:140175950:GTCA:Gacceptor_gain1.0000
3:140175950:GTCAA:Gacceptor_gain1.0000
3:140176069:TGCAG:Tdonor_loss1.0000
3:140176070:GCAGG:Gdonor_loss1.0000
3:140176071:CAG:Cdonor_loss1.0000
3:140176072:AGGTG:Adonor_loss1.0000
3:140176073:GG:Gdonor_loss1.0000
3:140176074:G:GCdonor_loss1.0000
3:140176075:T:Adonor_loss1.0000
3:140403624:T:Aacceptor_gain1.0000
3:140403626:CAGG:Cacceptor_loss1.0000
3:140403627:A:AGacceptor_gain1.0000
3:140403627:AG:Aacceptor_gain1.0000
3:140403627:AGG:Aacceptor_gain1.0000
3:140403627:AGGG:Aacceptor_gain1.0000
3:140403628:G:GAacceptor_gain1.0000
3:140403628:GG:Gacceptor_gain1.0000
3:140403628:GGG:Gacceptor_gain1.0000
3:140403628:GGGG:Gacceptor_gain1.0000

AlphaMissense

6353 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:140175966:C:AP42Q1.000
3:140175983:T:GY48D1.000
3:140175990:G:AG50E1.000
3:140176017:T:AV59D1.000
3:140176041:C:AA67D1.000
3:140403644:T:CF83S1.000
3:140403644:T:GF83C1.000
3:140403767:T:AI124N1.000
3:140404566:T:AV146D1.000
3:140404572:T:AI148K1.000
3:140421125:G:AG213D1.000
3:140421125:G:TG213V1.000
3:140459753:C:GC402W1.000
3:140466717:T:AW444R1.000
3:140466717:T:CW444R1.000
3:140532341:G:CW454C1.000
3:140532341:G:TW454C1.000
3:140175965:C:TP42S0.999
3:140175970:G:CW43C0.999
3:140175970:G:TW43C0.999
3:140175983:T:CY48H0.999
3:140175989:G:AG50R0.999
3:140175989:G:CG50R0.999
3:140176023:T:CL61S0.999
3:140176035:T:AL65Q0.999
3:140176035:T:CL65P0.999
3:140176046:G:CD69H0.999
3:140176047:A:CD69A0.999
3:140176047:A:TD69V0.999
3:140176052:G:CD71H0.999

dbSNP variants (sampled 300 via entrez): RS1000001013 (3:140004114 G>A), RS1000015825 (3:140520684 A>G), RS1000021689 (3:140440683 C>T), RS1000024043 (3:140316765 G>A), RS1000027679 (3:140027126 A>G,T), RS1000029026 (3:140271321 T>A), RS1000030162 (3:140199873 A>G), RS1000039650 (3:140130426 C>T), RS1000041169 (3:140036543 A>G), RS1000053491 (3:140003910 G>C), RS1000054250 (3:140247499 C>A), RS1000056927 (3:139976701 C>T), RS1000058431 (3:139936148 T>C), RS1000060430 (3:139958776 G>C,T), RS1000065710 (3:140045687 A>G)

Disease associations

OMIM: gene MIM:611323 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

17 associations (top):

StudyTraitp-value
GCST001104_4Sudden cardiac arrest2.000000e-06
GCST001523_21Visceral adipose tissue adjusted for BMI7.000000e-06
GCST001712_42Myopia (pathological)4.000000e-07
GCST001891_1Multiple sclerosis (OCB status)8.000000e-07
GCST002248_5Fasting insulin (dietary factor interaction)3.000000e-06
GCST002253_7Homeostasis model assessment of insulin resistance (dietary factor interaction)4.000000e-06
GCST002480_1Hodgkin’s lymphoma8.000000e-07
GCST002592_16Neuritic plaque6.000000e-06
GCST002685_7Refractive astigmatism5.000000e-06
GCST003262_626Post bronchodilator FEV11.000000e-06
GCST003264_772Post bronchodilator FEV1/FVC ratio3.000000e-07
GCST003831_27Asthma2.000000e-06
GCST004748_36Lung cancer7.000000e-06
GCST007741_25Iris color (b* coordinate)3.000000e-06
GCST008755_7Phenylephrine infusion rate during anesthesia2.000000e-06
GCST009311_6Letter-number span reordering6.000000e-06
GCST010292_5Response to lamotrigine and valproic acid in genetic generalized epilepsy4.000000e-06

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004278sudden cardiac arrest
EFO:0004340body mass index
EFO:0004207pathological myopia
EFO:0008111diet measurement
EFO:0004501HOMA-IR
EFO:0006798neuritic plaque measurement
EFO:0004314forced expiratory volume
EFO:0004713FEV/FVC ratio
EFO:0009764eye colour measurement
EFO:0004874memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression6
trichostatin Aaffects cotreatment, increases expression2
sodium arseniteincreases expression, affects methylation2
Panobinostataffects cotreatment, increases expression2
Aflatoxin B1decreases methylation, increases methylation2
aristolochic acid Idecreases expression1
methylmercuric chlorideincreases expression1
bisphenol Aaffects cotreatment, increases expression1
terbufosincreases methylation1
benzo(e)pyreneincreases methylation1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
incobotulinumtoxinAdecreases expression1
Arsenic Trioxideaffects cotreatment, decreases expression1
Benzo(a)pyreneincreases methylation1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Fonofosincreases methylation1
Formaldehydeincreases expression1
Indomethacinaffects cotreatment, increases expression1
Leadaffects expression1
Methapyrileneincreases methylation1
Nickeldecreases expression1
Parathionincreases methylation1
Phenylmercuric Acetateaffects cotreatment, increases expression1
Tobacco Smoke Pollutiondecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Hodgkins lymphoma