CTNNAL1

gene
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Also known as CLLPalpha-CATU

Summary

CTNNAL1 (catenin alpha like 1, HGNC:2512) is a protein-coding gene on chromosome 9q31.3, encoding Alpha-catulin (Q9UBT7). May modulate the Rho pathway signaling by providing a scaffold for the Lbc Rho guanine nucleotide exchange factor (ARHGEF1).

Predicted to enable actin filament binding activity and cadherin binding activity. Acts upstream of or within Rho protein signal transduction. Located in cytosol.

Source: NCBI Gene 8727 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 84 total
  • MANE Select transcript: NM_003798

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2512
Approved symbolCTNNAL1
Namecatenin alpha like 1
Location9q31.3
Locus typegene with protein product
StatusApproved
AliasesCLLP, alpha-CATU
Ensembl geneENSG00000119326
Ensembl biotypeprotein_coding
OMIM604785
Entrez8727

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000325551, ENST00000374593, ENST00000374594, ENST00000374595, ENST00000488130, ENST00000863428, ENST00000916573, ENST00000964500, ENST00000964501, ENST00000964502, ENST00000964503, ENST00000964504, ENST00000964505

RefSeq mRNA: 2 — MANE Select: NM_003798 NM_001286974, NM_003798

CCDS: CCDS6775, CCDS69638

Canonical transcript exons

ENST00000325551 — 19 exons

ExonStartEnd
ENSE00000805982108942961108943044
ENSE00000805985108943703108943816
ENSE00000805986108943962108944018
ENSE00000805989108948186108948234
ENSE00000805997108965378108965528
ENSE00000805998108970402108970494
ENSE00000806001108976962108977048
ENSE00000806004108983145108983315
ENSE00000806005108984347108984436
ENSE00000806006108990726108990845
ENSE00000806008108999067108999256
ENSE00001034206108955790108955827
ENSE00001137056108992632108992819
ENSE00001143716108979281108979481
ENSE00001867748109013302109013499
ENSE00001908714108942577108942834
ENSE00003559836108952444108952494
ENSE00003580907108952209108952363
ENSE00003603073108972675108972833

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 99.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.3287 / max 468.0629, expressed in 1775 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
10187135.12271768
1018691.2204759
1018700.5626330
1018680.4230200

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right adrenal gland cortexUBERON:003582799.16gold quality
right adrenal glandUBERON:000123399.09gold quality
left adrenal glandUBERON:000123498.99gold quality
adrenal cortexUBERON:000123598.98gold quality
left adrenal gland cortexUBERON:003582598.96gold quality
adrenal tissueUBERON:001830398.75gold quality
adrenal glandUBERON:000236998.60gold quality
tibial nerveUBERON:000132398.01gold quality
left ovaryUBERON:000211997.64gold quality
left lobe of thyroid glandUBERON:000112097.32gold quality
thyroid glandUBERON:000204697.22gold quality
pigmented layer of retinaUBERON:000178296.94gold quality
ovaryUBERON:000099296.89gold quality
right lobe of thyroid glandUBERON:000111996.86gold quality
mucosa of stomachUBERON:000119996.69gold quality
cartilage tissueUBERON:000241896.48gold quality
right ovaryUBERON:000211896.47gold quality
trigeminal ganglionUBERON:000167596.42gold quality
olfactory bulbUBERON:000226496.14gold quality
cardiac atriumUBERON:000208195.75gold quality
right atrium auricular regionUBERON:000663195.75gold quality
myocardiumUBERON:000234995.73gold quality
vena cavaUBERON:000408795.39gold quality
cardiac muscle of right atriumUBERON:000337995.35gold quality
dorsal root ganglionUBERON:000004494.88gold quality
heartUBERON:000094894.69gold quality
olfactory segment of nasal mucosaUBERON:000538694.63gold quality
heart left ventricleUBERON:000208494.58gold quality
cardiac ventricleUBERON:000208294.50gold quality
right testisUBERON:000453494.37gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-MTAB-6308yes1161.49
E-HCAD-11yes23.42
E-HCAD-10yes16.94
E-HCAD-9yes16.44
E-MTAB-6678yes12.36
E-MTAB-8271yes6.99
E-GEOD-130148yes6.39
E-MTAB-6524no212.02
E-MTAB-10137no6.70
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOXC1, LEF1, TFAP2A

miRNA regulators (miRDB)

18 targeting CTNNAL1, 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-3163100.0077.238605
HSA-MIR-433-3P99.9869.371203
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-432899.5771.064094
HSA-MIR-513A-3P99.3970.633620
HSA-MIR-513C-3P99.3970.633620
HSA-MIR-520A-5P99.3566.721632
HSA-MIR-525-5P99.3566.851615
HSA-MIR-2115-3P99.3169.682026
HSA-MIR-16-2-3P99.2970.601954
HSA-MIR-195-3P99.2970.611954
HSA-MIR-3606-3P99.1169.843254
HSA-MIR-6755-3P98.6166.90834
HSA-MIR-427597.9668.421549
HSA-MIR-383-5P96.8667.55820
HSA-MIR-4750-3P96.6564.38512
HSA-MIR-4772-5P95.6068.04617

Literature-anchored findings (GeneRIF, showing 20)

  • alpha-catulin maps precisely to the familial dysautonomia candidate region on 9q31. (PMID:11768226)
  • Results show that alpha-catulin co-expression leads to increased Lbc-induced serum response factor activation and may modulate Rho pathway signaling in vivo by providing a scaffold for the Lbc Rho guanine nucleotide exchange factor. (PMID:12270917)
  • Abnormal expression of alpha-catenin was seen in mucoepidermoid carcinoma. (PMID:12694354)
  • alpha-catenin and alpha-catulin have distinct activities that downregulate, respectively, beta-catenin and Ras signals converging on the cyclin D1 promoter (PMID:14993280)
  • CTNNAL1 mRNA expression is highly correlated to airway resistance; CTNNAL1 may contribute to the wound repair and proliferation of HBEC. Furthermore, it may serve to Fn mediated cell-extracellular adhesion and its signal transduction. (PMID:17647259)
  • Alpha-catulin has tumorigenic potential. (PMID:17952117)
  • Seven placental transcripts characterize HELLP-syndrome. (PMID:18374411)
  • the Lbc/alpha-catulin axis participates in 5-HT-induced PASMC mitogenesis and RhoA/ROCK signaling, and may be an interventional target in diseases involving vascular smooth muscle remodeling. (PMID:20696764)
  • Data show that alpha-dystrobrevin-1 recruits alpha-catulin, which supersensitizes alpha(1D)-AR functional responses by recruiting effector molecules to the signalosome. (PMID:21115837)
  • Study provides evidence that alpha-catulin promotes tumor growth by preventing cellular senescence and suggests that downregulating alpha-catulin may be a promising therapeutic approach for cancer treatment. (PMID:21278790)
  • a robust transcriptional CTNNAL1 up-regulation occurs during acute ozone-induced stress and is mediated at least in part by ozone-induced recruitments of LEF-1 and AP-2alpha to the human CTNNAL1 promoter (PMID:22359570)
  • these results strongly indicate that alpha-catulin contributes to the invasive behavior of metastatic cells and may be used as a prognostic marker and future therapeutic target for patients with cancer. (PMID:22648798)
  • findings show that alpha-catulin is highly expressed in melanoma cells; expression of alpha-catulin promoted melanoma progression and occurred concomitantly with the downregulation of E-cadherin and the upregulation of expression of mesenchymal genes (PMID:22733455)
  • our study shows that alpha-catulin plays a critical role in cancer metastasis (PMID:23047866)
  • Alpha-catulin contributes to drug-resistance of melanoma by activating NF-kappaB and AP-1 (PMID:25793618)
  • These data indicated that upregulated expression of alpha-catulin protein might have impact on the tumorigenesis of head and neck squamous cell carcinoma (PMID:26311049)
  • CTNNAL1 may play a role in airway EMT by repressing the expression of Twist1 mRNA and reducing the level of TGF-beta1. (PMID:29791759)
  • Genetic variants in RET, ARHGEF3 and CTNNAL1, and relevant interaction networks, contribute to the risk of Hirschsprung disease. (PMID:32139661)
  • alpha-Catulin promotes cancer stemness by antagonizing WWP1-mediated KLF5 degradation in lung cancer. (PMID:35154481)
  • CTNNAL1 deficiency suppresses CFTR expression in HDM-induced asthma mouse model through ROCK1-CAL signaling pathway. (PMID:37715489)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioctnnal1ENSDARG00000018162
mus_musculusCtnnal1ENSMUSG00000038816
rattus_norvegicusCtnnal1ENSRNOG00000010593
drosophila_melanogasteralpha-CatrFBGN0029105
caenorhabditis_elegansctn-1WBGENE00000832

Paralogs (4): VCL (ENSG00000035403), CTNNA1 (ENSG00000044115), CTNNA2 (ENSG00000066032), CTNNA3 (ENSG00000183230)

Protein

Protein identifiers

Alpha-catulinQ9UBT7 (reviewed: Q9UBT7)

Alternative names: Alpha-catenin-related protein, Catenin alpha-like protein 1

All UniProt accessions (3): Q9UBT7, Q5JTQ6, Q5JTQ9

UniProt curated annotations — full annotation on UniProt →

Function. May modulate the Rho pathway signaling by providing a scaffold for the Lbc Rho guanine nucleotide exchange factor (ARHGEF1).

Subunit / interactions. Interacts with ARHGEF1. Interacts with DTNA. The interaction is required for correct localization of both CTNL1 and DTNA.

Subcellular location. Cytoplasm. Cytoskeleton. Cell membrane.

Tissue specificity. Widely expressed. Expressed at lower level in neural tissues and at the highest level in the adrenal gland.

Induction. Down-regulated in cancer pancreatic cells undergoing differentiation and apoptosis.

Similarity. Belongs to the vinculin/alpha-catenin family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9UBT7-11yes
Q9UBT7-22, Alpha2-catulin
Q9UBT7-33

RefSeq proteins (2): NP_001273903, NP_003789* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001033Alpha_cateninFamily
IPR006077Vinculin/cateninFamily
IPR030045CTNNAL1Family
IPR036723Alpha-catenin/vinculin-like_sfHomologous_superfamily

Pfam: PF01044

UniProt features (13 total): sequence variant 7, modified residue 2, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UBT7-F184.600.66

Functional residue map

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

Post-translational modifications (2): 374, 538

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 229 (showing top): CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, MODULE_503, CEBPB_01, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, MAHAJAN_RESPONSE_TO_IL1A_DN, MODULE_195, FOSTER_TOLERANT_MACROPHAGE_UP, MARTINEZ_RB1_TARGETS_DN, BACH2_01, WTGAAAT_UNKNOWN, FOXJ2_01, TGANTCA_AP1_C, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, MODULE_147, OUYANG_PROSTATE_CANCER_PROGRESSION_DN

GO Biological Process (2): cell adhesion (GO:0007155), Rho protein signal transduction (GO:0007266)

GO Molecular Function (3): cadherin binding (GO:0045296), actin filament binding (GO:0051015), protein binding (GO:0005515)

GO Cellular Component (5): cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cellular process1
small GTPase-mediated signal transduction1
cell adhesion molecule binding1
actin binding1
protein-containing complex binding1
binding1
cytoplasm1
intracellular membraneless organelle1
membrane1
cell periphery1
intracellular anatomical structure1

Protein interactions and networks

STRING

1160 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CTNNAL1ACTL7AQ9Y615950
CTNNAL1ACTL7BQ9Y614935
CTNNAL1AKAP13Q12802817
CTNNAL1DTNAQ9Y4J8727
CTNNAL1RHOAP06749589
CTNNAL1ARHGEF28Q8N1W1559
CTNNAL1DMDP11532548
CTNNAL1FGD5Q6ZNL6531
CTNNAL1CTNNB1P35222526
CTNNAL1ILKP57043471
CTNNAL1IKBKBO14920469
CTNNAL1HOXB5P09067461
CTNNAL1GRPEL2Q8TAA5453
CTNNAL1ABITRAMQ9NX38453
CTNNAL1VCLP18206444

IntAct

100 interactions, top by confidence:

ABTypeScore
DMDDTNBpsi-mi:“MI:0914”(association)0.890
CTNNAL1DMDpsi-mi:“MI:0915”(physical association)0.880
DMDCTNNAL1psi-mi:“MI:0915”(physical association)0.880
CTNNAL1DMDpsi-mi:“MI:0914”(association)0.880
CTNNAL1RNF135psi-mi:“MI:0915”(physical association)0.780
RNF135CTNNAL1psi-mi:“MI:0915”(physical association)0.780
ADRA1DUTRNpsi-mi:“MI:0915”(physical association)0.770
LRFN4NCK2psi-mi:“MI:0914”(association)0.730
ADRA1DCTNNAL1psi-mi:“MI:0914”(association)0.710
RHPN1PODXLpsi-mi:“MI:0914”(association)0.690
CTNNAL1CBY2psi-mi:“MI:0915”(physical association)0.670
CBY2CTNNAL1psi-mi:“MI:0915”(physical association)0.670
SNTB2CASKpsi-mi:“MI:0914”(association)0.670
CTNNAL1DTNApsi-mi:“MI:0915”(physical association)0.620
DTNACTNNAL1psi-mi:“MI:0403”(colocalization)0.620
ADRA1DLIN7Apsi-mi:“MI:0914”(association)0.590
SLC16A3CASKpsi-mi:“MI:0914”(association)0.590
CTNNAL1PLCB2psi-mi:“MI:0915”(physical association)0.580
CTNNAL1BRME1psi-mi:“MI:0915”(physical association)0.560
USH1CCTNNAL1psi-mi:“MI:0915”(physical association)0.560
BRME1CTNNAL1psi-mi:“MI:0915”(physical association)0.560

BioGRID (85): CTNNAL1 (Two-hybrid), USH1C (Two-hybrid), C19orf57 (Two-hybrid), RNF135 (Two-hybrid), SPERT (Two-hybrid), CTNNAL1 (Synthetic Lethality), CTNNAL1 (Proximity Label-MS), CTNNAL1 (Affinity Capture-MS), CTNNAL1 (Affinity Capture-MS), CTNNAL1 (Affinity Capture-MS), CTNNAL1 (Affinity Capture-MS), CTNNAL1 (Affinity Capture-MS), CTNNAL1 (Affinity Capture-MS), CTNNAL1 (Affinity Capture-MS), CTNNAL1 (Affinity Capture-MS)

ESM2 similar proteins: A2CEI4, A3KNI7, B7ZC77, E7FBU4, G8JYB2, O35095, O43156, O46037, O75800, O88327, O95273, P0DX19, P26231, P35220, P35221, Q08CY4, Q0V9L1, Q14746, Q2KIZ9, Q2KJ97, Q3MHM6, Q3TVC7, Q4R809, Q59I72, Q5BK06, Q5RC06, Q5RFN4, Q5U4I3, Q65CL1, Q69ZR2, Q6GPP1, Q6NVK9, Q6NY52, Q7T006, Q803M5, Q8BTG3, Q8C3S2, Q8JGR7, Q8K2Z4, Q91V83

Diamond homologs: G8JYB2, O88327, Q5RC06, Q9UBT7, P26232, P30997, Q5R416, Q61301, A4IGI7, B7ZC77, P26231, P35220, P35221, P90947, Q04615, Q3MHM6, Q59I72, Q65CL1, Q6GLP0, Q9PVF8, Q9UI47

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 76 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Formation of the dystrophin-glycoprotein complex (DGC)634.9×5e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance67
Likely benign3
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3507 predictions. Top by Δscore:

VariantEffectΔscore
9:108942956:CTCA:Cdonor_loss1.0000
9:108942957:TCA:Tdonor_loss1.0000
9:108942958:CACCT:Cdonor_loss1.0000
9:108942959:A:Cdonor_loss1.0000
9:108942960:C:CGdonor_loss1.0000
9:108942960:CCTT:Cdonor_gain1.0000
9:108943041:CAAC:Cacceptor_gain1.0000
9:108943042:AACC:Aacceptor_loss1.0000
9:108943045:CTA:Cacceptor_loss1.0000
9:108943046:T:Aacceptor_loss1.0000
9:108943698:TTTA:Tdonor_loss1.0000
9:108943700:TACCT:Tdonor_loss1.0000
9:108943702:C:Gdonor_loss1.0000
9:108943740:A:ACdonor_gain1.0000
9:108943741:C:CCdonor_gain1.0000
9:108943741:CTGT:Cdonor_gain1.0000
9:108943813:TCAG:Tacceptor_gain1.0000
9:108943814:CAG:Cacceptor_gain1.0000
9:108943814:CAGC:Cacceptor_gain1.0000
9:108943816:GCTG:Gacceptor_loss1.0000
9:108943817:C:CCacceptor_gain1.0000
9:108943817:C:Tacceptor_loss1.0000
9:108952238:A:ACdonor_gain1.0000
9:108952239:C:CCdonor_gain1.0000
9:108952239:CTGGA:Cdonor_gain1.0000
9:108952271:ATTCT:Adonor_gain1.0000
9:108952438:TCTTA:Tdonor_loss1.0000
9:108952439:CTTA:Cdonor_loss1.0000
9:108952440:TTACC:Tdonor_loss1.0000
9:108952441:TAC:Tdonor_loss1.0000

AlphaMissense

4824 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:108984360:A:GL239P1.000
9:108990772:C:TG198E1.000
9:108990783:G:CF194L1.000
9:108990783:G:TF194L1.000
9:108990785:A:GF194L1.000
9:108984347:C:AK243N0.999
9:108984347:C:GK243N0.999
9:108984355:C:GA241P0.999
9:108984360:A:TL239H0.999
9:108984363:A:GL238P0.999
9:108984384:A:GL231P0.999
9:108990732:T:AR211S0.999
9:108990732:T:GR211S0.999
9:108990772:C:AG198V0.999
9:108990773:C:GG198R0.999
9:108990773:C:TG198R0.999
9:108990793:A:TV191D0.999
9:108992672:T:AD160V0.999
9:108992672:T:GD160A0.999
9:108992684:A:CL156W0.999
9:108992684:A:GL156S0.999
9:108992708:A:GL148P0.999
9:108992718:C:GA145P0.999
9:108999070:C:GA110P0.999
9:108999078:G:TA107D0.999
9:108999079:C:GA107P0.999
9:108999141:C:TG86E0.999
9:108999142:C:GG86R0.999
9:108999142:C:TG86R0.999
9:108999152:A:CF82L0.999

dbSNP variants (sampled 300 via entrez): RS1000006986 (9:108985084 T>C), RS1000012990 (9:108975330 C>T), RS1000154177 (9:108946347 T>A), RS1000204190 (9:108944264 A>G), RS1000208301 (9:108985386 T>C), RS1000258177 (9:108946008 A>C,G,T), RS1000284551 (9:108991029 T>C), RS1000288916 (9:108989086 G>A), RS1000456073 (9:109009214 G>A,C), RS1000483964 (9:108957852 T>C), RS1000581879 (9:109008961 CA>C), RS1000590947 (9:108981782 G>A), RS1000639371 (9:108988747 C>G), RS1000698872 (9:108951451 T>C,G), RS1000702481 (9:108996394 G>A)

Disease associations

OMIM: gene MIM:604785 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Air Pollutantsdecreases reaction, increases expression, affects cotreatment, increases abundance, increases oxidation (+1 more)4
Ozoneaffects cotreatment, increases oxidation, increases abundance, decreases expression, decreases reaction (+1 more)4
Cisplatinaffects cotreatment, decreases expression, increases expression, affects response to substance3
Cyclosporineincreases expression3
Particulate Matterincreases abundance, decreases expression3
Coumestrolaffects reaction, affects cotreatment, increases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Tretinoindecreases expression2
Valproic Acidaffects expression, increases expression2
Aflatoxin B1decreases methylation, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
bisphenol Adecreases expression1
sodium arsenateincreases abundance, increases expression1
kojic aciddecreases expression1
beta-lapachonedecreases expression1
perfluorooctanoic aciddecreases expression1
benzo(e)pyrenedecreases methylation1
2,3-bis(3’-hydroxybenzyl)butyrolactoneincreases expression, affects cotreatment1
aflatoxin B2decreases methylation1
nickel sulfatedecreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
tamibarotenedecreases expression1
perfluorooctane sulfonic aciddecreases expression1
deguelinincreases expression1
fenpyroximateincreases expression1
ICG 001affects expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.