Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CGNL1 Gene

Aliases for CGNL1 Gene

  • Cingulin Like 1 2 3 5
  • Junction-Associated Coiled-Coil Protein 2 3 4
  • Paracingulin 2 3 4
  • JACOP 3 4
  • Cingulin-Like Protein 1 3
  • KIAA1749 4
  • PCING 3

External Ids for CGNL1 Gene

Previous GeneCards Identifiers for CGNL1 Gene

  • GC15P055456
  • GC15P057668
  • GC15P034553

Summaries for CGNL1 Gene

Entrez Gene Summary for CGNL1 Gene

  • This gene encodes a member of the cingulin family. The encoded protein localizes to both adherens and tight cell-cell junctions and mediates junction assembly and maintenance by regulating the activity of the small GTPases RhoA and Rac1. Heterozygous chromosomal rearrangements resulting in association of the promoter for this gene with the aromatase gene are a cause of aromatase excess syndrome. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011]

GeneCards Summary for CGNL1 Gene

CGNL1 (Cingulin Like 1) is a Protein Coding gene. Diseases associated with CGNL1 include Aromatase Excess Syndrome and Estrogen Excess. Among its related pathways are Tight junction. Gene Ontology (GO) annotations related to this gene include motor activity. An important paralog of this gene is CGN.

UniProtKB/Swiss-Prot for CGNL1 Gene

  • May be involved in anchoring the apical junctional complex, especially tight junctions, to actin-based cytoskeletons.

Additional gene information for CGNL1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CGNL1 Gene

Genomics for CGNL1 Gene

GeneHancer (GH) Regulatory Elements for CGNL1 Gene

Promoters and enhancers for CGNL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J057375 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650.7 +0.9 880 1.8 FOXA2 ARID4B SIN3A RAD21 YY1 GLIS2 SCRT2 ZNF202 SP3 RXRA CGNL1 GC15P057377
GH15J057417 Promoter 0.6 EPDnew 650.3 +41.1 41087 0.1 KDM1A CGNL1 RNU6-844P GC15P057377 GC15P057471
GH15J057504 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 19.1 +130.1 130081 4.1 ELF3 PKNOX1 FOXA2 NEUROD1 SIN3A RAD21 SCRT2 ZNF143 FOS MXD4 CGNL1 RNU6-844P GC15P057504 ENSG00000261265
GH15J057474 Enhancer 1.1 Ensembl ENCODE 15.5 +101.4 101361 4.8 FOXA2 MLX ARID4B DMAP1 ZNF48 ETS1 YY1 SLC30A9 RXRA ZHX2 ENSG00000261489 CGNL1 RNU6-844P GC15P057471
GH15J057485 Enhancer 1 Ensembl ENCODE 17 +110.1 110138 1.7 ELF3 TFAP4 PKNOX1 SAP130 JUN BACH1 RAD21 THRB RARA ETS1 CGNL1 RNU6-844P GCOM1 POLR2M ENSG00000261489 GC15P057500 PIR54453 GC15P057503 GC15P057502 GC15P057501
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CGNL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CGNL1 gene promoter:

Genomic Locations for CGNL1 Gene

Genomic Locations for CGNL1 Gene
174,761 bases
Plus strand

Genomic View for CGNL1 Gene

Genes around CGNL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CGNL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CGNL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CGNL1 Gene

Proteins for CGNL1 Gene

  • Protein details for CGNL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Cingulin-like protein 1
    Protein Accession:
    Secondary Accessions:
    • Q05BZ4
    • Q52LR0
    • Q695C7
    • Q7Z2L3
    • Q96JV2
    • Q96MN6
    • Q9C0B4

    Protein attributes for CGNL1 Gene

    1302 amino acids
    Molecular mass:
    149079 Da
    Quaternary structure:
    • Homodimer or oligomer (By similarity). Interacts with CD2AP and SH3BP1; probably part of a complex at cell junctions (PubMed:22891260).
    • Sequence=AAH30995.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Alternative splice isoforms for CGNL1 Gene


neXtProt entry for CGNL1 Gene

Post-translational modifications for CGNL1 Gene

  • Ubiquitination at Lys681 and posLast=525525
  • Modification sites at PhosphoSitePlus

Other Protein References for CGNL1 Gene

No data available for DME Specific Peptides for CGNL1 Gene

Domains & Families for CGNL1 Gene

Gene Families for CGNL1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CGNL1 Gene


Suggested Antigen Peptide Sequences for CGNL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The head region is responsible for both junction and actin filament-based distribution.
  • Belongs to the cingulin family.
  • The head region is responsible for both junction and actin filament-based distribution.
  • Belongs to the cingulin family.
genes like me logo Genes that share domains with CGNL1: view

Function for CGNL1 Gene

Molecular function for CGNL1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in anchoring the apical junctional complex, especially tight junctions, to actin-based cytoskeletons.

Phenotypes From GWAS Catalog for CGNL1 Gene

Gene Ontology (GO) - Molecular Function for CGNL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003774 motor activity IEA --
GO:0005515 protein binding IPI 22891260
genes like me logo Genes that share ontologies with CGNL1: view
genes like me logo Genes that share phenotypes with CGNL1: view

Animal Model Products

miRNA for CGNL1 Gene

miRTarBase miRNAs that target CGNL1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CGNL1 Gene

Localization for CGNL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CGNL1 Gene

Cell junction, tight junction. Note=Localizes to the apical junction complex composed of tight and adherens junctions (PubMed:22891260). In the liver and kidney, it is also found along non-junctional actin filament bundles in addition to the apical junction (By similarity). {ECO:0000250 UniProtKB:Q6AW69, ECO:0000269 PubMed:22891260}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CGNL1 gene
Compartment Confidence
cytoskeleton 4
nucleus 4
cytosol 3
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CGNL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005923 bicellular tight junction IEA --
GO:0016459 myosin complex IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with CGNL1: view

Pathways & Interactions for CGNL1 Gene

SuperPathways for CGNL1 Gene

SuperPathway Contained pathways
1 Tight junction
genes like me logo Genes that share pathways with CGNL1: view

Pathways by source for CGNL1 Gene

1 KEGG pathway for CGNL1 Gene

Interacting Proteins for CGNL1 Gene

Gene Ontology (GO) - Biological Process for CGNL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007015 actin filament organization IMP 22891260
GO:0051058 negative regulation of small GTPase mediated signal transduction IMP 22891260
genes like me logo Genes that share ontologies with CGNL1: view

No data available for SIGNOR curated interactions for CGNL1 Gene

Drugs & Compounds for CGNL1 Gene

No Compound Related Data Available

Transcripts for CGNL1 Gene

Unigene Clusters for CGNL1 Gene

Cingulin-like 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CGNL1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP3: - - -
SP4: - - -
SP7: - - - -

ExUns: 23 ^ 24

Relevant External Links for CGNL1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CGNL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CGNL1 Gene

mRNA differential expression in normal tissues according to GTEx for CGNL1 Gene

This gene is overexpressed in Kidney - Cortex (x5.2).

Protein differential expression in normal tissues from HIPED for CGNL1 Gene

This gene is overexpressed in Cervix (13.2), Adrenal (12.8), and Placenta (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CGNL1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CGNL1 Gene:


SOURCE GeneReport for Unigene cluster for CGNL1 Gene:


mRNA Expression by UniProt/SwissProt for CGNL1 Gene:

Tissue specificity: Smooth muscle, spleen, testis, fetal brain, amygdala, corpus callosum, cerebellum, thalamus and subthalamic nucleus of adult brain.

Evidence on tissue expression from TISSUES for CGNL1 Gene

  • Kidney(4.6)
  • Liver(4.4)
  • Nervous system(4.3)
  • Intestine(4.1)
genes like me logo Genes that share expression patterns with CGNL1: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CGNL1 Gene

Orthologs for CGNL1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CGNL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CGNL1 34 33
  • 99.41 (n)
(Canis familiaris)
Mammalia CGNL1 34 33
  • 86.12 (n)
(Bos Taurus)
Mammalia CGNL1 34 33
  • 85.29 (n)
(Mus musculus)
Mammalia Cgnl1 16 34 33
  • 82 (n)
(Rattus norvegicus)
Mammalia Cgnl1 33
  • 81.41 (n)
(Monodelphis domestica)
Mammalia CGNL1 34
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 60 (a)
-- 34
  • 53 (a)
(Gallus gallus)
Aves CGNL1 34 33
  • 66.38 (n)
(Anolis carolinensis)
Reptilia CGNL1 34
  • 60 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cgnl1 33
  • 65.75 (n)
Str.15211 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.7082 33
(Danio rerio)
Actinopterygii cgnl1 34 33
  • 58.26 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ASF2 36
Species where no ortholog for CGNL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CGNL1 Gene

Gene Tree for CGNL1 (if available)
Gene Tree for CGNL1 (if available)
Evolutionary constrained regions (ECRs) for CGNL1: view image

Paralogs for CGNL1 Gene

Paralogs for CGNL1 Gene

(1) SIMAP similar genes for CGNL1 Gene using alignment to 2 proteins:

  • Q6P5Q2_HUMAN
genes like me logo Genes that share paralogs with CGNL1: view

Variants for CGNL1 Gene

Sequence variations from dbSNP and Humsavar for CGNL1 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs483352760 conflicting-interpretations-of-pathogenicity, not provided 57,461,811(+) T/C coding_sequence_variant, synonymous_variant
rs1000007593 -- 57,435,287(+) G/A intron_variant
rs1000011608 -- 57,402,074(+) G/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000036848 -- 57,435,079(+) G/A intron_variant
rs1000053863 -- 57,517,940(+) G/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CGNL1 Gene

Variant ID Type Subtype PubMed ID
dgv2607n100 CNV gain 25217958
dgv4556n54 CNV gain 21841781
esv2454508 CNV deletion 19546169
esv2751536 CNV gain 17911159
esv2761873 CNV gain 21179565
esv2763103 CNV loss 21179565
esv3636608 CNV gain 21293372
esv3636609 CNV gain 21293372
nsv1045611 CNV gain 25217958
nsv1054547 CNV gain 25217958
nsv1116074 CNV deletion 24896259
nsv457166 CNV gain 19166990
nsv516366 CNV gain+loss 19592680
nsv569590 CNV loss 21841781
nsv569591 CNV loss 21841781
nsv569592 CNV gain 21841781
nsv7266 OTHER inversion 18451855
nsv833021 CNV gain 17160897
nsv833022 CNV gain 17160897

Variation tolerance for CGNL1 Gene

Residual Variation Intolerance Score: 88.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.93; 93.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CGNL1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CGNL1 Gene

Disorders for CGNL1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CGNL1 Gene - From: HGMD and GeneCards

Disorder Aliases PubMed IDs
aromatase excess syndrome
  • aexs
estrogen excess
  • hyperestrogenism
- elite association - COSMIC cancer census association via MalaCards
Search CGNL1 in MalaCards View complete list of genes associated with diseases


  • Aromatase excess syndrome (AEXS) [MIM:139300]: An autosomal dominant disorder characterized by increased extraglandular aromatization of steroids that presents with heterosexual precocity in males and isosexual precocity in females. {ECO:0000269 PubMed:12736278}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration inv(15)(q21.2;q21.3) has been found in patients with aromatase excess syndrome. The inversion moves the promoter of the CGNL1 gene into a 5-prime position in relation to the aromatase coding region.

Additional Disease Information for CGNL1

genes like me logo Genes that share disorders with CGNL1: view

No data available for Genatlas for CGNL1 Gene

Publications for CGNL1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11214970) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  2. Distinct domains of paracingulin are involved in its targeting to the actin cytoskeleton and regulation of apical junction assembly. (PMID: 22315225) Paschoud S … Citi S (The Journal of biological chemistry 2012) 2 3 58
  3. Epithelial junction formation requires confinement of Cdc42 activity by a novel SH3BP1 complex. (PMID: 22891260) Elbediwy A … Balda MS (The Journal of cell biology 2012) 3 4 58
  4. Genome-wide association analysis of age at onset and psychotic symptoms in bipolar disorder. (PMID: 21305692) Belmonte Mahon P … Zandi PP (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2011) 3 44 58
  5. Paracingulin regulates the activity of Rac1 and RhoA GTPases by recruiting Tiam1 and GEF-H1 to epithelial junctions. (PMID: 18653465) Guillemot L … Citi S (Molecular biology of the cell 2008) 3 22 58

Products for CGNL1 Gene

Sources for CGNL1 Gene

Loading form....