Aliases for CNN1 Gene

Aliases for CNN1 Gene

  • Calponin 1 2 3 5
  • Calponin 1, Basic, Smooth Muscle 2 3
  • Calponin H1, Smooth Muscle 3 4
  • Basic Calponin 3 4
  • Calponin-1 3 4
  • Sm-Calp 2 3
  • SMCC 2 3
  • Epididymis Secretory Protein Li 14 3
  • Calponins, Basic 3
  • HEL-S-14 3
  • CNN1 5

External Ids for CNN1 Gene

Previous GeneCards Identifiers for CNN1 Gene

  • GC19P011781
  • GC19P011494
  • GC19P011510
  • GC19P011649
  • GC19P011224

Summaries for CNN1 Gene

GeneCards Summary for CNN1 Gene

CNN1 (Calponin 1) is a Protein Coding gene. Diseases associated with CNN1 include Infantile Digital Fibromatosis and Nipple Benign Neoplasm. Among its related pathways are Myometrial Relaxation and Contraction Pathways and Mesenchymal Stem Cell Differentiation Pathways and Lineage-specific Markers. Gene Ontology (GO) annotations related to this gene include actin binding and calmodulin binding. An important paralog of this gene is CNN3.

UniProtKB/Swiss-Prot Summary for CNN1 Gene

  • Thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin and tropomyosin. The interaction of calponin with actin inhibits the actomyosin Mg-ATPase activity (By similarity).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CNN1 Gene

Genomics for CNN1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CNN1 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
GH19J011534 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 269.8 -0.9 -934 5.9 TBP ZBTB10 SP1 MXD4 NR2C1 IKZF1 BRCA1 SMAD5 IRF2 CTCF CNN1 MF281430-040 ZNF136 ZNF627 ILF3 ZNF625 ZNF439 ZNF709 ZNF788P ZNF442
GH19J011504 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.3 -33.1 -33054 2.6 TBP SP1 MXD4 SIX5 NR2C1 SMAD5 ETS1 MBD2 ZNF217 POLR2A ENSG00000267477 NONHSAG024846.2 ZNF653 lnc-ECSIT-1 CNN1 ILF3 ZNF136 ZNF627 ZNF788P ZNF439
GH19J010717 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 19.1 -819.9 -819893 4.3 CHD2 TBP MXD4 SP1 FEZF1 CEBPA SIX5 NR2C1 MNT DEK DNM2 MIR638 ILF3 KRI1 EIF3G ZNF627 FBXL12 PPAN RAVER1 UBE2L4
GH19J011434 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 19.3 -103.1 -103077 2.6 TBP ZBTB10 BCL11A SP1 SIX5 NR2C1 MNT IKZF1 SMAD5 ETS1 PRKCSH ODAD3 lnc-RGL3-1 ZNF20 ZNF44 CNN1 ZNF763 KRI1 ZNF136 ZNF799
GH19J011047 Enhancer 0.7 ENCODE 19.2 -489.2 -489190 3.2 SP1 EBF1 CBFB BHLHE40 POLR2A SRF IKZF1 NR2F1 TCF12 ARID3A KANK2 CNN1 SPC24 SMARCA4 ILF3-DT piR-45578 HSALNG0123984 LDLR
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNN1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CNN1

Top Transcription factor binding sites by QIAGEN in the CNN1 gene promoter:
  • ATF6
  • CREB
  • FOXO3
  • FOXO3a
  • FOXO3b
  • FOXO4
  • MAZR
  • Pax-5
  • RREB-1
  • Sox9

Genomic Locations for CNN1 Gene

Latest Assembly
11,557 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
11,473 bases
Plus strand

(GRCh37/hg19 by Ensembl)
11,607 bases
Plus strand

Genomic View for CNN1 Gene

Genes around CNN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNN1 Gene

Proteins for CNN1 Gene

  • Protein details for CNN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2R868
    • B4DUX6
    • O00638
    • Q15416
    • Q8IY93
    • Q99438

    Protein attributes for CNN1 Gene

    297 amino acids
    Molecular mass:
    33170 Da
    Quaternary structure:
    • Part of cGMP kinase signaling complex at least composed of ACTA2/alpha-actin, CNN1/calponin H1, PLN/phospholamban, PRKG1 and ITPR1.

    Three dimensional structures from OCA and Proteopedia for CNN1 Gene

    Alternative splice isoforms for CNN1 Gene


neXtProt entry for CNN1 Gene

Post-translational modifications for CNN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibodies for research

No data available for DME Specific Peptides for CNN1 Gene

Domains & Families for CNN1 Gene

Gene Families for CNN1 Gene

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

Protein Domains for CNN1 Gene

  • Calponin-like actin-binding
  • Calponin signature
  • Calponin-like actin-binding subtype

Suggested Antigen Peptide Sequences for CNN1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59763, highly similar to Calponin-1 (B4DUX6_HUMAN)
  • cDNA, FLJ79305, highly similar to Calponin-1 (B7Z7E1_HUMAN)
  • Calponin H1, smooth muscle (CNN1_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the calponin family.
  • Belongs to the calponin family.
genes like me logo Genes that share domains with CNN1: view

Function for CNN1 Gene

Molecular function for CNN1 Gene

UniProtKB/Swiss-Prot Function:
Thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin and tropomyosin. The interaction of calponin with actin inhibits the actomyosin Mg-ATPase activity (By similarity).
GENATLAS Biochemistry:
calponin,basic,cytoskeletal protein of smooth muscle cells,33kDa,expressed in aorta,actin,calmodulin,tropomyosin binding,down-regulated during dedifferentiation of vascular smooth muscle cell

Phenotypes From GWAS Catalog for CNN1 Gene

Gene Ontology (GO) - Molecular Function for CNN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0005515 protein binding IEA,IPI 27107012
GO:0005516 calmodulin binding IEA --
genes like me logo Genes that share ontologies with CNN1: view
genes like me logo Genes that share phenotypes with CNN1: view

Animal Models for CNN1 Gene

MGI Knock Outs for CNN1:
  • Cnn1 Cnn1<tm1Tkhi>
  • Cnn1 Cnn1<tm1.1Jomm>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNN1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for CNN1 Gene

Localization for CNN1 Gene

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 CNN1 gene
Compartment Confidence
cytoskeleton 5
cytosol 3
plasma membrane 2
extracellular 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 1
endosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CNN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005856 cytoskeleton IDA 8616889
GO:0005925 focal adhesion HDA 21423176
genes like me logo Genes that share ontologies with CNN1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for CNN1 Gene

Pathways & Interactions for CNN1 Gene

genes like me logo Genes that share pathways with CNN1: view

Pathways by source for CNN1 Gene

1 Cell Signaling Technology pathway for CNN1 Gene

SIGNOR curated interactions for CNN1 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for CNN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006940 regulation of smooth muscle contraction TAS 14550641
GO:0031032 actomyosin structure organization IEA --
GO:1904706 negative regulation of vascular smooth muscle cell proliferation IGI 26315405
genes like me logo Genes that share ontologies with CNN1: view

Drugs & Compounds for CNN1 Gene

(1) Drugs for CNN1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with CNN1: view

Transcripts for CNN1 Gene

mRNA/cDNA for CNN1 Gene

13 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNN1

Alternative Splicing Database (ASD) splice patterns (SP) for CNN1 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b
SP1: - - - - -
SP3: - -
SP4: -
SP5: - -

Relevant External Links for CNN1 Gene

GeneLoc Exon Structure for

Expression for CNN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CNN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CNN1 Gene

This gene is overexpressed in Colon - Sigmoid (x7.0), Esophagus - Muscularis (x5.8), Esophagus - Gastroesophageal Junction (x5.4), and Artery - Tibial (x5.1).

Protein differential expression in normal tissues from HIPED for CNN1 Gene

This gene is overexpressed in Seminal vesicle (9.9), Prostate (9.0), Uterus (8.1), Cardia (8.1), Rectum (6.6), Colon (6.6), and Colon muscle (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CNN1 Gene

Protein tissue co-expression partners for CNN1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CNN1

SOURCE GeneReport for Unigene cluster for CNN1 Gene:


mRNA Expression by UniProt/SwissProt for CNN1 Gene:

Tissue specificity: Smooth muscle, and tissues containing significant amounts of smooth muscle.

Evidence on tissue expression from TISSUES for CNN1 Gene

  • Intestine(4.8)
  • Nervous system(4.5)
  • Heart(4)
  • Muscle(3.9)
  • Stomach(3.2)
  • Lung(2.2)
  • Gall bladder(2.1)
  • Kidney(2)
genes like me logo Genes that share expression patterns with CNN1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CNN1 Gene

Orthologs for CNN1 Gene

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

Orthologs for CNN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CNN1 30 31
  • 99.66 (n)
(Canis familiaris)
Mammalia -- 31
  • 99 (a)
CNN1 30
  • 91.58 (n)
-- 31
  • 72 (a)
(Monodelphis domestica)
Mammalia CNN1 31
  • 94 (a)
(Bos Taurus)
Mammalia CNN1 30 31
  • 91.58 (n)
(Mus musculus)
Mammalia Cnn1 30 17 31
  • 89 (n)
(Rattus norvegicus)
Mammalia Cnn1 30
  • 87.09 (n)
(Ornithorhynchus anatinus)
Mammalia CNN1 31
  • 85 (a)
(Anolis carolinensis)
Reptilia CNN1 31
  • 84 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cnn2 30
  • 73.42 (n)
Str.8537 30
African clawed frog
(Xenopus laevis)
Amphibia MGC68737 30
(Danio rerio)
Actinopterygii LOC572250 30
  • 73.8 (n)
cnn1b 31
  • 71 (a)
cnn1a 31
  • 60 (a)
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8817 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000749 30
  • 55.35 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG5023 30
  • 52.26 (n)
Chd64 32
  • 40 (a)
Mp20 31
  • 34 (a)
(Caenorhabditis elegans)
Secernentea cpn-2 31
  • 36 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SCP1 31
  • 25 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.7148 31
  • 40 (a)
Species where no ortholog for CNN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Chicken (Gallus gallus)
  • 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)
  • 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)

Evolution for CNN1 Gene

Gene Tree for CNN1 (if available)
Gene Tree for CNN1 (if available)
Evolutionary constrained regions (ECRs) for CNN1: view image

Paralogs for CNN1 Gene

Paralogs for CNN1 Gene

(5) SIMAP similar genes for CNN1 Gene using alignment to 9 proteins:

  • B7Z7E1_HUMAN
  • K7EQ72_HUMAN
  • K7ER02_HUMAN
genes like me logo Genes that share paralogs with CNN1: view

Variants for CNN1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CNN1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CNN1 Gene

Variant ID Type Subtype PubMed ID
nsv509721 CNV insertion 20534489
nsv519802 CNV loss 19592680

Variation tolerance for CNN1 Gene

Residual Variation Intolerance Score: 63.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.14; 23.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CNN1 Gene

Disorders for CNN1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CNN1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
infantile digital fibromatosis
  • asymptomatic nodular proliferation of fibrous tissue on the dorsal and lateral aspects of the fingers or toes
subareolar duct papillomatosis
  • adenoma of the nipple
nipple benign neoplasm
  • tumor of nipple
marfan syndrome
  • mfs
aortic valve disease 1
  • aovd1
- elite association - COSMIC cancer census association via MalaCards
Search CNN1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CNN1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CNN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CNN1 Gene

Publications for CNN1 Gene

  1. Expression, genomic structure and high resolution mapping to 19p13.2 of the human smooth muscle cell calponin gene. (PMID: 9332369) Miano JM … Olson EN (Gene 1997) 2 3 4
  2. Molecular cloning and gene mapping of human basic and acidic calponins. (PMID: 8526917) Maguchi M … Hiwada K (Biochemical and biophysical research communications 1995) 2 3 4
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Maternal serum calponin 1 level as a biomarker for the short-term prediction of preterm birth in women with threatened preterm labor. (PMID: 28068849) Cetin O … Sahin HG (The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians 2018) 3

Products for CNN1 Gene

Sources for CNN1 Gene