Aliases for CLMN Gene

Aliases for CLMN Gene

  • Calmin 2 3 4 5
  • Calponin-Like Transmembrane Domain Protein 3 4
  • Calmin (Calponin-Like, Transmembrane) 2 3
  • KIAA1188 4

External Ids for CLMN Gene

Previous GeneCards Identifiers for CLMN Gene

  • GC14M093167
  • GC14M089474
  • GC14M093644
  • GC14M093647
  • GC14M094727
  • GC14M095648
  • GC14M075832

Summaries for CLMN Gene

GeneCards Summary for CLMN Gene

CLMN (Calmin) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include actin binding. An important paralog of this gene is SYNE1.

Additional gene information for CLMN Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLMN Gene

Genomics for CLMN Gene

GeneHancer (GH) Regulatory Elements for CLMN Gene

Promoters and enhancers for CLMN 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
GH14J095317 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 757.4 +0.2 157 3.6 MNT NKRF SP1 CEBPG MLLT1 SP7 ZSCAN21 CREM EGR1 KLF14 CLMN LINC02292 ENSG00000258866 ENSG00000258729 lnc-GLRX5-5
GH14J095259 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 26.7 +56.8 56754 9.5 ZNF785 SIN3A ZNF24 SP1 SREBF1 RBPJ TCF7L2 CTBP1 NR2F6 CREB1 SNHG10 SCARNA13 DICER1 CLMN ENSG00000258866 piR-36588-165 piR-38352-184
GH14J095254 Enhancer 1.2 ENCODE CraniofacialAtlas dbSUPER 28.1 +64.2 64182 2.2 ETV6 SP1 SP7 ZSCAN21 ZNF548 PRDM1 CREM IKZF1 GLIS2 CREB1 SNHG10 CLMN SCARNA13 DICER1 piR-36588-165 piR-38352-184
GH14J095182 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 21.4 +134.6 134571 4.5 MYC ELF1 HLF CEBPB MAX TEAD4 SP1 MAFK CEBPG CBFA2T2 ENSG00000259143 CLMN lnc-GLRX5-2
GH14J095248 Enhancer 0.9 ENCODE dbSUPER 28.6 +70.3 70298 2.8 RBPJ HLF ZBTB33 ELF3 SP1 MAFK CEBPG ZNF644 IKZF1 CEBPA CLMN piR-36588-165 piR-38352-184
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLMN on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLMN gene promoter:
  • aMEF-2
  • AML1a
  • Cdc5
  • MEF-2A
  • Nkx2-2
  • Nkx6-1
  • p300
  • RORalpha1
  • RORalpha2
  • Sp1

Genomic Locations for CLMN Gene

Genomic Locations for CLMN Gene
137,970 bases
Minus strand
137,970 bases
Minus strand

Genomic View for CLMN Gene

Genes around CLMN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CLMN Gene

Proteins for CLMN Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2RAR7
    • Q9H713
    • Q9HA23
    • Q9HA57
    • Q9UFP4
    • Q9ULN2

    Protein attributes for CLMN Gene

    1002 amino acids
    Molecular mass:
    111651 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAB13999.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB14036.1; Type=Frameshift; Positions=493; Evidence={ECO:0000305}; Sequence=BAB14036.1; Type=Miscellaneous discrepancy; Note=Chimeric cDNA.; Evidence={ECO:0000305};

neXtProt entry for CLMN Gene

Post-translational modifications for CLMN Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLMN Gene

Domains & Families for CLMN Gene

Gene Families for CLMN Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CLMN Gene

Suggested Antigen Peptide Sequences for CLMN Gene

GenScript: Design optimal peptide antigens:
  • CLMN protein (A0PJD0_HUMAN)
  • CLMN protein (A1A4B9_HUMAN)
  • Calponin-like transmembrane domain protein (CLMN_HUMAN)
  • Calmin (Calponin-like, transmembrane) (Q6NUQ2_HUMAN)
genes like me logo Genes that share domains with CLMN: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CLMN Gene

Function for CLMN Gene

Phenotypes From GWAS Catalog for CLMN Gene

Gene Ontology (GO) - Molecular Function for CLMN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0051015 actin filament binding IBA 21873635
genes like me logo Genes that share ontologies with CLMN: view
genes like me logo Genes that share phenotypes with CLMN: view

Animal Model Products

CRISPR Products

Clone Products

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

Localization for CLMN Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLMN Gene

Membrane; Single-pass type IV membrane protein.

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 CLMN gene
Compartment Confidence
plasma membrane 3
nucleus 3
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLMN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005640 nuclear outer membrane IBA 21873635
GO:0005737 cytoplasm IEA,IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0034993 meiotic nuclear membrane microtubule tethering complex IBA 21873635
genes like me logo Genes that share ontologies with CLMN: view

Pathways & Interactions for CLMN Gene

PathCards logo

SuperPathways for CLMN Gene

No Data Available

Gene Ontology (GO) - Biological Process for CLMN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007097 nuclear migration IBA 21873635
GO:0008285 negative regulation of cell proliferation IBA,IEA 21873635
GO:0031175 neuron projection development IEA --
GO:0051647 nucleus localization IBA 21873635
GO:0090286 cytoskeletal anchoring at nuclear membrane IBA 21873635
genes like me logo Genes that share ontologies with CLMN: view

No data available for Pathways by source and SIGNOR curated interactions for CLMN Gene

Drugs & Compounds for CLMN Gene

No Compound Related Data Available

Transcripts for CLMN Gene

mRNA/cDNA for CLMN Gene

CRISPR Products

Clone Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b · 15c ^ 16 ^ 17a · 17b
SP1: - -
SP2: -
SP3: -
SP4: - - - -
SP5: - - -
SP6: -

Relevant External Links for CLMN Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLMN Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLMN Gene

This gene is overexpressed in Islet of Langerhans (17.1), Urine (16.8), and Lung (6.6).

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

Protein tissue co-expression partners for CLMN Gene

NURSA nuclear receptor signaling pathways regulating expression of CLMN Gene:


SOURCE GeneReport for Unigene cluster for CLMN Gene:


mRNA Expression by UniProt/SwissProt for CLMN Gene:

Tissue specificity: Widely expressed at intermediate level.

Evidence on tissue expression from TISSUES for CLMN Gene

  • Nervous system(4.6)
  • Liver(4.3)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with CLMN: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLMN Gene

Orthologs for CLMN Gene

This gene was present in the common ancestor of animals.

Orthologs for CLMN Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLMN 33 32
  • 99.39 (n)
(Bos Taurus)
Mammalia CLMN 33 32
  • 81.83 (n)
(Canis familiaris)
Mammalia CLMN 33 32
  • 81.67 (n)
(Mus musculus)
Mammalia Clmn 17 33 32
  • 76.84 (n)
(Rattus norvegicus)
Mammalia Clmn 32
  • 76.5 (n)
(Monodelphis domestica)
Mammalia CLMN 33
  • 52 (a)
(Ornithorhynchus anatinus)
Mammalia CLMN 33
  • 45 (a)
(Gallus gallus)
Aves CLMN 33
  • 44 (a)
(Anolis carolinensis)
Reptilia CLMN 33
  • 74 (a)
(Danio rerio)
Actinopterygii CLMN 33
  • 35 (a)
fruit fly
(Drosophila melanogaster)
Insecta kst 33
  • 4 (a)
(Caenorhabditis elegans)
Secernentea M116.5 33
  • 15 (a)
Species where no ortholog for CLMN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for CLMN Gene

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

Paralogs for CLMN Gene

(14) SIMAP similar genes for CLMN Gene using alignment to 8 proteins:

  • A1A4B9_HUMAN
  • G3V3D8_HUMAN
  • G3V4C0_HUMAN
  • G3V5E0_HUMAN
  • G3V5U3_HUMAN
genes like me logo Genes that share paralogs with CLMN: view

Variants for CLMN Gene

Sequence variations from dbSNP and Humsavar for CLMN Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1000036213 -- 95,186,546(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000057528 -- 95,185,419(-) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000063679 -- 95,243,977(-) T/C intron_variant
rs1000089567 -- 95,289,744(-) G/ intron_variant
rs1000095017 -- 95,193,252(-) A/G genic_downstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
dgv1325e59 CNV duplication 20981092
dgv384n67 CNV gain 20364138
dgv675e212 CNV loss 25503493
dgv89e55 CNV gain 17911159
esv2250778 CNV deletion 18987734
esv2749047 CNV deletion 23290073
esv3306150 CNV mobile element insertion 20981092
esv3395087 CNV insertion 20981092
esv3551998 CNV deletion 23714750
esv3635396 CNV gain 21293372
esv3635399 CNV loss 21293372
nsv1036738 CNV gain 25217958
nsv1070233 CNV deletion 25765185
nsv1070652 CNV deletion 25765185
nsv1131160 CNV deletion 24896259
nsv1143756 CNV deletion 24896259
nsv1412 CNV insertion 18451855
nsv472215 CNV novel sequence insertion 20440878
nsv476271 CNV novel sequence insertion 20440878
nsv528121 CNV loss 19592680
nsv565630 CNV loss 21841781

Variation tolerance for CLMN Gene

Residual Variation Intolerance Score: 86.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.53; 55.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLMN 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 CLMN Gene

Disorders for CLMN Gene

Additional Disease Information for CLMN

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CLMN Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLMN Gene

Publications for CLMN Gene

  1. Calmin, a protein with calponin homology and transmembrane domains expressed in maturing spermatogenic cells. (PMID: 11386753) Ishisaki Z … Huh N (Genomics 2001) 2 3 4 23 56
  2. Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. (PMID: 20195266) Adkins DE … van den Oord EJ (Molecular psychiatry 2011) 3 43 56
  3. Genome-wide association of lipid-lowering response to statins in combined study populations. (PMID: 20339536) Barber MJ … Krauss RM (PloS one 2010) 3 43 56
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  5. The DNA sequence and analysis of human chromosome 14. (PMID: 12508121) Heilig R … Weissenbach J (Nature 2003) 3 4 56

Products for CLMN Gene

Sources for CLMN Gene