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 2 4
  • FLJ12383 2
  • KIAA0500 2
  • CLMN 5

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. Diseases associated with CLMN include Smith-Mccort Dysplasia 1 and Psoriasis 2. Gene Ontology (GO) annotations related to this gene include actin binding. An important paralog of this gene is SYNE1.

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 Pubs

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 257.4 +0.2 157 3.6 ZBTB10 ZIC2 ZNF610 SIN3A VEZF1 SAP130 KLF7 ZNF341 RXRA ETV4 CLMN LINC02292 DICER1
GH14J095259 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 26.7 +56.8 56754 9.5 BCL11A MXD4 SP1 CEBPA DEK ZNF217 ELF1 ZIC2 HOMEZ THAP11 SNHG10 SCARNA13 DICER1 CLMN piR-36588-165 piR-38352-184
GH14J095254 Enhancer 1.2 ENCODE CraniofacialAtlas dbSUPER 28.1 +64.2 64182 2.2 FEZF1 ELF1 ZIC2 CEBPB EBF1 CTBP1 KLF9 ZSCAN23 INSM2 ZNF24 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 CEBPA NR2C1 HES1 BHLHE40 FOXA2 VEZF1 MAFF GABPA TAL1 RXRA ENSG00000259143 MK280150 CLMN lnc-GLRX5-2 DICER1
GH14J095248 Enhancer 0.9 ENCODE dbSUPER 28.6 +70.3 70298 2.8 CEBPA FOXA2 SAP130 RXRA TEAD3 JUND HMG20A HNF4A CTCF RBPJ CLMN piR-36588-165 piR-38352-184 DICER1
- 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 the GeneHancer Hub at the UCSC Golden Path

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

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

Latest Assembly
137,969 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
137,969 bases
Minus strand

(GRCh37/hg19 by Ensembl)
137,967 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; 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

  • Actin-binding, actinin-type

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:0003779 actin binding IEA --
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 Models for CLMN Gene

MGI Knock Outs for CLMN:
  • Clmn Clmn<tm1b(EUCOMM)Wtsi>

Inhibitory RNAs for research

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

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
extracellular 1
cytoskeleton 1

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 IEA,IBA 21873635
GO:0031175 neuron projection development IEA --
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

16 NCBI additional mRNA sequence :
9 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 CLMN

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

Expression for CLMN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

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

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(4.7)
  • Liver(4.4)
  • Intestine(4.3)
genes like me logo Genes that share expression patterns with CLMN: view

Primer products for research

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 30 31
  • 99.39 (n)
(Bos Taurus)
Mammalia CLMN 30 31
  • 81.83 (n)
(Canis familiaris)
Mammalia CLMN 30 31
  • 81.67 (n)
(Mus musculus)
Mammalia Clmn 30 17 31
  • 76.84 (n)
(Rattus norvegicus)
Mammalia Clmn 30
  • 76.5 (n)
(Monodelphis domestica)
Mammalia CLMN 31
  • 52 (a)
(Ornithorhynchus anatinus)
Mammalia CLMN 31
  • 45 (a)
(Gallus gallus)
Aves CLMN 31
  • 44 (a)
(Anolis carolinensis)
Reptilia CLMN 31
  • 74 (a)
(Danio rerio)
Actinopterygii CLMN 31
  • 35 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta kst 31
  • 4 (a)
(Caenorhabditis elegans)
Secernentea M116.5 31
  • 15 (a)
Species where no ortholog for CLMN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLMN Gene

SNP ID Clinical significance and condition Chr 14 pos Variation AA Info Type
rs10131338 Benign: not provided 95,203,795(-) G/A
NM_024734.4(CLMN):c.1554C>T (p.His518=)
rs10149705 Benign: not provided. - 95,191,685(-) G/Ap.Pro963Leu
NM_024734.4(CLMN):c.2888C>T (p.Pro963Leu)
rs114143013 Benign: not provided 95,203,150(-) C/T
NM_024734.4(CLMN):c.2199G>A (p.Glu733=)
rs116654567 Benign: not provided 95,203,884(-) C/A
NM_024734.4(CLMN):c.1465G>T (p.Val489Phe)
rs118150470 Likely Benign: not provided 95,209,454(-) C/T
NM_024734.4(CLMN):c.826G>A (p.Glu276Lys)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLMN 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 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 Assays for research

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

Disorders for CLMN Gene

MalaCards: The human disease database

(6) MalaCards diseases for CLMN Gene - From: COP

Disorder Aliases PubMed IDs
smith-mccort dysplasia 1
  • smc1
psoriasis 2
  • psors2
fraser syndrome 1
  • frasrs1
psoriasis 3
  • psoriasis 3, susceptibility to
dyggve-melchior-clausen disease
  • dmc
- elite association - COSMIC cancer census association via MalaCards
Search CLMN in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLMN

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 CLMN: view

No data available for 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
  2. Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. (PMID: 20195266) Adkins DE … van den Oord EJ (Molecular psychiatry 2011) 3 41
  3. Genome-wide association of lipid-lowering response to statins in combined study populations. (PMID: 20339536) Barber MJ … Krauss RM (PloS one 2010) 3 41
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The DNA sequence and analysis of human chromosome 14. (PMID: 12508121) Heilig R … Weissenbach J (Nature 2003) 3 4

Products for CLMN Gene

Sources for CLMN Gene