Human Gene CNMD (ENST00000377962.8) from GENCODE V44
  Description: Homo sapiens chondromodulin (CNMD), transcript variant 1, mRNA. (from RefSeq NM_007015)
RefSeq Summary (NM_007015): This gene encodes a glycosylated transmembrane protein that is cleaved to form a mature, secreted protein. The N-terminus of the precursor protein shares characteristics with other surfactant proteins and is sometimes called chondrosurfactant protein although no biological activity has yet been defined for it. The C-terminus of the precursor protein contains a 25 kDa mature protein called leukocyte cell-derived chemotaxin-1 or chondromodulin-1. The mature protein promotes chondrocyte growth and inhibits angiogenesis. This gene is expressed in the avascular zone of prehypertrophic cartilage and its expression decreases during chondrocyte hypertrophy and vascular invasion. The mature protein likely plays a role in endochondral bone development by permitting cartilaginous anlagen to be vascularized and replaced by bone. It may be involved also in the broad control of tissue vascularization during development. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000377962.8
Gencode Gene: ENSG00000136110.13
Transcript (Including UTRs)
   Position: hg38 chr13:52,703,264-52,739,820 Size: 36,557 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg38 chr13:52,703,595-52,739,701 Size: 36,107 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr13:52,703,264-52,739,820)mRNA (may differ from genome)Protein (334 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHPRD
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Leukocyte cell-derived chemotaxin 1; Contains: RecName: Full=Chondrosurfactant protein; Short=CH-SP; Contains: RecName: Full=Chondromodulin-1; AltName: Full=Chondromodulin-I; Short=ChM-I; Flags: Precursor;
FUNCTION: Bifunctional growth regulator that stimulates the growth of cultured chondrocytes in the presence of basic fibroblast growth factor (FGF) but inhibits the growth of cultured vascular endothelial cells. May contribute to the rapid growth of cartilage and vascular invasion prior to the replacement of cartilage by bone during endochondral bone development. Inhibits in vitro tube formation and mobilization of endothelial cells. Plays a role as antiangiogenic factor in cardiac valves to suppress neovascularization.
SUBCELLULAR LOCATION: Chondromodulin-1: Secreted. Note=Accumulated in the inter-territorial matrix of cartilage.
SUBCELLULAR LOCATION: Chondrosurfactant protein: Endomembrane system; Single-pass membrane protein (Potential).
TISSUE SPECIFICITY: Detected in cartilage and cardiac valves (at protein level). Detected in the laminae fibrosa, spongiosa and ventricularis layers of normal cardiac valves (at protein level). Expression is decreased cardiac valves of patients with valvular heart disease (at protein level). Weakly expressed in chondrosarcoma.
DEVELOPMENTAL STAGE: Expressed at 9 weeks in developing cartilagenous bone rudiments.
PTM: After cleavage, the post-translationally modified ChM-I is secreted as a glycoprotein.
SIMILARITY: Belongs to the chondromodulin-1 family.
SIMILARITY: Contains 1 BRICHOS domain.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: CNMD
Diseases sorted by gene-association score: chondrosarcoma (8), aortic valve disease 2 (2)

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.37 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 20.25 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -52.30119-0.439 Picture PostScript Text
3' UTR -64.20331-0.194 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007084 - BRICHOS_dom

Pfam Domains:
PF04089 - BRICHOS domain

ModBase Predicted Comparative 3D Structure on O75829
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0001501 skeletal system development
GO:0006029 proteoglycan metabolic process
GO:0007275 multicellular organism development
GO:0016525 negative regulation of angiogenesis
GO:0030154 cell differentiation
GO:0051216 cartilage development

Cellular Component:
GO:0005576 extracellular region
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  BC025659 - Homo sapiens leukocyte cell derived chemotaxin 1, mRNA (cDNA clone MGC:34671 IMAGE:5198878), complete cds.
AB006000 - Homo sapiens mRNA for chondromodulin-I precursor, complete cds.
JD410019 - Sequence 391043 from Patent EP1572962.
JD440987 - Sequence 422011 from Patent EP1572962.
AB005999 - Homo sapiens mRNA for chondromodulin-I, partial cds.
E09362 - Human cDNA encoding chondromodulin-I.
E09363 - Human cDNA encoding chondromodulin-I.
E09364 - Human cDNA encoding chondromodulin-I.
CR541910 - Homo sapiens full open reading frame cDNA clone RZPDo834F0533D for gene LECT1, leukocyte cell derived chemotaxin 1; complete cds, without stopcodon.
KJ898346 - Synthetic construct Homo sapiens clone ccsbBroadEn_07740 LECT1 gene, encodes complete protein.
AY368652 - Homo sapiens multiple myeloma susceptibility tumor suppressor protein mRNA, complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: CHMI, ENST00000377962.1, ENST00000377962.2, ENST00000377962.3, ENST00000377962.4, ENST00000377962.5, ENST00000377962.6, ENST00000377962.7, LECT1, LECT1_HUMAN, NM_007015, O75829, Q5TAM4, Q8TAY6, Q9UM18, uc001vhf.1, uc001vhf.2, uc001vhf.3, uc001vhf.4, uc001vhf.5
UCSC ID: ENST00000377962.8
RefSeq Accession: NM_007015
Protein: O75829 (aka LECT1_HUMAN or CHM1_HUMAN)
CCDS: CCDS9437.1, CCDS45051.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.