CLMP Gene (Protein Coding)

CXADR Like Membrane Protein

GC11M123069
GIFtS:
40
This gene encodes a type I transmembrane protein that is localized to junctional complexes between endothelial and epithelial cells and may have a role in cell-cell adhesion. Expression of this gene in white adipose tissue is implicated in adipocyte maturation and development of obesity. This gene is also essential for normal intestinal development and mutations in the gene are... See more...

Aliases for CLMP Gene

Aliases for CLMP Gene

  • CXADR Like Membrane Protein 2 3 5
  • Coxsackie- And Adenovirus Receptor-Like Membrane Protein 2 3 4
  • ACAM 2 3 4
  • ASAM 2 3 4
  • Adipocyte-Specific Adhesion Molecule 2 3
  • Adipocyte Adhesion Molecule 2 4
  • CXADR-Like Membrane Protein 3 4
  • CAR-Like Membrane Protein 3 4
  • FLJ22415 2
  • CSBM 3
  • CSBS 3
  • CLMP 5

External Ids for CLMP Gene

Previous GeneCards Identifiers for CLMP Gene

  • GC11M122943

Summaries for CLMP Gene

Entrez Gene Summary for CLMP Gene

  • This gene encodes a type I transmembrane protein that is localized to junctional complexes between endothelial and epithelial cells and may have a role in cell-cell adhesion. Expression of this gene in white adipose tissue is implicated in adipocyte maturation and development of obesity. This gene is also essential for normal intestinal development and mutations in the gene are associated with congenital short bowel syndrome. [provided by RefSeq, Aug 2015]

GeneCards Summary for CLMP Gene

CLMP (CXADR Like Membrane Protein) is a Protein Coding gene. Diseases associated with CLMP include Congenital Short Bowel Syndrome and Intestinal Pseudo-Obstruction. An important paralog of this gene is CXADR.

UniProtKB/Swiss-Prot Summary for CLMP Gene

  • May be involved in the cell-cell adhesion. May play a role in adipocyte differentiation and development of obesity. Is required for normal small intestine development.

Additional gene information for CLMP Gene

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

Genomics for CLMP Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CLMP Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH11J123192 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 259.1 +0.7 722 4.7 CEBPA POLR2A CEBPB ZNF341 MAX SP2 YY1 TCF7L2 ZBTB48 TAF1 CLMP lnc-GRAMD1B-5 UBASH3B ENSG00000254710 HSPA8
GH11J123357 Promoter/Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas 19.5 -163.3 -163299 1.7 BCLAF1 ZNF654 ZNF600 SIN3A TRIM22 ZNF341 CTCF ZNF610 IRF4 CBFB GRAMD1B lnc-JHY-7 CLMP HSALNG0087826 SCN3B
GH11J123055 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 12.2 +134.1 134136 10.9 BCLAF1 SP1 ZNF207 MYC ZNF600 SSRP1 JUND POLR2A CEBPA ZNF10 ENSG00000288061 LOC101929289 HSPA8 lnc-CLMP-3 SNORD14C piR-59038 piR-61486 ZNF202 CLMP SCN3B
GH11J123740 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 12.1 -546.5 -546548 4.4 BCLAF1 ZNF207 ZNF600 MYC NCOR1 POLR2A NFIC YY1 MXD4 REST ZNF202 lnc-ZNF202-1 lnc-GRAMD1B-6 VWA5A CLMP OR6X1 OR10G7 OR6M1 OR10G4 OR8G2P
GH11J123172 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas dbSUPER 23.2 +20.3 20344 5 JUND ZNF223 CEBPB MAX EP300 RFX5 TCF7L2 SCRT1 ATF4 ATF2 CLMP ENSG00000254710 RF00017-959 HSPA8
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Genomic Locations for CLMP Gene

Latest Assembly
chr11:123,069,872-123,195,248
(GRCh38/hg38)
Size:
125,377 bases
Orientation:
Minus strand

Previous Assembly
chr11:122,940,580-123,065,956
(GRCh37/hg19 by Entrez Gene)
Size:
125,377 bases
Orientation:
Minus strand

chr11:122,943,035-123,065,989
(GRCh37/hg19 by Ensembl)
Size:
122,955 bases
Orientation:
Minus strand

Genomic View for CLMP Gene

Genes around CLMP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CLMP Gene

Proteins for CLMP Gene

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

    Protein Symbol:
    Q9H6B4-CLMP_HUMAN
    Recommended name:
    CXADR-like membrane protein
    Protein Accession:
    Q9H6B4

    Protein attributes for CLMP Gene

    Size:
    373 amino acids
    Molecular mass:
    41281 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CLMP Gene

Protein Expression for CLMP Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CLMP Gene

  • Glycosylation at Asn74 and Asn197
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for CLMP Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLMP Gene

Domains & Families for CLMP Gene

Gene Families for CLMP Gene

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

Protein Domains for CLMP Gene

InterPro:
Blocks:
  • Immunoglobulin C-2 type
  • Immunoglobulin V-set

Suggested Antigen Peptide Sequences for CLMP Gene

GenScript: Design optimal peptide antigens:
  • Coxsackie- and adenovirus receptor-like membrane protein (CLMP_HUMAN)
genes like me logo Genes that share domains with CLMP: view

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

Function for CLMP Gene

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  4. Inhibitory RNAs for research
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  6. Cell Lines for research

Molecular function for CLMP Gene

UniProtKB/Swiss-Prot Function:
May be involved in the cell-cell adhesion. May play a role in adipocyte differentiation and development of obesity. Is required for normal small intestine development.
UniProtKB/Swiss-Prot Induction:
Up-regulated in mature adipocytes and adipocyte tissue of obese individuals.

Phenotypes From GWAS Catalog for CLMP Gene

Gene Ontology (GO) - Molecular Function for CLMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with CLMP: view
genes like me logo Genes that share phenotypes with CLMP: view

Human Phenotype Ontology for CLMP Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLMP Gene

MGI Knock Outs for CLMP:

Animal Models for research

  • Taconic Biosciences Mouse Models for CLMP

Inhibitory RNAs for research

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

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CLMP Gene

Localization for CLMP Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLMP Gene

Cell junction, tight junction. Cell membrane. Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
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 CLMP gene
Compartment Confidence
cytoskeleton 5
plasma membrane 4
extracellular 2
nucleus 2
cytosol 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for CLMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005881 cytoplasmic microtubule IDA 23264731
GO:0005886 plasma membrane IEA --
GO:0005923 bicellular tight junction IEA,IDA 22155368
GO:0009986 cell surface HDA 19581412
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CLMP: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLMP Gene

Pathways & Interactions for CLMP Gene

PathCards logo

SuperPathways for CLMP Gene

No Data Available

Gene Ontology (GO) - Biological Process for CLMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0048565 digestive tract development IMP 22155368
genes like me logo Genes that share ontologies with CLMP: view

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

Drugs & Compounds for CLMP Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for CLMP Gene

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mRNA/cDNA for CLMP Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
4 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 CLMP

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

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b
SP1:
SP2: -

Relevant External Links for CLMP Gene

GeneLoc Exon Structure for
CLMP

Expression for CLMP Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

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

mRNA expression in normal human tissues for CLMP Gene
mRNA expression by GTEx for CLMP GenemRNA expression by BioGPS for CLMP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Artery - Aorta (x4.2).

Protein differential expression in normal tissues from HIPED for CLMP Gene

This gene is overexpressed in Urine (32.0), Gallbladder (12.8), Adipocyte (10.4), and Fetal Brain (8.5).

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



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

SOURCE GeneReport for Unigene cluster for CLMP Gene:

Hs.591949

mRNA Expression by UniProt/SwissProt for CLMP Gene:

Q9H6B4-CLMP_HUMAN
Tissue specificity: Predominantly expressed in epithelial cells within different tissues and in the white adipose tissue. Expressed at high levels in small intestine and placenta, at intermediate levels in the heart, skeletal muscle, colon, spleen, kidney and lung and at low levels in the liver and peripheral blood leukocytes. Highly abundant in the intestine during embryo and fetal development (at protein level).

Evidence on tissue expression from TISSUES for CLMP Gene

  • Muscle(4.3)
  • Heart(2.1)
  • Nervous system(2.1)
  • Intestine(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLMP Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeleton
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • head
  • lip
  • nose
  • outer ear
  • skull
Thorax:
  • esophagus
  • heart
Abdomen:
  • biliary tract
  • duodenum
  • intestine
  • large intestine
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • anus
  • rectum
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • skin
genes like me logo Genes that share expression patterns with CLMP: view

Primer products for research

No data available for Protein tissue co-expression partners for CLMP Gene

Orthologs for CLMP Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLMP Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CLMP 29 30
  • 100 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CLMP 29 30
  • 93.13 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia ASAM 30
  • 90 (a)
 OneToOne
CLMP 29
  • 89.19 (n)
Mouse
(Mus musculus)
 Mammalia Clmp 29 16 30
  • 87.82 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Clmp 29
  • 87.73 (n)
Oppossum
(Monodelphis domestica)
 Mammalia CLMP 30
  • 80 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia CLMP 30
  • 71 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CLMP 29 30
  • 68.47 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CLMP 30
  • 61 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia clmp 29
  • 59.22 (n)
Zebrafish
(Danio rerio)
 Actinopterygii LOC100330877 29
  • 55.48 (n)
CLMP 30
  • 44 (a)
 OneToOne
Species where no ortholog for CLMP 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)
  • 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 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CLMP Gene

ENSEMBL:
Gene Tree for CLMP (if available)
TreeFam:
Gene Tree for CLMP (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLMP: view image
Alliance of Genome Resources:
Additional Orthologs for CLMP

Paralogs for CLMP Gene

Paralogs for CLMP Gene

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

  • CLMP_HUMAN
genes like me logo Genes that share paralogs with CLMP: view

Variants for CLMP Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLMP Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs112659755 Benign: not provided 123,083,783(-) C/T
NM_024769.5(CLMP):c.453G>A (p.Leu151=) 		SYNONYMOUS
rs142239120 Benign: not provided 123,073,708(-) G/A
NM_024769.5(CLMP):c.888C>T (p.Ser296=) 		SYNONYMOUS
rs142456942 Benign: not provided 123,073,585(-) C/T
NM_024769.5(CLMP):c.1011G>A (p.Gly337=) 		SYNONYMOUS
rs146055456 Benign: not provided 123,097,818(-) C/T
NM_024769.5(CLMP):c.163G>A (p.Asp55Asn) 		MISSENSE
rs202047829 Benign: not provided 123,083,828(-) C/T
NM_024769.5(CLMP):c.408G>A (p.Lys136=) 		SYNONYMOUS

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

Variant ID Type Subtype PubMed ID
esv2745163 CNV deletion 23290073
esv2745165 CNV deletion 23290073
esv3548445 CNV deletion 23714750
nsv1039284 CNV gain 25217958
nsv1122675 CNV deletion 24896259
nsv1146235 CNV deletion 26484159

Variation tolerance for CLMP Gene

Residual Variation Intolerance Score: 24.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.47; 54.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLMP Gene

Human Gene Mutation Database (HGMD)
CLMP
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLMP
Leiden Open Variation Database (LOVD)
CLMP

SNP Genotyping and Copy Number Assays for research

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

Disorders for CLMP Gene

MalaCards: The human disease database

(6) MalaCards diseases for CLMP Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
congenital short bowel syndrome
  • csbs
intestinal pseudo-obstruction
  • chronic intestinal pseudo-obstruction
short bowel syndrome
  • acquired short bowel syndrome
interstitial myocarditis
testicular thecoma
- elite association - COSMIC cancer census association via MalaCards
Search CLMP in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CLMP_HUMAN
  • Congenital short bowel syndrome (CSBS) [MIM:615237]: A disease characterized by a shortened small intestine, intestinal malrotation, and malabsorption. The mean length of the small intestine in CSBS patients is approximately 50 cm, compared with a normal length at birth of 190-280 cm. Patients with CSBS may develop severe malnutrition as a result of the hugely reduced absorptive surface of the small intestine. Infants require parenteral nutrition for survival. However, parenteral nutrition itself causes life-threatening complications such as sepsis and liver failure which are associated with a high rate of mortality early in life. {ECO:0000269 PubMed:22155368}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for CLMP

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CLMP: view

No data available for Genatlas for CLMP Gene

Publications for CLMP Gene

  1. CLMP, a novel member of the CTX family and a new component of epithelial tight junctions. (PMID: 14573622) Raschperger E … Fuxe J (The Journal of biological chemistry 2004) 2 3 4 22
  2. CLMP is required for intestinal development, and loss-of-function mutations cause congenital short-bowel syndrome. (PMID: 22155368) Van Der Werf CS … Hofstra RM (Gastroenterology 2012) 3 4 72
  3. Identification of adipocyte adhesion molecule (ACAM), a novel CTX gene family, implicated in adipocyte maturation and development of obesity. (PMID: 15563274) Eguchi J … Makino H (The Biochemical journal 2005) 3 4 22
  4. IGSF11 gene, frequently up-regulated in intestinal-type gastric cancer, encodes adhesion molecule homologous to CXADR, FLJ22415 and ESAM. (PMID: 12851705) Katoh M … Katoh M (International journal of oncology 2003) 2 3 22
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4

ExternalLinks

View latest publications for CLMP gene in Mastermind

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