Human Gene L1CAM (ENST00000370060.7) from GENCODE V44
  Description: Homo sapiens L1 cell adhesion molecule (L1CAM), transcript variant 4, mRNA. (from RefSeq NM_001278116)
RefSeq Summary (NM_001278116): The protein encoded by this gene is an axonal glycoprotein belonging to the immunoglobulin supergene family. The ectodomain, consisting of several immunoglobulin-like domains and fibronectin-like repeats (type III), is linked via a single transmembrane sequence to a conserved cytoplasmic domain. This cell adhesion molecule plays an important role in nervous system development, including neuronal migration and differentiation. Mutations in the gene cause X-linked neurological syndromes known as CRASH (corpus callosum hypoplasia, retardation, aphasia, spastic paraplegia and hydrocephalus). Alternative splicing of this gene results in multiple transcript variants, some of which include an alternate exon that is considered to be specific to neurons. [provided by RefSeq, May 2013].
Gencode Transcript: ENST00000370060.7
Gencode Gene: ENSG00000198910.14
Transcript (Including UTRs)
   Position: hg38 chrX:153,861,516-153,886,173 Size: 24,658 Total Exon Count: 29 Strand: -
Coding Region
   Position: hg38 chrX:153,862,663-153,875,836 Size: 13,174 Coding Exon Count: 28 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:153,861,516-153,886,173)mRNA (may differ from genome)Protein (1257 aa)
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HGNCLynxMalacardsMGImyGene2neXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: L1CAM_HUMAN
DESCRIPTION: RecName: Full=Neural cell adhesion molecule L1; Short=N-CAM-L1; Short=NCAM-L1; AltName: CD_antigen=CD171; Flags: Precursor;
FUNCTION: Cell adhesion molecule with an important role in the development of the nervous system. Involved in neuron-neuron adhesion, neurite fasciculation, outgrowth of neurites, etc. Binds to axonin on neurons.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.
DISEASE: Defects in L1CAM are the cause of hydrocephalus due to stenosis of the aqueduct of Sylvius (HSAS) [MIM:307000]. Hydrocephalus is a condition in which abnormal accumulation of cerebrospinal fluid in the brain causes increased intracranial pressure inside the skull. This is usually due to blockage of cerebrospinal fluid outflow in the brain ventricles or in the subarachnoid space at the base of the brain. In children is typically characterized by enlargement of the head, prominence of the forehead, brain atrophy, mental deterioration, and convulsions. In adults the syndrome includes incontinence, imbalance, and dementia. HSAS is characterized by mental retardation and enlarged brain ventricles. Note=L1CAM mutations have also been found in few patients affected by hydrocephalus with Hirschsprung disease, suggesting a role of this gene acting either in a direct or indirect way in the pathogenesis of Hirschsprung disease (PubMed:22344793).
DISEASE: Defects in L1CAM are the cause of mental retardation- aphasia-shuffling gait-adducted thumbs syndrome (MASA) [MIM:303350]; also known as corpus callosum hypoplasia, psychomotor retardation, adducted thumbs, spastic paraparesis, and hydrocephalus or CRASH syndrome. MASA is an X-linked recessive syndrome with a highly variable clinical spectrum. Main clinical features include spasticity and hyperreflexia of lower limbs, shuffling gait, mental retardation, aphasia and adducted thumbs. The features of spasticity have been referred to as complicated spastic paraplegia type 1 (SPG1). Some patients manifest corpus callosum hypoplasia and hydrocephalus. Inter- and intrafamilial variability is very wide, such that patients with hydrocephalus, MASA, SPG1, and agenesis of corpus callosum can be present within the same family.
DISEASE: Defects in L1CAM are the cause of spastic paraplegia X- linked type 1 (SPG1) [MIM:303350]. Spastic paraplegia is a degenerative spinal cord disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs.
DISEASE: Note=Defects in L1CAM may contribute to Hirschsprung disease by modifying the effects of Hirschsprung disease- associated genes to cause intestinal aganglionosis.
DISEASE: Defects in L1CAM are a cause of partial agenesis of the corpus callosum (ACCPX) [MIM:304100]. A syndrome characterized by partial corpus callosum agenesis, hypoplasia of inferior vermis and cerebellum, mental retardation, seizures and spasticity. Other features include microcephaly, unusual facies, and Hirschsprung disease in some patients.
SIMILARITY: Belongs to the immunoglobulin superfamily. L1/neurofascin/NgCAM family.
SIMILARITY: Contains 5 fibronectin type-III domains.
SIMILARITY: Contains 6 Ig-like C2-type (immunoglobulin-like) domains.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/L1CAMID44110chXq28.html";
WEB RESOURCE: Name=L1CAM; Note=L1CAM mutation Web Page; URL="http://www.rug.nl/umcg/faculteit/disciplinegroepen/medischegenetica/hereditarydiseases/L1cam/index";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/L1CAM";

-  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: L1CAM
Diseases sorted by gene-association score: masa syndrome* (1689), hydrocephalus due to aqueductal stenosis* (1550), corpus callosum, partial agenesis of* (1550), spastic paraplegia 1* (500), hydrocephalus* (470), hydrocephalus due to congenital stenosis of aqueduct of sylvius* (400), x-linked complicated corpus callosum agenesis* (400), x-linked complicated spastic paraplegia type 1* (350), x-linked hydrocephalus with stenosis of the aqueduct of sylvius* (100), aphasia (54), adducted thumbs syndrome (31), congenital hydrocephalus (29), corpus callosum agenesis (14), acrocallosal syndrome (8), diabetes insipidus, nephrogenic (8), porencephaly (7), intestinal pseudo-obstruction (7), cerebral degeneration (6), hirschsprung disease 1 (5), speech and communication disorders (5), hereditary spastic paraplegia (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 111.35 RPKM in Brain - Cerebellum
Total median expression: 603.71 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 -104.90217-0.483 Picture PostScript Text
3' UTR -418.001147-0.364 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
IPR026966 - Fibronectin_III_C
IPR003961 - Fibronectin_type3
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003599 - Ig_sub
IPR003598 - Ig_sub2

Pfam Domains:
PF13882 - Bravo-like intracellular region
PF00041 - Fibronectin type III domain
PF07679 - Immunoglobulin I-set domain

ModBase Predicted Comparative 3D Structure on P32004
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-  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     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019904 protein domain specific binding

Biological Process:
GO:0006935 chemotaxis
GO:0007155 cell adhesion
GO:0007160 cell-matrix adhesion
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0007411 axon guidance
GO:0016477 cell migration
GO:0030154 cell differentiation
GO:0031175 neuron projection development
GO:0045773 positive regulation of axon extension
GO:0050808 synapse organization
GO:0050900 leukocyte migration
GO:0061564 axon development

Cellular Component:
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030424 axon
GO:0030425 dendrite
GO:0030426 growth cone
GO:0031012 extracellular matrix
GO:0042995 cell projection
GO:0043025 neuronal cell body
GO:0044295 axonal growth cone


-  Descriptions from all associated GenBank mRNAs
  BC021858 - Homo sapiens L1 cell adhesion molecule, mRNA (cDNA clone IMAGE:4940156), **** WARNING: chimeric clone ****.
BC025843 - Homo sapiens L1 cell adhesion molecule, mRNA (cDNA clone IMAGE:4907142), partial cds.
M77640 - Homo sapiens L1 cell adhesion molecule (L1CAM) mRNA, complete cds.
JD250916 - Sequence 231940 from Patent EP1572962.
JD563949 - Sequence 544973 from Patent EP1572962.
JD494764 - Sequence 475788 from Patent EP1572962.
JD253319 - Sequence 234343 from Patent EP1572962.
BC126229 - Homo sapiens L1 cell adhesion molecule, mRNA (cDNA clone MGC:161507 IMAGE:8991945), complete cds.
BC136447 - Homo sapiens L1 cell adhesion molecule, mRNA (cDNA clone MGC:168059 IMAGE:9020436), complete cds.
JD490355 - Sequence 471379 from Patent EP1572962.
JD104392 - Sequence 85416 from Patent EP1572962.
AK289754 - Homo sapiens cDNA FLJ76744 complete cds, highly similar to Homo sapiens L1 cell adhesion molecule (L1CAM), transcript variant 1, mRNA.
JD041203 - Sequence 22227 from Patent EP1572962.
JD036838 - Sequence 17862 from Patent EP1572962.
JD379157 - Sequence 360181 from Patent EP1572962.
M74387 - Human cell adhesion molecule L1 (L1CAM) mRNA, complete cds.
JD445216 - Sequence 426240 from Patent EP1572962.
JD277316 - Sequence 258340 from Patent EP1572962.
JD190469 - Sequence 171493 from Patent EP1572962.
JD107119 - Sequence 88143 from Patent EP1572962.
JD205284 - Sequence 186308 from Patent EP1572962.
AB102653 - Homo sapiens L1CAM mRNA for L1 cell adhesion molecule, partial cds.
EF506611 - Homo sapiens non-neural L1CAM (L1CAM) mRNA, complete cds.
X59847 - H.sapiens mRNA for neural cell adhesion molecule L1.
AB384393 - Synthetic construct DNA, clone: pF1KSDB0238, Homo sapiens L1CAM gene for neural cell adhesion molecule L1 precursor, complete cds, without stop codon, in Flexi system.
X58776 - Human CAM-L1 mRNA for cell adhesion molecule L1, partial cds.
AY927629 - Homo sapiens mRNA sequence.
M55271 - Human neural adhesion molecule L1 mRNA, partial cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance
hsa04514 - Cell adhesion molecules (CAMs)

Reactome (by CSHL, EBI, and GO)

Protein P32004 (Reactome details) participates in the following event(s):

R-HSA-374669 L1 binds NRP1
R-HSA-374672 Cis-heterodimerization of L1 and Axonin-1
R-HSA-374673 L1 binds RanBPM
R-HSA-374680 L1 trans-homophilic interaction
R-HSA-374681 L1 and NCAM1 engaged in cis-interaction
R-HSA-374683 Interaction of L1 with Neurocan
R-HSA-374686 L1 interaction with Integrins
R-HSA-392748 L1 binds to AP-2 Clathrin complex
R-HSA-392752 Phosphorylation of L1 by CK-II
R-HSA-437234 Heat-Stable Antigen binds L1
R-HSA-443780 Cis-heterodimerization of L1 and DM-GRASP/ALCAM/BEN
R-HSA-443783 Interaction of NUMB with L1
R-HSA-443784 Cis-heterodimerization of L1 and Contactin-1/F3/F11
R-HSA-443817 Phosphorylation of L1 by EPHB2
R-NUL-445066 Phosphorylation of L1 by p90rsk
R-HSA-445069 L1-EGFR trans-heterodimerization
R-HSA-445084 Phosphorylation of L1 by SRC
R-HSA-445071 Reinsertion of L1 into the plasma membrane
R-HSA-445089 Dephosphorylation of pL1 (Y1176)
R-HSA-373736 Shootin-1 links L1 and retrograde actin flow
R-HSA-374677 L1 binds ERM family members
R-NUL-443049 L1 dimer binds Ankyrin
R-HSA-443779 Linkage of L1 with treadmilling F-actin
R-HSA-392749 Transport of L1 into endosomes
R-HSA-555065 Formation of clathrin coated vesicle
R-HSA-374696 Phosphorylation of L1 by p90rsk
R-HSA-445077 Transport of L1 from C-domain to P-domain
R-HSA-445079 Phosphorylation of L1 by ERK
R-HSA-443778 Interaction of L1 with Laminin-1
R-HSA-445076 Phosphorylation of Y1229 in L1
R-HSA-374675 L1 dimer binds Ankyrin
R-HSA-437230 L1-FGFR cis-heterodimerization
R-HSA-375133 Basigin binds Mannose-carrying cell recognition molecules
R-HSA-392751 L1 linked to actin cytoskeleton by ankyrin
R-HSA-445144 Signal transduction by L1
R-HSA-373760 L1CAM interactions
R-HSA-437239 Recycling pathway of L1
R-HSA-445095 Interaction between L1 and Ankyrins
R-HSA-210991 Basigin interactions
R-HSA-422475 Axon guidance
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-1266738 Developmental Biology
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: A0AV65, B2RMU7, CAML1, ENST00000370060.1, ENST00000370060.2, ENST00000370060.3, ENST00000370060.4, ENST00000370060.5, ENST00000370060.6, L1CAM_HUMAN, MIC5, NM_001278116, P32004, Q8TA87, uc031tks.1, uc031tks.2, uc031tks.3, uc031tks.4
UCSC ID: ENST00000370060.7
RefSeq Accession: NM_001278116
Protein: P32004 (aka L1CAM_HUMAN or CAML_HUMAN)
CCDS: CCDS14733.1, CCDS14734.1, CCDS48192.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene L1CAM:
hsp (Hereditary Spastic Paraplegia Overview)
l1cam (L1 Syndrome)

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