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    L1CAM L1 cell adhesion molecule [ Homo sapiens (human) ]

    Gene ID: 3897, updated on 2-Nov-2024

    Summary

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    Official Symbol
    L1CAMprovided by HGNC
    Official Full Name
    L1 cell adhesion moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:6470
    See related
    Ensembl:ENSG00000198910 MIM:308840; AllianceGenome:HGNC:6470
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    S10; HSAS; HYCX; MASA; MIC5; SPG1; CAML1; CD171; HSAS1; N-CAML1; NCAM-L1; N-CAM-L1
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 23.7), adrenal (RPKM 13.5) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See L1CAM in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153861514..153886173, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152135195..152159857, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153126969..153151627, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene PDZ domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21072 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:153092379-153092957 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153099642-153099888 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:153110079-153110947 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:153110948-153111815 Neighboring gene CYCS pseudogene 45 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153128028-153128886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153128887-153129745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153147023-153148020 Neighboring gene L1CAM antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153174367-153175060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153175061-153175753 Neighboring gene arginine vasopressin receptor 2 Neighboring gene Rho GTPase activating protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153186395-153186896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153188877-153189377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21073

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Novel mutations in the L1CAM gene support the complexity of L1 syndrome. Bertolin C, et al. J Neurol Sci, 2010 Jul 15. PMID 20447653
    2. Expression of l1 cell adhesion molecule and morphologic features at the invasive front of colorectal cancer. Kajiwara Y, et al. Am J Clin Pathol, 2011 Jul. PMID 21685041
    3. Circulating levels of cell adhesion molecule L1 as a prognostic marker in gastrointestinal stromal tumor patients. Zander H, et al. BMC Cancer, 2011 May 22. PMID 21600041, Free PMC Article
    4. L1 cell adhesion molecule as a novel independent poor prognostic factor in gallbladder carcinoma. Choi SY, et al. Hum Pathol, 2011 Oct. PMID 21496863
    5. Two alcohol binding residues interact across a domain interface of the L1 neural cell adhesion molecule and regulate cell adhesion. Dou X, et al. J Biol Chem, 2011 May 6. PMID 21367865, Free PMC Article

    See all (331) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression of L1 Cell Adhesion Molecule, a Nephronal Principal Cell Marker, in Nephrogenic Adenoma.
      Title: Expression of L1 Cell Adhesion Molecule, a Nephronal Principal Cell Marker, in Nephrogenic Adenoma.
    2. Reciprocal regulation of forkhead box C1 and L1 cell adhesion molecule contributes to triple-negative breast cancer progression.
      Title: Reciprocal regulation of forkhead box C1 and L1 cell adhesion molecule contributes to triple-negative breast cancer progression.
    3. Cyclic increase in the ADAMTS1-L1CAM-EGFR axis promotes the EMT and cervical lymph node metastasis of oral squamous cell carcinoma.
      Title: Cyclic increase in the ADAMTS1-L1CAM-EGFR axis promotes the EMT and cervical lymph node metastasis of oral squamous cell carcinoma.
    4. VAMP7j: A Splice Variant of Human VAMP7 That Modulates Neurite Outgrowth by Regulating L1CAM Transport to the Plasma Membrane.
      Title: VAMP7j: A Splice Variant of Human VAMP7 That Modulates Neurite Outgrowth by Regulating L1CAM Transport to the Plasma Membrane.
    5. A novel splicing variation in L1CAM is responsible for recurrent fetal hydrocephalus.
      Title: A novel splicing variation in L1CAM is responsible for recurrent fetal hydrocephalus.
    6. L1CAM Is Not a Predictive Factor in Early-stage Squamous-cell Cervical Cancer.
      Title: L1CAM Is Not a Predictive Factor in Early-stage Squamous-cell Cervical Cancer.
    7. An Increase in Mucin2 Expression Is Required for Colon Cancer Progression Mediated by L1.
      Title: An Increase in Mucin2 Expression Is Required for Colon Cancer Progression Mediated by L1.
    8. Clinical significance of L1CAM expression in metastatic tubo-ovarian high-grade serous carcinoma.
      Title: Clinical significance of L1CAM expression in metastatic tubo-ovarian high-grade serous carcinoma.
    9. ZNF133 is a potent suppressor in breast carcinogenesis through dampening L1CAM, a driver for tumor progression.
      Title: ZNF133 is a potent suppressor in breast carcinogenesis through dampening L1CAM, a driver for tumor progression.
    10. Knocking out alpha-synuclein in melanoma cells downregulates L1CAM and decreases motility.
      Title: Knocking out alpha-synuclein in melanoma cells downregulates L1CAM and decreases motility.
    Submit: New GeneRIF Correction See all GeneRIFs (215)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-12-02)

    ClinGen Genome Curation PagePubMed
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-12-02)

    ClinGen Genome Curation PagePubMed

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables axon guidance receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein domain specific binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in axon development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in axon guidance IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell adhesion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cell migration IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell-matrix adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chemotaxis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in neuron projection development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of axon extension ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synapse organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in axonal growth cone ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cell surface HDA PubMed 
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in focal adhesion HDA PubMed 
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in neuronal cell body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    neural cell adhesion molecule L1
    Names
    antigen identified by monoclonal antibody R1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009645.4 RefSeqGene

      Range
      5001..29658
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_14

    mRNA and Protein(s)

    1. NM_000425.5 → NP_000416.1  neural cell adhesion molecule L1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_000416.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as FL-L1CAM) differs in the 5' UTR and represents use of an alternate promoter, compared to variant 4. Variants 1 and 4 encode the same isoform (1).
      Source sequence(s)
      BC025843, BC126229, HY119527
      Consensus CDS
      CCDS14733.1
      UniProtKB/Swiss-Prot
      A0AV65, A4ZYW4, B2RMU7, G3XAF4, P32004, Q8TA87
      UniProtKB/TrEMBL
      A8K139
      Conserved Domains (10) summary
      cd05731
      Location:260 → 330
      Ig3_L1-CAM_like; Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
      cd05733
      Location:53 → 130
      Ig6_L1-CAM_like; Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins
      cd05867
      Location:347 → 422
      Ig4_L1-CAM_like; Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
      smart00408
      Location:532 → 594
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:249 → 329
      IG_like; Immunoglobulin like
      cd00063
      Location:612 → 709
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:519 → 608
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:824 → 907
      fn3; Fibronectin type III domain
      pfam13882
      Location:1144 → 1233
      Bravo_FIGEY; Bravo-like intracellular region
      cl11960
      Location:134 → 228
      Ig; Immunoglobulin domain

    2. NM_001143963.2 → NP_001137435.1  neural cell adhesion molecule L1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001137435.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as SV-L1CAM) lacks two alternate in-frame exons, one in the 5' coding region and the other (neuron-specific exon) in the 3' coding region, compared to variant 4. The resulting isoform (3) is shorter, and lacks an internal segment in the N-terminus and is missing a tyrosine-based sorting motif in the C-terminus, compared to isoform 1.
      Source sequence(s)
      AI361399, BC025843, BC126229, EF506611
      Consensus CDS
      CCDS48192.1
      UniProtKB/TrEMBL
      A8K139
      Related
      ENSP00000354712.3, ENST00000361981.7
      Conserved Domains (9) summary
      cd05731
      Location:255 → 325
      Ig3_L1-CAM_like; Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
      cd05733
      Location:48 → 125
      Ig6_L1-CAM_like; Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins
      cd05867
      Location:342 → 417
      Ig4_L1-CAM_like; Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
      smart00408
      Location:527 → 589
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:244 → 324
      IG_like; Immunoglobulin like
      cd00063
      Location:607 → 704
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:819 → 902
      fn3; Fibronectin type III domain
      pfam13882
      Location:1139 → 1224
      Bravo_FIGEY; Bravo-like intracellular region
      cl11960
      Location:129 → 223
      Ig; Immunoglobulin domain

    3. NM_001278116.2 → NP_001265045.1  neural cell adhesion molecule L1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001265045.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents the longest transcript and its 5' UTR structure is inferred based on experimental data in PMID 20799950. Variants 1 and 4 encode the same isoform (1).
      Source sequence(s)
      BC025843, BC126229, DA122729
      Consensus CDS
      CCDS14733.1
      UniProtKB/Swiss-Prot
      A0AV65, A4ZYW4, B2RMU7, G3XAF4, P32004, Q8TA87
      UniProtKB/TrEMBL
      A8K139
      Related
      ENSP00000359077.1, ENST00000370060.7
      Conserved Domains (10) summary
      cd05731
      Location:260 → 330
      Ig3_L1-CAM_like; Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
      cd05733
      Location:53 → 130
      Ig6_L1-CAM_like; Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins
      cd05867
      Location:347 → 422
      Ig4_L1-CAM_like; Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
      smart00408
      Location:532 → 594
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:249 → 329
      IG_like; Immunoglobulin like
      cd00063
      Location:612 → 709
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:519 → 608
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:824 → 907
      fn3; Fibronectin type III domain
      pfam13882
      Location:1144 → 1233
      Bravo_FIGEY; Bravo-like intracellular region
      cl11960
      Location:134 → 228
      Ig; Immunoglobulin domain

    4. NM_024003.3 → NP_076493.1  neural cell adhesion molecule L1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_076493.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame neuron-specific exon in the 3' coding region, compared to variant 4. The resulting isoform (2) is shorter and lacks an internal segment containing a tyrosine-based sorting motif, compared to isoform 1.
      Source sequence(s)
      AI361399, BC025843, BC126229, M74387
      Consensus CDS
      CCDS14734.1
      UniProtKB/TrEMBL
      A8K139
      Related
      ENSP00000355380.4, ENST00000361699.8
      Conserved Domains (10) summary
      cd05731
      Location:260 → 330
      Ig3_L1-CAM_like; Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
      cd05733
      Location:53 → 130
      Ig6_L1-CAM_like; Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins
      cd05867
      Location:347 → 422
      Ig4_L1-CAM_like; Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
      smart00408
      Location:532 → 594
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:249 → 329
      IG_like; Immunoglobulin like
      cd00063
      Location:612 → 709
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:519 → 608
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:824 → 907
      fn3; Fibronectin type III domain
      pfam13882
      Location:1144 → 1229
      Bravo_FIGEY; Bravo-like intracellular region
      cl11960
      Location:134 → 228
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      153861514..153886173 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152135195..152159857 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P32004.2 GenPept UniProtKB/Swiss-Prot:P32004

    Gene LinkOut

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