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

Gene ID: 3897, updated on 1-Jun-2020

Summary

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
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; 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

Genomic context

See L1CAM in Genome Data Viewer
Location:
Xq28
Exon count:
29
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (153861514..153886173, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153126969..153151628, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene PDZ domain containing 4 Neighboring gene CYCS pseudogene 45 Neighboring gene lung carcinoma-associated 10 Neighboring gene arginine vasopressin receptor 2 Neighboring gene Rho GTPase activating protein 4

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

ClinGen Genome Curation Page

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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

NCBI Reference Sequences (RefSeq)

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_009645.3 RefSeqGene

    Range
    38210..52708
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000425.5NP_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
    P32004
    Conserved Domains (10) summary
    cd05731
    Location:260330
    Ig3_L1-CAM_like; Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
    cd05733
    Location:53130
    Ig6_L1-CAM_like; Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins
    cd05867
    Location:347422
    Ig4_L1-CAM_like; Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
    smart00408
    Location:532594
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:249329
    IG_like; Immunoglobulin like
    cd00063
    Location:612709
    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:519608
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:824907
    fn3; Fibronectin type III domain
    pfam13882
    Location:11441233
    Bravo_FIGEY; Bravo-like intracellular region
    cl11960
    Location:134228
    Ig; Immunoglobulin domain
  2. NM_001143963.2NP_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/Swiss-Prot
    P32004
    Related
    ENSP00000354712.3, ENST00000361981.7
    Conserved Domains (9) summary
    cd05731
    Location:255325
    Ig3_L1-CAM_like; Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
    cd05733
    Location:48125
    Ig6_L1-CAM_like; Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins
    cd05867
    Location:342417
    Ig4_L1-CAM_like; Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
    smart00408
    Location:527589
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:244324
    IG_like; Immunoglobulin like
    cd00063
    Location:607704
    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:819902
    fn3; Fibronectin type III domain
    pfam13882
    Location:11391224
    Bravo_FIGEY; Bravo-like intracellular region
    cl11960
    Location:129223
    Ig; Immunoglobulin domain
  3. NM_001278116.2NP_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
    P32004
    Related
    ENSP00000359077.1, ENST00000370060.7
    Conserved Domains (10) summary
    cd05731
    Location:260330
    Ig3_L1-CAM_like; Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
    cd05733
    Location:53130
    Ig6_L1-CAM_like; Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins
    cd05867
    Location:347422
    Ig4_L1-CAM_like; Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
    smart00408
    Location:532594
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:249329
    IG_like; Immunoglobulin like
    cd00063
    Location:612709
    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:519608
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:824907
    fn3; Fibronectin type III domain
    pfam13882
    Location:11441233
    Bravo_FIGEY; Bravo-like intracellular region
    cl11960
    Location:134228
    Ig; Immunoglobulin domain
  4. NM_024003.3NP_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/Swiss-Prot
    P32004
    Related
    ENSP00000355380.4, ENST00000361699.8
    Conserved Domains (10) summary
    cd05731
    Location:260330
    Ig3_L1-CAM_like; Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
    cd05733
    Location:53130
    Ig6_L1-CAM_like; Sixth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins
    cd05867
    Location:347422
    Ig4_L1-CAM_like; Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM)
    smart00408
    Location:532594
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:249329
    IG_like; Immunoglobulin like
    cd00063
    Location:612709
    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:519608
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:824907
    fn3; Fibronectin type III domain
    pfam13882
    Location:11441229
    Bravo_FIGEY; Bravo-like intracellular region
    cl11960
    Location:134228
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

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