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CADM3 cell adhesion molecule 3 [ Homo sapiens (human) ]

Gene ID: 57863, updated on 2-Nov-2024

Summary

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Official Symbol
CADM3provided by HGNC
Official Full Name
cell adhesion molecule 3provided by HGNC
Primary source
HGNC:HGNC:17601
See related
Ensembl:ENSG00000162706 MIM:609743; AllianceGenome:HGNC:17601
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
BIgR; NECL1; TSLL1; CMT2FF; IGSF4B; Necl-1; synCAM3
Summary
The protein encoded by this gene is a calcium-independent cell-cell adhesion protein that can form homodimers or heterodimers with other nectin proteins. The encoded protein has both homophilic and heterophilic cell-cell adhesion activity. This gene is reported to be a tumor suppressor gene. [provided by RefSeq, Oct 2016]
Expression
Biased expression in brain (RPKM 106.6), placenta (RPKM 39.2) and 4 other tissues See more
Orthologs
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Genomic context

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See CADM3 in Genome Data Viewer
Location:
1q23.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (159171615..159203313)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (158308647..158340339)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (159141405..159173103)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene absent in melanoma 2 Neighboring gene RAD1 pseudogene 2 Neighboring gene tRNA-Arg (anticodon TCT) 4-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159140542-159141042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1453 Neighboring gene RNA, 5S ribosomal pseudogene 60 Neighboring gene CADM3 antisense RNA 1 Neighboring gene atypical chemokine receptor 1 (Duffy blood group) Neighboring gene mucosal pentraxin 1 (pseudogene)

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. A CADM3 variant causes Charcot-Marie-Tooth disease with marked upper limb involvement. Rebelo AP, et al. Brain, 2021 May 7. PMID 33889941, Free PMC Article
  2. [Effect of NECL1 on the proliferation of T98G glioma cell line]. Gao J, et al. Zhongguo Yi Xue Ke Xue Yuan Xue Bao, 2008 Jun. PMID 18686605
  3. [Neural adhesion molecule NECL1 inhibits migration, invasion, and potentially induces differentiation of glioma cell]. Yin B, et al. Zhongguo Yi Xue Ke Xue Yuan Xue Bao, 2009 Dec. PMID 20078932
  4. Crystal Structure of the cis-Dimer of Nectin-1: implications for the architecture of cell-cell junctions. Narita H, et al. J Biol Chem, 2011 Apr 8. PMID 21325282, Free PMC Article
  5. Clinical significance of low expression of CADM3 in breast cancer and preliminary exploration of related mechanisms. Ren H, et al. BMC Cancer, 2024 Mar 21. PMID 38515057, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical significance of low expression of CADM3 in breast cancer and preliminary exploration of related mechanisms.
    Title: Clinical significance of low expression of CADM3 in breast cancer and preliminary exploration of related mechanisms.
  2. A CADM3 variant causes Charcot-Marie-Tooth disease with marked upper limb involvement.
    Title: A CADM3 variant causes Charcot-Marie-Tooth disease with marked upper limb involvement.
  3. CADM3 expression was increased in retinoblastoma tissues and cells. miR-140-5p inhibited CADM3 expression possibly by targeting the 3'-UTR.
    Title: miR-140-5p suppresses retinoblastoma cell proliferation, migration, and invasion by targeting CEMIP and CADM3.
  4. Nectin-based cell-cell adhesion was formed at the apical side of the junctional adhesion molecule (JAM)-based cell-cell adhesion; cadherin and claudin were recruited to the nectin-3 and JAM-based cell-cell adhesion sites to form AJ- and TJ-like domains.
    Title: Nectin and junctional adhesion molecule are critical cell adhesion molecules for the apico-basal alignment of adherens and tight junctions in epithelial cells.
  5. NECL1 can inhibit the migration and invasion of glioma cells and induce differentiation.
    Title: [Neural adhesion molecule NECL1 inhibits migration, invasion, and potentially induces differentiation of glioma cell].
  6. A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration.
    Title: Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration.
  7. Findings clearly reveal the structural basis for the cis-dimerization of nectins through the first Ig-like domains.
    Title: Crystal Structure of the cis-Dimer of Nectin-1: implications for the architecture of cell-cell junctions.
  8. A link might exist between NECL1 and the extracellular matrix protein OPN in inhibiting the migration and invasion of U251 glioma ce
    Title: Nectin-like molecule 1 inhibits the migration and invasion of U251 glioma cells by regulating the expression of an extracellular matrix protein osteopontin.
  9. NECL1 may inhibit the proliferation of T98G cells by inducing its apoptosis.
    Title: [Effect of NECL1 on the proliferation of T98G glioma cell line].
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: New genetic associations detected in a host response study to hepatitis B vaccine.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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

Associated conditions

Description Tests
Charcot-Marie-Tooth disease, axonal, type 2FF
MedGen: C5561981 OMIM: 619519 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
A genome-wide association scan on the levels of markers of inflammation in Sardinians reveals associations that underpin its complex regulation.
EBI GWAS Catalog
Genome-wide association with select biomarker traits in the Framingham Heart Study.
EBI GWAS Catalog

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

Clone Names

  • FLJ10698

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Process Evidence Code Pubs
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Component Evidence Code Pubs
located_in cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
is_active_in presynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
cell adhesion molecule 3
Names
TSLC1-like 1
brain immunoglobulin receptor
immunoglobulin superfamily member 4B
synaptic cell adhesion molecule 3

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_051933.1 RefSeqGene

    Range
    5052..36750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001127173.3 → NP_001120645.1  cell adhesion molecule 3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001120645.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF363367, DA221489, HY346099
    Consensus CDS
    CCDS44251.1
    UniProtKB/Swiss-Prot
    Q8IZQ9, Q8N126, Q9NVJ5, Q9UJP1
    Related
    ENSP00000357107.4, ENST00000368125.9
    Conserved Domains (5) summary
    smart00294
    Location:354 → 369
    4.1m; putative band 4.1 homologues' binding motif
    cd05882
    Location:32 → 126
    Ig1_Necl-1; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1, also known as cell adhesion molecule3 (CADM3))
    cd07705
    Location:147 → 229
    Ig2_Necl-1; Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1, also known as cell adhesion molecule3 (CADM3))
    smart00410
    Location:245 → 316
    IG_like; Immunoglobulin like
    pfam13895
    Location:237 → 302
    Ig_2; Immunoglobulin domain

  2. NM_001346510.2 → NP_001333439.1  cell adhesion molecule 3 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AL035403
    UniProtKB/Swiss-Prot
    Q8N126

  3. NM_021189.5 → NP_067012.1  cell adhesion molecule 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_067012.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF363367, AK289541, AL035403, HY346099
    Consensus CDS
    CCDS1182.1
    UniProtKB/Swiss-Prot
    Q8N126
    Related
    ENSP00000357106.4, ENST00000368124.8
    Conserved Domains (4) summary
    cd05882
    Location:66 → 160
    Ig1_Necl-1; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1, also known as cell adhesion molecule3 (CADM3))
    cd07705
    Location:181 → 263
    Ig2_Necl-1; Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1, also known as cell adhesion molecule3 (CADM3))
    smart00410
    Location:279 → 350
    IG_like; Immunoglobulin like
    pfam13895
    Location:271 → 336
    Ig_2; 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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    159171615..159203313
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024448760.2 → XP_024304528.1  cell adhesion molecule 3 isoform X1

    Conserved Domains (4) summary
    smart00294
    Location:437 → 452
    4.1m; putative band 4.1 homologues' binding motif
    cd05882
    Location:115 → 209
    Ig1_Necl-1; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1, also known as cell adhesion molecule3 (CADM3))
    cd07705
    Location:230 → 312
    Ig2_Necl-1; Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1, also known as cell adhesion molecule3 (CADM3))
    smart00410
    Location:328 → 399
    IG_like; Immunoglobulin like

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    158308647..158340339
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337944.1 → XP_054193919.1  cell adhesion molecule 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N126.1 GenPept UniProtKB/Swiss-Prot:Q8N126

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