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

Summary

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: mouse all
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Genomic context

Location:: 1q23.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (159171615..159203313)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (158308647..158340339)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (159141405..159173103)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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].
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.
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.
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.
NECL1 may inhibit the proliferation of T98G cells by inducing its apoptosis.
Title: [Effect of NECL1 on the proliferation of T98G glioma cell line].
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 EBI GWAS CatalogPubMed
Genome-wide association with select biomarker traits in the Framingham Heart Study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S2635 (e-PCR), detects polymorphism
- UniSTS:62214

D1S3501 (e-PCR)
- UniSTS:83215

RH12336 (e-PCR)
- UniSTS:15916

STS-T65055 (e-PCR)
- UniSTS:41065

A001Y21 (e-PCR)
- UniSTS:25766

RH11558 (e-PCR)
- UniSTS:56535

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

NG_051933.1 RefSeqGene

Range

5052..36750

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

159171615..159203313

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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