CADM3

cell adhesion molecule 3, the group of V-set domain containing|C2-set domain containing|Nectins and nectin-like molecules

Basic information

Region (hg38): 1:159171608-159203313

Previous symbols: [ "IGSF4B" ]

Links

ENSG00000162706 ∙ NCBI:57863 ∙ OMIM:609743 ∙ HGNC:17601 ∙ Uniprot:Q8N126 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Charcot-Marie-Tooth disease, axonal, type 2FF (Limited), mode of inheritance: AD
• Charcot-Marie-Tooth disease, axonal, type 2FF (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Charcot-Marie-Tooth disease, axonal, type 2FF	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	33889941

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CADM3 gene.

• Inborn genetic diseases (14 variants)
• Charcot-Marie-Tooth disease, axonal, type 2FF (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CADM3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			15			15
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in CADM3

This is a list of pathogenic ClinVar variants found in the CADM3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-159171815-G-A		Inborn genetic diseases	Uncertain significance (Dec 26, 2023)
1-159171838-A-C		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)
1-159191945-C-T		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)
1-159191947-T-C		Inborn genetic diseases	Uncertain significance (Dec 28, 2023)
1-159191983-G-A		Inborn genetic diseases	Uncertain significance (Apr 13, 2022)
1-159192007-G-A		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
1-159192042-T-G			Likely benign (Feb 01, 2023)
1-159192608-C-T		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
1-159192614-C-T		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)
1-159192718-G-A		Inborn genetic diseases	Uncertain significance (Jan 02, 2024)
1-159192730-G-C		Malignant tumor of prostate	Uncertain significance (-)
1-159193421-AG-A		Charcot-Marie-Tooth disease, axonal, type 2FF	Uncertain significance (Oct 26, 2022)
1-159193453-A-G		Charcot-Marie-Tooth disease, axonal, type 2FF	Likely pathogenic (Mar 29, 2024)
1-159193458-T-C		Inborn genetic diseases	Uncertain significance (May 18, 2023)
1-159193467-C-T		Inborn genetic diseases	Uncertain significance (May 17, 2023)
1-159193507-G-A		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
1-159193872-G-A		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
1-159193944-A-G		Inborn genetic diseases	Uncertain significance (Jul 05, 2023)
1-159193968-A-G		Inborn genetic diseases	Uncertain significance (Dec 17, 2023)
1-159193971-G-A		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
1-159196392-C-A		Inborn genetic diseases	Uncertain significance (Jun 27, 2022)
1-159196401-T-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
1-159196406-G-A		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
1-159199789-G-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
1-159199798-G-T		Charcot-Marie-Tooth disease, axonal, type 2FF	Uncertain significance (Apr 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CADM3	protein_coding	protein_coding	ENST00000368124	10	31705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.934	0.0661	125739	0	5	125744	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	168	242	0.694	0.0000137	2789
Missense in Polyphen		42	81.713	0.514		928
Synonymous	0.0532	99	99.7	0.993	0.00000631	867
Loss of Function	3.74	3	21.9	0.137	0.00000115	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000278	0.0000264
Middle Eastern	0.0000556	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the cell-cell adhesion. Has both calcium- independent homophilic cell-cell adhesion activity and calcium- independent heterophilic cell-cell adhesion activity with IGSF4, NECTIN1 and NECTIN3. Interaction with EPB41L1 may regulate structure or function of cell-cell junctions (By similarity). {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Splicing factor NOVA regulated synaptic proteins;Cell-cell junction organization;Nectin/Necl trans heterodimerization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.459

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.235
• hipred: Y
• hipred_score: 0.685
• ghis: 0.679

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cadm3
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;protein localization;adherens junction organization
• Cellular component: plasma membrane;cell-cell junction;parallel fiber to Purkinje cell synapse;integral component of presynaptic membrane
• Molecular function: protein homodimerization activity