CADM2

cell adhesion molecule 2, the group of I-set domain containing|V-set domain containing|C2-set domain containing|Nectins and nectin-like molecules|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:84958988-86074429

Previous symbols: [ "IGSF4D" ]

Links

ENSG00000175161 ∙ NCBI:253559 ∙ OMIM:609938 ∙ HGNC:29849 ∙ Uniprot:Q8N3J6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CADM2 gene.

• Inborn genetic diseases (9 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CADM2 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					3	3
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	9	0	4

Variants in CADM2

This is a list of pathogenic ClinVar variants found in the CADM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-85883396-T-C		not specified	Uncertain significance (Aug 12, 2021)
3-85886210-A-T		not specified	Uncertain significance (Nov 22, 2021)
3-85886263-C-T			Benign (Jul 31, 2018)
3-85912505-C-T		not specified	Uncertain significance (Nov 20, 2023)
3-85912527-G-C		not specified	Uncertain significance (Feb 06, 2024)
3-85961477-C-T		not specified	Uncertain significance (Nov 15, 2021)
3-85961548-A-T		not specified	Uncertain significance (Dec 03, 2021)
3-85979212-C-A		not specified	Uncertain significance (Nov 10, 2022)
3-85979226-A-G		not specified	Uncertain significance (Jul 14, 2022)
3-85979286-A-G			Benign (Dec 31, 2019)
3-86065607-C-T		not specified	Uncertain significance (Apr 17, 2023)
3-86065615-T-C			Benign (Jul 10, 2018)
3-86065684-G-C			Benign (May 24, 2018)
3-86065706-G-C		not specified	Uncertain significance (Dec 18, 2023)
3-86066761-A-G		not specified	Uncertain significance (Sep 14, 2022)
3-86066778-A-G		not specified	Uncertain significance (Jun 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CADM2	protein_coding	protein_coding	ENST00000405615	10	1115448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.891	0.109	125707	0	6	125713	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.98	151	237	0.638	0.0000118	2831
Missense in Polyphen		31	81.528	0.38024		1012
Synonymous	-1.60	108	88.8	1.22	0.00000489	875
Loss of Function	3.57	3	20.4	0.147	0.00000101	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adhesion molecule that engages in homo- and heterophilic interactions with the other nectin-like family members, leading to cell aggregation. Important for synapse organization, providing regulated trans-synaptic adhesion. Preferentially binds to oligodendrocytes. {ECO:0000269|PubMed:17967169}.
• Pathway: Type 2 papillary renal cell carcinoma;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.201
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.518
• hipred: Y
• hipred_score: 0.783
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cadm2

Gene ontology

• Biological process: cell adhesion;adherens junction organization
• Cellular component: plasma membrane;integral component of membrane;cell junction;axon;synapse