CADM4

cell adhesion molecule 4, the group of Nectins and nectin-like molecules|V-set domain containing|C2-set domain containing

Basic information

Region (hg38): 19:43622368-43639850

Previous symbols: [ "IGSF4C" ]

Links

ENSG00000105767 ∙ NCBI:199731 ∙ OMIM:609744 ∙ HGNC:30825 ∙ Uniprot:Q8NFZ8 ∙ 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 CADM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CADM4 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in CADM4

This is a list of pathogenic ClinVar variants found in the CADM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-43624201-C-T		not specified	Uncertain significance (Oct 25, 2022)
19-43625111-G-A		not specified	Uncertain significance (Mar 06, 2023)
19-43625158-G-A		not specified	Uncertain significance (Jun 11, 2024)
19-43625231-T-G		not specified	Uncertain significance (Mar 14, 2024)
19-43625993-T-C		not specified	Uncertain significance (Dec 22, 2023)
19-43626168-G-A		not specified	Uncertain significance (Dec 06, 2021)
19-43626219-C-T		not specified	Uncertain significance (Oct 18, 2021)
19-43626251-G-C		not specified	Uncertain significance (Apr 05, 2023)
19-43627271-C-G		not specified	Uncertain significance (Aug 08, 2022)
19-43627722-G-C		not specified	Uncertain significance (Aug 21, 2023)
19-43639775-G-T		not specified	Uncertain significance (May 11, 2022)
19-43639786-C-A		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CADM4	protein_coding	protein_coding	ENST00000222374	9	17472

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00238	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	130	253	0.514	0.0000174	2466
Missense in Polyphen		37	91.108	0.40611		882
Synonymous	2.75	73	110	0.666	0.00000800	819
Loss of Function	3.90	0	17.7	0.00	7.55e-7	212

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the cell-cell adhesion. Has calcium- and magnesium-independent cell-cell adhesion activity. May have tumor- suppressor activity. {ECO:0000269|PubMed:16261159}.

Recessive Scores

• pRec: 0.0888

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.285
• hipred: Y
• hipred_score: 0.707
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.275

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cadm4
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: cadm4
• Affected structure: bulbus arteriosus
• Phenotype tag: abnormal
• Phenotype quality: elongated

Gene ontology

• Biological process: cell adhesion
• Cellular component: integral component of membrane