JCAD

junctional cadherin 5 associated

Basic information

Region (hg38): 10:30012802-30115494

Previous symbols: [ "KIAA1462" ]

Links

ENSG00000165757 ∙ NCBI:57608 ∙ OMIM:614398 ∙ HGNC:29283 ∙ Uniprot:Q9P266 ∙ 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 JCAD gene.

• Inborn genetic diseases (27 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JCAD 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				2	1	3
missense			26	2	4	32
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	27	4	5

Variants in JCAD

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

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

Position	Type	Phenotype	Significance	ClinVar
10-30026119-T-G		not specified	Uncertain significance (Sep 06, 2022)
10-30026169-T-C		not specified	Uncertain significance (Apr 13, 2022)
10-30026252-G-A			Benign (Oct 09, 2017)
10-30026262-C-A		not specified	Uncertain significance (Sep 20, 2023)
10-30026293-G-A			Benign (Jul 20, 2018)
10-30026310-C-T			Benign (Jul 04, 2018)
10-30026339-C-G		not specified	Uncertain significance (Feb 28, 2024)
10-30026339-C-T		not specified	Uncertain significance (Nov 08, 2022)
10-30026340-G-A		not specified	Uncertain significance (Dec 01, 2022)
10-30026375-C-T		not specified	Uncertain significance (Feb 03, 2022)
10-30026390-C-T		not specified	Uncertain significance (Jan 24, 2023)
10-30026399-G-A		not specified	Uncertain significance (Dec 13, 2022)
10-30026429-A-G		not specified	Uncertain significance (Dec 04, 2023)
10-30026456-T-C		not specified	Uncertain significance (Dec 20, 2023)
10-30026465-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-30026478-G-A		not specified	Uncertain significance (Oct 30, 2023)
10-30026484-T-C		not specified	Uncertain significance (Nov 09, 2021)
10-30026544-C-T		not specified	Uncertain significance (May 17, 2023)
10-30026643-C-G		not specified	Uncertain significance (May 30, 2023)
10-30026645-C-T		not specified	Uncertain significance (Dec 28, 2022)
10-30026646-G-C		not specified	Uncertain significance (May 16, 2023)
10-30026685-T-C		not specified	Likely benign (Jan 16, 2024)
10-30026694-C-T		not specified	Uncertain significance (Dec 15, 2023)
10-30026698-C-A		not specified	Uncertain significance (Aug 18, 2023)
10-30026721-C-G		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JCAD	protein_coding	protein_coding	ENST00000375377	3	102695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00300	0.997	124800	0	38	124838	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.253	799	779	1.03	0.0000488	8872
Missense in Polyphen		180	201.72	0.89233		2683
Synonymous	-1.35	357	326	1.10	0.0000227	2762
Loss of Function	4.27	13	43.3	0.300	0.00000248	511

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000296	0.000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.000146	0.000139
European (Non-Finnish)	0.000177	0.000159
Middle Eastern	0.0000556	0.0000556
South Asian	0.000196	0.000196
Other	0.000170	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0891

Intolerance Scores

• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.16

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.273
• ghis: 0.484

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Jcad

Gene ontology

• Biological process: cell adhesion;positive regulation of MAPK cascade;positive regulation of cell migration involved in sprouting angiogenesis;positive regulation of vascular endothelial growth factor signaling pathway;positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis
• Cellular component: cell-cell junction;adherens junction;ruffle membrane;perinuclear region of cytoplasm