JCAD

protein-coding

junctional cadherin 5 associated

Gene summary

This gene encodes an endothelial cell-to-cell junction protein. Naturally occurring mutations in this gene are associated with coronary artery disease, late onset alzheimer disease, and emphysema distribution. [provided by RefSeq, Mar 2017]

Previous symbols:

KIAA1462

MANE transcript

NM_020848.4

Inheritance

—

ClinVar variants

U:256B:31

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr10:30,012,803-30,115,494

External References & Databases

Ensembl (ENSG00000165757)

Transcript & Mutation Effects

hg38 • Region Span ~102.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JCAD variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 266

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020848.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	1 clinvar	5
missense			251 clinvar	24 clinvar	4 clinvar	279
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	256	26	5	287

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020848.4	RefSeq	NP_065899.1	3	MANE Select
ENST00000375377.2	Ensembl	ENSP00000364526.1	3	MANE Select
NM_001350001.2	RefSeq	NP_001336930.1	2	Standard
NM_001350021.2	RefSeq	NP_001336950.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375377
Coding exons: 3
Length: 102695
Individuals with no LoFs: 124800
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 124838
p: 0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.253	799	779	1.03	0.0000488	8872
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000064	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.00015	0.00014	rare
European (Non-Finnish)	0.00018	0.00016	rare
South Asian	0.00020	0.00020	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0891

Intolerance Scores

RVIS EVS: 1.22
RVIS percentile EVS: 93.16

Essentials

Essential (gene trap): N