CXADR

CXADR Ig-like cell adhesion molecule, the group of V-set domain containing|IgCAM CXADR-related subfamily

Basic information

Region (hg38): 21:17513042-17593579

Links

ENSG00000154639 ∙ NCBI:1525 ∙ OMIM:602621 ∙ HGNC:2559 ∙ Uniprot:P78310 ∙ 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 CXADR gene.

• Inborn genetic diseases (13 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXADR 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	1

Variants in CXADR

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

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

Position	Type	Phenotype	Significance	ClinVar
21-17513154-C-T		not specified	Uncertain significance (Jul 12, 2022)
21-17547120-G-A		not specified	Uncertain significance (Mar 06, 2023)
21-17547125-G-A		not specified	Uncertain significance (Oct 24, 2023)
21-17547138-C-T		not specified	Uncertain significance (Nov 17, 2023)
21-17551768-A-G		not specified	Uncertain significance (May 09, 2023)
21-17551861-C-T		not specified	Uncertain significance (Dec 21, 2022)
21-17551887-A-T		not specified	Uncertain significance (Aug 02, 2021)
21-17551895-G-T		not specified	Uncertain significance (Mar 04, 2024)
21-17559055-A-C		not specified	Uncertain significance (Aug 03, 2022)
21-17560709-T-A			Benign (Jun 14, 2018)
21-17560807-G-C		not specified	Uncertain significance (Dec 21, 2023)
21-17561391-C-G		not specified	Uncertain significance (Sep 25, 2023)
21-17561406-C-T		not specified	Uncertain significance (Mar 12, 2024)
21-17561425-G-A		not specified	Likely benign (Oct 12, 2021)
21-17561433-C-T		not specified	Uncertain significance (Jan 26, 2023)
21-17565463-C-T		not specified	Uncertain significance (Apr 12, 2023)
21-17565464-T-A		not specified	Likely benign (Feb 05, 2024)
21-17565479-C-T		not specified	Likely benign (Nov 22, 2023)
21-17565480-G-A		not specified	Uncertain significance (Apr 15, 2022)
21-17565558-C-T		not specified	Uncertain significance (Feb 26, 2024)
21-17565577-G-A		not specified	Uncertain significance (Feb 10, 2023)
21-17565596-T-G		not specified	Likely benign (Dec 28, 2023)
21-17565655-T-C		not specified	Uncertain significance (Jun 21, 2023)
21-17565675-G-A		not specified	Uncertain significance (Nov 02, 2023)
21-17565677-T-G		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXADR	protein_coding	protein_coding	ENST00000284878	7	81198

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.369	0.631	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.979	163	202	0.806	0.0000110	2356
Missense in Polyphen		38	64.707	0.58726		790
Synonymous	-0.234	77	74.4	1.03	0.00000447	713
Loss of Function	3.02	4	17.8	0.225	9.95e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000536	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the epithelial apical junction complex that may function as a homophilic cell adhesion molecule and is essential for tight junction integrity. Also involved in transepithelial migration of leukocytes through adhesive interactions with JAML a transmembrane protein of the plasma membrane of leukocytes. The interaction between both receptors also mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. Upon epithelial CXADR-binding, JAML induces downstream cell signaling events in gamma-delta T-cells through PI3-kinase and MAP kinases. It results in proliferation and production of cytokines and growth factors by T-cells that in turn stimulate epithelial tissues repair. {ECO:0000269|PubMed:11734628, ECO:0000269|PubMed:12297051, ECO:0000269|PubMed:15800062, ECO:0000269|PubMed:19064666, ECO:0000269|PubMed:9096397}.; FUNCTION: (Microbial infection) Acts as a receptor for Coxsackievirus B1 to B6. {ECO:0000269|PubMed:10814575, ECO:0000269|PubMed:14978041}.
• Pathway: Viral myocarditis - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.228

Intolerance Scores

• loftool: 0.319
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.518
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cxadr
• Phenotype: immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: cxadr
• Affected structure: podocyte
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: mitochondrion organization;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;heart development;germ cell migration;epithelial structure maintenance;neutrophil chemotaxis;actin cytoskeleton reorganization;cell-cell junction organization;gamma-delta T cell activation;viral entry into host cell;cardiac muscle fiber development;regulation of immune response;leukocyte migration;negative regulation of cardiac muscle cell proliferation;transepithelial transport;AV node cell to bundle of His cell communication;AV node cell-bundle of His cell adhesion involved in cell communication;regulation of AV node cell action potential
• Cellular component: acrosomal vesicle;extracellular region;nucleoplasm;cytoplasm;plasma membrane;integral component of plasma membrane;cell-cell junction;adherens junction;cell-cell adherens junction;bicellular tight junction;intercalated disc;basolateral plasma membrane;apicolateral plasma membrane;cell junction;filopodium;growth cone;protein-containing complex;neuron projection;cell body;membrane raft
• Molecular function: virus receptor activity;integrin binding;protein binding;beta-catenin binding;PDZ domain binding;cell adhesion molecule binding;connexin binding;cell adhesive protein binding involved in AV node cell-bundle of His cell communication