RDX

radixin, the group of FERM domain containing

Basic information

Region (hg38): 11:109864294-110296712

Previous symbols: [ "DFNB24" ]

Links

ENSG00000137710 ∙ NCBI:5962 ∙ OMIM:179410 ∙ HGNC:9944 ∙ Uniprot:P35241 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 24 (Strong), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 24 (Strong), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 24 (Strong), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 24	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	17226784; 19215054

ClinVar

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

• not provided (104 variants)
• Autosomal recessive nonsyndromic hearing loss 24 (94 variants)
• Inborn genetic diseases (44 variants)
• not specified (28 variants)
• Nonsyndromic Hearing Loss, Recessive (26 variants)
• Hearing impairment (2 variants)
• X-linked Alport syndrome (1 variants)
• Rare genetic deafness (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RDX 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			4	28		32
missense			54	2		56
nonsense	2	2	1			5
start loss						0
frameshift	5	2				7
inframe indel						0
splice donor/acceptor (+/-2bp)	1	1				2
splice region			3	2		5
non coding			105	23	16	144
Total	8	5	164	53	16

Highest pathogenic variant AF is 0.0000131

Variants in RDX

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

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

Position	Type	Phenotype	Significance	ClinVar
11-110093424-G-C		not specified	Uncertain significance (Aug 09, 2021)
11-110136669-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-110136723-C-T		not specified	Uncertain significance (Nov 07, 2022)
11-110136724-G-A		not specified	Likely benign (Aug 03, 2022)
11-110136760-A-G		not specified	Uncertain significance (Sep 12, 2023)
11-110136768-G-A		not specified	Likely benign (Jan 23, 2024)
11-110136886-A-G		not specified	Uncertain significance (Sep 19, 2022)
11-110136915-G-A		not specified	Uncertain significance (May 02, 2023)
11-110136981-A-G		not specified	Uncertain significance (Dec 16, 2023)
11-110136996-C-G		X-linked Alport syndrome	Uncertain significance (Jul 14, 2021)
11-110137018-T-C		not specified	Uncertain significance (Jan 27, 2022)
11-110137021-A-T		not specified	Uncertain significance (Nov 15, 2021)
11-110137023-C-T		not specified	Uncertain significance (Jun 16, 2023)
11-110137028-C-G		not specified	Uncertain significance (Jul 14, 2023)
11-110137039-G-T		not specified	Uncertain significance (May 09, 2023)
11-110137086-T-A		not specified	Uncertain significance (Jul 07, 2022)
11-110137110-G-A		not specified	Uncertain significance (Sep 27, 2021)
11-110137120-G-A		not specified	Uncertain significance (Apr 22, 2022)
11-110137168-A-G		not specified	Uncertain significance (May 15, 2023)
11-110137353-G-T		not specified	Uncertain significance (Jul 08, 2021)
11-110137410-A-G		not specified	Uncertain significance (Oct 26, 2022)
11-110152933-A-C		not specified	Uncertain significance (Apr 13, 2022)
11-110159271-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-110159348-G-A		not specified	Uncertain significance (Oct 27, 2022)
11-110159488-C-G		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RDX	protein_coding	protein_coding	ENST00000405097	14	121843

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.852	0.148	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.908	275	321	0.857	0.0000173	4011
Missense in Polyphen		86	111.95	0.76821		1467
Synonymous	-0.387	111	106	1.05	0.00000557	1035
Loss of Function	4.82	8	41.5	0.193	0.00000246	467

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000220	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.0000983	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably plays a crucial role in the binding of the barbed end of actin filaments to the plasma membrane.
• Disease: DISEASE: Deafness, autosomal recessive, 24 (DFNB24) [MIM:611022]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:17226784}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Tight junction - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Regulation of Actin Cytoskeleton;Developmental Biology;RAGE;Recycling pathway of L1;KitReceptor;L1CAM interactions;Axon guidance;RhoA signaling pathway (Consensus)

Recessive Scores

• pRec: 0.268

Intolerance Scores

• loftool: 0.203
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.506
• hipred: Y
• hipred_score: 0.814
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rdx
• 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); hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; 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); reproductive system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of cell shape;regulation of cell size;positive regulation of gene expression;protein kinase A signaling;microvillus assembly;positive regulation of cell migration;regulation of actin filament bundle assembly;regulation of Rap protein signal transduction;negative regulation of homotypic cell-cell adhesion;negative regulation of GTPase activity;cellular response to platelet-derived growth factor stimulus;regulation of GTPase activity;apical protein localization;establishment of protein localization;negative regulation of cell size;barbed-end actin filament capping;establishment of endothelial barrier;protein localization to plasma membrane;cellular response to thyroid hormone stimulus;regulation of ruffle assembly;positive regulation of G1/S transition of mitotic cell cycle;regulation of organelle assembly;positive regulation of protein localization to early endosome;positive regulation of cellular protein catabolic process;negative regulation of adherens junction organization;positive regulation of early endosome to late endosome transport
• Cellular component: ruffle;extracellular space;plasma membrane;microvillus;cell-cell adherens junction;focal adhesion;apical plasma membrane;lamellipodium;filopodium;T-tubule;midbody;cortical actin cytoskeleton;cleavage furrow;stereocilium;myelin sheath;cell tip;extracellular exosome;cell periphery
• Molecular function: RNA binding;actin binding;protein binding;protein domain specific binding;protein homodimerization activity;cadherin binding;protein kinase A binding;ATPase binding