TAX1BP3

Tax1 binding protein 3, the group of PDZ domain containing

Basic information

Region (hg38): 17:3662894-3668679

Links

ENSG00000213977 ∙ NCBI:30851 ∙ OMIM:616484 ∙ HGNC:30684 ∙ Uniprot:O14907 ∙ 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 TAX1BP3 gene.

• Ocular cystinosis (10 variants)
• Nephropathic cystinosis (10 variants)
• not provided (8 variants)
• Inborn genetic diseases (8 variants)
• TAX1BP3-related arrhythmogenic right ventricular cardiomyopathy (1 variants)
• Primary familial dilated cardiomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAX1BP3 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	2
missense			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			6		4	10
Total	0	0	17	0	7

Variants in TAX1BP3

This is a list of pathogenic ClinVar variants found in the TAX1BP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3662896-G-A		Nephropathic cystinosis • Ocular cystinosis	Uncertain significance (Jan 13, 2018)
17-3662915-G-C		Ocular cystinosis • Nephropathic cystinosis	Benign (Jan 13, 2018)
17-3662919-G-A		Ocular cystinosis • Nephropathic cystinosis	Benign (Jan 12, 2018)
17-3662937-G-C		Nephropathic cystinosis • Ocular cystinosis	Uncertain significance (Jan 13, 2018)
17-3662938-C-T		Nephropathic cystinosis • Ocular cystinosis	Benign (Jan 13, 2018)
17-3662953-C-T		Ocular cystinosis • Nephropathic cystinosis	Uncertain significance (Jan 13, 2018)
17-3662962-A-T		Nephropathic cystinosis • Ocular cystinosis	Uncertain significance (Jan 13, 2018)
17-3662997-C-T		Ocular cystinosis • Nephropathic cystinosis	Uncertain significance (Jan 12, 2018)
17-3663031-G-A		Ocular cystinosis • Nephropathic cystinosis	Uncertain significance (Jan 13, 2018)
17-3663086-A-G		Nephropathic cystinosis • Ocular cystinosis	Uncertain significance (Jan 13, 2018)
17-3663755-A-G			Benign (Jan 22, 2024)
17-3663765-G-T		not specified	Uncertain significance (Jun 21, 2023)
17-3663767-T-C			Uncertain significance (Jul 13, 2023)
17-3663771-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-3663792-G-A		not specified	Uncertain significance (Aug 14, 2023)
17-3663794-G-A			Uncertain significance (Jul 07, 2023)
17-3663869-A-G		not specified	Uncertain significance (Feb 13, 2024)
17-3664199-A-G		TAX1BP3-related arrhythmogenic right ventricular cardiomyopathy • Primary familial dilated cardiomyopathy	Conflicting classifications of pathogenicity (Apr 16, 2020)
17-3664222-C-G			Benign (Jan 29, 2024)
17-3664257-G-A		not specified	Uncertain significance (Sep 14, 2022)
17-3664265-T-C		not specified	Uncertain significance (Jan 16, 2024)
17-3664270-A-G			Benign (Nov 12, 2022)
17-3664289-C-A			Likely benign (Aug 25, 2023)
17-3664679-C-A			Uncertain significance (May 12, 2023)
17-3664705-G-T		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAX1BP3	protein_coding	protein_coding	ENST00000225525	4	5781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00524	0.722	125721	0	6	125727	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.896	60	83.0	0.723	0.00000544	791
Missense in Polyphen		24	35.532	0.67545		344
Synonymous	0.782	27	32.7	0.826	0.00000217	250
Loss of Function	0.762	4	6.02	0.665	2.55e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate a number of protein-protein interactions by competing for PDZ domain binding sites. Binds CTNNB1 and may thereby act as an inhibitor of the Wnt signaling pathway. Competes with LIN7A for KCNJ4 binding, and thereby promotes KCNJ4 internalization. May play a role in the Rho signaling pathway. May play a role in activation of CDC42 by the viral protein HPV16 E6. {ECO:0000269|PubMed:10940294, ECO:0000269|PubMed:16855024, ECO:0000269|PubMed:21139582}.
• Pathway: Signal Transduction;RHO GTPases Activate Rhotekin and Rhophilins;RHO GTPase Effectors;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.684
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.131
• hipred: Y
• hipred_score: 0.685
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tax1bp3

Zebrafish Information Network

• Gene name: tax1bp3
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: Rho protein signal transduction;negative regulation of cell population proliferation;Wnt signaling pathway;negative regulation of Wnt signaling pathway;activation of GTPase activity;negative regulation of protein localization to cell surface
• Cellular component: fibrillar center;cytoplasm;cytosol;plasma membrane;actin cytoskeleton;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: protein binding;beta-catenin binding;protein C-terminus binding