DTX4

deltex E3 ubiquitin ligase 4, the group of Ring finger proteins

Basic information

Region (hg38): 11:59171430-59208588

Links

ENSG00000110042 ∙ NCBI:23220 ∙ OMIM:616110 ∙ HGNC:29151 ∙ Uniprot:Q9Y2E6 ∙ 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 DTX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DTX4 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					3	3
missense			30		1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	33	0	4

Variants in DTX4

This is a list of pathogenic ClinVar variants found in the DTX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59172638-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-59172663-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-59172695-G-A		not specified	Uncertain significance (Jan 29, 2024)
11-59172708-C-T		not specified	Uncertain significance (May 29, 2024)
11-59172749-C-G		not specified	Uncertain significance (Dec 13, 2023)
11-59172803-A-T		not specified	Uncertain significance (Sep 12, 2023)
11-59172804-C-G		not specified	Uncertain significance (Sep 20, 2023)
11-59181760-G-C		not specified	Uncertain significance (Nov 03, 2023)
11-59181765-T-C		not specified	Uncertain significance (Jun 11, 2021)
11-59181781-C-T		not specified	Uncertain significance (Apr 07, 2022)
11-59181822-A-C		not specified	Uncertain significance (Apr 17, 2023)
11-59181829-C-G		not specified	Uncertain significance (Nov 21, 2022)
11-59181835-C-T		not specified	Uncertain significance (Dec 06, 2023)
11-59181961-G-A		not specified	Uncertain significance (Feb 06, 2024)
11-59181981-C-T		not specified	Uncertain significance (Feb 10, 2022)
11-59181987-C-T		not specified	Uncertain significance (Mar 15, 2024)
11-59181990-C-T		not specified	Uncertain significance (Aug 02, 2023)
11-59181991-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-59182005-A-G		not specified	Uncertain significance (Jan 23, 2024)
11-59182038-G-A		not specified	Uncertain significance (Mar 23, 2023)
11-59182107-T-C		not specified	Uncertain significance (May 18, 2023)
11-59182121-G-A		not specified	Uncertain significance (Nov 08, 2021)
11-59182224-C-T		not specified	Uncertain significance (Jan 23, 2023)
11-59182246-T-C		not specified	Uncertain significance (Oct 20, 2023)
11-59182297-T-G			Benign (Apr 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DTX4	protein_coding	protein_coding	ENST00000227451	9	37158

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.217	0.783	124927	0	18	124945	0.0000720

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	284	375	0.758	0.0000221	3956
Missense in Polyphen		90	132.03	0.68167		1333
Synonymous	-0.0192	151	151	1.00	0.00000905	1295
Loss of Function	3.47	6	24.6	0.244	0.00000128	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000667	0.0000632
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000555
Finnish	0.0000497	0.0000464
European (Non-Finnish)	0.0000977	0.0000972
Middle Eastern	0.0000557	0.0000555
South Asian	0.000102	0.0000980
Other	0.000168	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations (By similarity). Functions as a ubiquitin ligase protein in vivo, mediating 'Lys48'-linked polyubiquitination and promoting degradation of TBK1, targeting to TBK1 requires interaction with NLRP4. {ECO:0000250, ECO:0000269|PubMed:22388039}.
• Pathway: Notch signaling pathway - Homo sapiens (human);NOTCH-Ncore;Notch Signaling Pathway;Pathways Affected in Adenoid Cystic Carcinoma;Notch Signaling Pathway;Signal Transduction;IRF3 mediated activation of type 1 IFN;ZBP1(DAI) mediated induction of type I IFNs;STING mediated induction of host immune responses;Regulation of innate immune responses to cytosolic DNA;Innate Immune System;Immune System;IRF3-mediated induction of type I IFN;Signaling by NOTCH1;Signaling by NOTCH;Cytosolic sensors of pathogen-associated DNA ;Activated NOTCH1 Transmits Signal to the Nucleus (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.377
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.42

Haploinsufficiency Scores

• pHI: 0.262
• hipred: Y
• hipred_score: 0.580
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dtx4

Gene ontology

• Biological process: Notch signaling pathway;protein ubiquitination;regulation of type I interferon production
• Cellular component: cytosol
• Molecular function: ubiquitin-protein transferase activity;zinc ion binding