DTX3

deltex E3 ubiquitin ligase 3, the group of Ring finger proteins

Basic information

Region (hg38): 12:57604622-57609804

Links

ENSG00000178498 ∙ NCBI:196403 ∙ OMIM:613142 ∙ HGNC:24457 ∙ Uniprot:Q8N9I9 ∙ 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 DTX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DTX3 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						0
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in DTX3

This is a list of pathogenic ClinVar variants found in the DTX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57606873-G-C		not specified	Uncertain significance (Jan 07, 2022)
12-57606931-A-G		not specified	Uncertain significance (Apr 06, 2024)
12-57606961-C-A		not specified	Uncertain significance (Aug 27, 2024)
12-57606984-C-T		not specified	Uncertain significance (Aug 07, 2024)
12-57606985-G-A		not specified	Uncertain significance (Aug 02, 2022)
12-57607069-C-G		not specified	Uncertain significance (Dec 01, 2022)
12-57607071-G-A		not specified	Uncertain significance (May 26, 2024)
12-57607102-A-G		not specified	Uncertain significance (Sep 27, 2022)
12-57607160-G-C		not specified	Uncertain significance (Mar 16, 2022)
12-57607167-C-G		not specified	Uncertain significance (Jan 26, 2023)
12-57607188-G-C		not specified	Uncertain significance (Dec 03, 2024)
12-57607221-G-A		not specified	Uncertain significance (Oct 26, 2021)
12-57607269-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-57607278-C-T		not specified	Uncertain significance (Jul 30, 2024)
12-57607281-C-G		not specified	Uncertain significance (Jun 23, 2023)
12-57607287-C-T		not specified	Uncertain significance (Oct 13, 2023)
12-57607303-C-T		not specified	Uncertain significance (Aug 08, 2023)
12-57607317-C-T		not specified	Uncertain significance (Apr 12, 2022)
12-57607324-G-T		not specified	Uncertain significance (Oct 01, 2024)
12-57607455-G-T		not specified	Uncertain significance (Jan 23, 2024)
12-57607590-G-A		not specified	Uncertain significance (Oct 02, 2023)
12-57609093-C-T		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DTX3	protein_coding	protein_coding	ENST00000548198	4	5183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.888	0.112	124791	0	4	124795	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	134	224	0.598	0.0000143	2202
Missense in Polyphen		9	45.896	0.19609		466
Synonymous	0.944	82	93.6	0.876	0.00000569	774
Loss of Function	2.87	1	11.5	0.0870	5.62e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000584	0.0000584
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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. Probably acts both as a positive and negative regulator of Notch, depending on the developmental and cell context (By similarity). Functions as an ubiquitin ligase protein in vitro, suggesting that it may regulate the Notch pathway via some ubiquitin ligase activity. {ECO:0000250}.
• Pathway: Notch signaling pathway - Homo sapiens (human);Notch Signaling Pathway;Notch Signaling Pathway;Notch (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.191
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.265
• hipred: Y
• hipred_score: 0.707
• ghis: 0.688

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.460

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dtx3

Gene ontology

• Biological process: Notch signaling pathway;protein ubiquitination
• Cellular component: cytoplasm
• Molecular function: protein binding;transferase activity;metal ion binding