DTX2

deltex E3 ubiquitin ligase 2, the group of Ring finger proteins

Basic information

Region (hg38): 7:76461676-76505995

Links

ENSG00000091073 ∙ NCBI:113878 ∙ OMIM:613141 ∙ HGNC:15973 ∙ Uniprot:Q86UW9 ∙ 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 DTX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DTX2 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				6	1	7
missense			45	4		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	45	10	1

Variants in DTX2

This is a list of pathogenic ClinVar variants found in the DTX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-76480525-A-G		not specified	Uncertain significance (Jul 07, 2024)
7-76480543-G-A		not specified	Uncertain significance (Dec 26, 2023)
7-76480598-C-T		not specified	Uncertain significance (Dec 13, 2022)
7-76480612-A-G		not specified	Uncertain significance (Jul 27, 2022)
7-76480621-G-A		not specified	Uncertain significance (Sep 27, 2021)
7-76480666-C-T		not specified	Uncertain significance (Sep 08, 2024)
7-76480671-T-G		not specified	Uncertain significance (Aug 16, 2021)
7-76480702-T-G		not specified	Uncertain significance (Apr 13, 2023)
7-76480729-C-A		not specified	Uncertain significance (Aug 10, 2024)
7-76480765-C-T		not specified	Uncertain significance (Jun 05, 2023)
7-76480774-A-C		not specified	Uncertain significance (Oct 27, 2023)
7-76482532-A-G		not specified	Uncertain significance (Jul 12, 2023)
7-76482562-G-A		not specified	Uncertain significance (Oct 04, 2024)
7-76482570-G-A		not specified	Uncertain significance (May 02, 2024)
7-76482588-G-A		not specified	Uncertain significance (Dec 18, 2023)
7-76482639-C-G		not specified	Uncertain significance (Oct 24, 2024)
7-76482644-G-T		not specified	Uncertain significance (Jun 05, 2023)
7-76482665-C-T			Likely benign (Nov 01, 2023)
7-76482676-C-A		not specified	Uncertain significance (Mar 25, 2024)
7-76482703-A-G		not specified	Uncertain significance (May 04, 2022)
7-76482708-A-G		not specified	Likely benign (Aug 04, 2021)
7-76482739-G-T		not specified	Uncertain significance (Jan 22, 2024)
7-76482759-C-T		not specified	Uncertain significance (Sep 14, 2023)
7-76482760-G-A		not specified	Uncertain significance (Dec 17, 2023)
7-76482798-G-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DTX2	protein_coding	protein_coding	ENST00000324432	9	44320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0289	0.971	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.931	325	376	0.865	0.0000236	3957
Missense in Polyphen		126	162.21	0.77679		1737
Synonymous	0.179	162	165	0.982	0.0000117	1266
Loss of Function	3.09	7	23.0	0.304	0.00000107	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000123
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000137	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000164	0.000163

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. Mediates the antineural activity of Notch, possibly by inhibiting the transcriptional activation mediated by MATCH1. Functions as a ubiquitin ligase protein in vitro, suggesting that it may regulate the Notch pathway via some ubiquitin ligase activity.
• Pathway: Notch signaling pathway - Homo sapiens (human);Notch Signaling Pathway;Notch Signaling Pathway;Signal Transduction;Notch;Signaling by NOTCH1;Signaling by NOTCH;Activated NOTCH1 Transmits Signal to the Nucleus (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.514
• rvis_EVS: -0.68
• rvis_percentile_EVS: 15.36

Haploinsufficiency Scores

• pHI: 0.258
• hipred: Y
• hipred_score: 0.725
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.548

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dtx2

Gene ontology

• Biological process: Notch signaling pathway;protein ubiquitination
• Cellular component: nucleoplasm;cytoplasm;nuclear membrane
• Molecular function: protein binding;zinc ion binding;transferase activity