DTX1

deltex E3 ubiquitin ligase 1, the group of Ring finger proteins

Basic information

Region (hg38): 12:113056730-113098028

Links

ENSG00000135144 ∙ NCBI:1840 ∙ OMIM:602582 ∙ HGNC:3060 ∙ Uniprot:Q86Y01 ∙ 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 DTX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DTX1 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	1	3
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	1

Variants in DTX1

This is a list of pathogenic ClinVar variants found in the DTX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113058256-G-T		not specified	Uncertain significance (Sep 13, 2023)
12-113058317-C-T		not specified	Uncertain significance (Aug 05, 2023)
12-113058364-G-A		not specified	Uncertain significance (Jun 21, 2021)
12-113058396-G-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
12-113058412-A-G		not specified	Uncertain significance (May 26, 2024)
12-113058440-G-A		not specified	Uncertain significance (Aug 17, 2021)
12-113077467-G-T			Benign (May 21, 2018)
12-113077507-G-T		not specified	Uncertain significance (Sep 06, 2022)
12-113077530-T-G		Neoplasm	- (-)
12-113077624-A-T		not specified	Uncertain significance (Oct 05, 2021)
12-113077841-C-A		not specified	Uncertain significance (Jun 18, 2021)
12-113077856-C-T		not specified	Uncertain significance (Nov 30, 2022)
12-113077873-C-T		not specified	Uncertain significance (Sep 12, 2023)
12-113077877-C-G		not specified	Uncertain significance (Mar 28, 2024)
12-113077930-G-T		not specified	Uncertain significance (Jul 21, 2021)
12-113077963-G-C		not specified	Uncertain significance (Feb 17, 2023)
12-113077995-A-G			Likely benign (Sep 01, 2023)
12-113078000-G-A		not specified	Uncertain significance (Oct 27, 2022)
12-113078026-A-C		not specified	Uncertain significance (Jul 09, 2021)
12-113078051-G-C		not specified	Uncertain significance (May 30, 2023)
12-113078054-C-G		not specified	Uncertain significance (Jul 14, 2021)
12-113078078-T-A		not specified	Uncertain significance (Feb 01, 2023)
12-113078093-C-T		not specified	Uncertain significance (Nov 17, 2023)
12-113093574-C-A		not specified	Uncertain significance (Dec 13, 2021)
12-113093604-A-T		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DTX1	protein_coding	protein_coding	ENST00000257600	9	41320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000990	0.997	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	229	379	0.604	0.0000259	3908
Missense in Polyphen		71	119.92	0.59206		1135
Synonymous	0.683	159	170	0.933	0.0000128	1313
Loss of Function	2.67	9	22.7	0.396	0.00000106	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000536	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a ubiquitin ligase protein in vivo, mediating ubiquitination and promoting degradation of MEKK1, suggesting that it may regulate the Notch pathway via some ubiquitin ligase activity (By similarity). Regulator of Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations. Mainly acts as a positive regulator of Notch, but it also acts as a negative regulator, depending on the developmental and cell context. Mediates the antineural activity of Notch, possibly by inhibiting the transcriptional activation mediated by MATCH1. Involved in neurogenesis, lymphogenesis and myogenesis, and may also be involved in MZB (Marginal zone B) cell differentiation. Promotes B-cell development at the expense of T- cell development, suggesting that it can antagonize NOTCH1. {ECO:0000250, ECO:0000269|PubMed:11564735, ECO:0000269|PubMed:11869684, ECO:0000269|PubMed:9590294}.
• Pathway: Notch signaling pathway - Homo sapiens (human);NOTCH-Ncore;Notch Signaling Pathway;Notch Signaling Pathway;Notch Signaling Pathway;Notch;Signal Transduction;Notch;Signaling by NOTCH1;Signaling by NOTCH;Presenilin action in Notch and Wnt signaling;Activated NOTCH1 Transmits Signal to the Nucleus (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.456
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.37

Haploinsufficiency Scores

• pHI: 0.482
• hipred: Y
• hipred_score: 0.646
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dtx1
• Phenotype: respiratory system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; normal phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: dtx1
• Affected structure: glial cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: transcription, DNA-templated;transcription by RNA polymerase II;cell surface receptor signaling pathway;Notch signaling pathway;regulation of Notch signaling pathway;glial cell differentiation;protein ubiquitination;negative regulation of T cell differentiation;negative regulation of neuron differentiation;positive regulation of nucleic acid-templated transcription;cellular response to leukemia inhibitory factor
• Cellular component: nucleoplasm;cytoplasm;cytosol;nuclear body
• Molecular function: transcription coactivator activity;Notch binding;protein binding;zinc ion binding;transferase activity;SH3 domain binding;ubiquitin protein ligase binding