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.

not_specified (68 variants)
not_provided (4 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

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. These statistics are base on transcript: NM_000004416.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			67 clinvar	3 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	68	5	1

Loading clinvar variants...

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