DET1

DET1 partner of COP1 E3 ubiquitin ligase

Basic information

Region (hg38): 15:88494440-88546681

Links

ENSG00000140543 ∙ NCBI:55070 ∙ OMIM:608727 ∙ HGNC:25477 ∙ Uniprot:Q7L5Y6 ∙ 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 DET1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DET1 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			30
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	30	3	0

Variants in DET1

This is a list of pathogenic ClinVar variants found in the DET1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-88512970-A-T		not specified	Uncertain significance (Dec 15, 2023)
15-88513020-G-A		not specified	Likely benign (Mar 28, 2024)
15-88513029-A-T		not specified	Uncertain significance (Jan 24, 2024)
15-88513096-G-A		not specified	Uncertain significance (Nov 11, 2024)
15-88513132-G-A		not specified	Uncertain significance (Jun 11, 2024)
15-88516876-C-T		not specified	Uncertain significance (Nov 15, 2024)
15-88516973-C-T		not specified	Likely benign (Nov 13, 2023)
15-88527623-T-A		not specified	Uncertain significance (Aug 17, 2021)
15-88527625-G-T		not specified	Uncertain significance (Mar 18, 2024)
15-88527649-C-T			Likely benign (Feb 01, 2023)
15-88527706-C-G		not specified	Uncertain significance (Apr 25, 2022)
15-88527720-C-G		not specified	Uncertain significance (Jan 24, 2024)
15-88527743-A-G		not specified	Uncertain significance (Oct 01, 2024)
15-88527754-C-T			Likely benign (Jul 01, 2022)
15-88527755-G-A		not specified	Uncertain significance (Oct 12, 2021)
15-88527762-T-G		not specified	Uncertain significance (Jun 16, 2023)
15-88527770-A-G		not specified	Uncertain significance (Dec 16, 2023)
15-88530633-T-A		not specified	Uncertain significance (Sep 10, 2024)
15-88530693-T-A		not specified	Uncertain significance (Oct 27, 2021)
15-88530793-G-A		not specified	Uncertain significance (Dec 17, 2021)
15-88530796-A-G		not specified	Uncertain significance (Aug 12, 2024)
15-88530809-C-A		not specified	Uncertain significance (Oct 26, 2022)
15-88530870-C-A		not specified	Uncertain significance (Dec 05, 2024)
15-88530870-C-G		not specified	Uncertain significance (Apr 12, 2022)
15-88530945-C-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DET1	protein_coding	protein_coding	ENST00000564406	5	35117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.679	0.321	124643	0	8	124651	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.826	297	340	0.874	0.0000215	3686
Missense in Polyphen		82	118.08	0.69442		1297
Synonymous	-2.25	155	123	1.26	0.00000636	1125
Loss of Function	3.46	4	21.2	0.189	0.00000131	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000458	0.0000442
Middle Eastern	0.000111	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the E3 ubiquitin ligase DCX DET1-COP1 complex, which is required for ubiquitination and subsequent degradation of target proteins. The complex is involved in JUN ubiquitination and degradation. {ECO:0000269|PubMed:14739464}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.17

Haploinsufficiency Scores

• pHI: 0.216
• hipred: Y
• hipred_score: 0.825
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Det1

Gene ontology

• Biological process: protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;protein-containing complex assembly
• Cellular component: nucleus;Cul4A-RING E3 ubiquitin ligase complex;Cul4-RING E3 ubiquitin ligase complex
• Molecular function: protein binding;ubiquitin protein ligase binding;protein-containing complex binding;protein binding, bridging involved in substrate recognition for ubiquitination