DCUN1D3

defective in cullin neddylation 1 domain containing 3

Basic information

Region (hg38): 16:20854925-20900358

Links

ENSG00000188215 ∙ NCBI:123879 ∙ OMIM:616167 ∙ HGNC:28734 ∙ Uniprot:Q8IWE4 ∙ 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 DCUN1D3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCUN1D3 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in DCUN1D3

This is a list of pathogenic ClinVar variants found in the DCUN1D3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20859939-T-C		not specified	Uncertain significance (Apr 13, 2023)
16-20859953-C-G		not specified	Uncertain significance (May 08, 2023)
16-20860227-C-A		not specified	Uncertain significance (Jan 23, 2024)
16-20860250-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-20860307-C-T		not specified	Uncertain significance (Oct 25, 2023)
16-20860341-T-C		not specified	Uncertain significance (Apr 19, 2024)
16-20862273-T-G		not specified	Uncertain significance (Dec 05, 2024)
16-20862330-G-A		not specified	Uncertain significance (Jun 25, 2024)
16-20862345-G-T		not specified	Uncertain significance (Oct 20, 2024)
16-20862361-C-T		not specified	Uncertain significance (Jan 17, 2024)
16-20862376-C-T		not specified	Uncertain significance (Mar 28, 2024)
16-20862382-C-T		not specified	Uncertain significance (Jan 17, 2025)
16-20862387-A-G		not specified	Uncertain significance (Dec 28, 2024)
16-20862396-C-T		not specified	Uncertain significance (Mar 25, 2024)
16-20862430-G-A		not specified	Uncertain significance (Jun 17, 2022)
16-20862453-T-C		not specified	Uncertain significance (May 26, 2024)
16-20862468-G-A		not specified	Uncertain significance (Mar 31, 2024)
16-20862474-C-T		not specified	Uncertain significance (Nov 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCUN1D3	protein_coding	protein_coding	ENST00000324344	2	45460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.867	0.133	125729	0	4	125733	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	119	170	0.698	0.0000104	2008
Missense in Polyphen		20	53.834	0.37151		704
Synonymous	0.566	61	66.9	0.912	0.00000388	587
Loss of Function	2.79	1	11.0	0.0912	6.26e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Antagonizes DCUN1D1-mediated CUL1 neddylation by sequestering CUL1 at the cell membrane (PubMed:25349211). When overexpressed in transformed cells, may promote mesenchymal to epithelial-like changes and inhibit colony formation in soft agar (PubMed:25349211). {ECO:0000269|PubMed:25349211}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Intolerance Scores

• loftool: 0.167
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.738
• hipred: Y
• hipred_score: 0.728
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.176

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcun1d3

Gene ontology

• Biological process: response to UV-C;response to gamma radiation;negative regulation of cell growth;positive regulation of apoptotic process;post-translational protein modification;protein neddylation;positive regulation of ubiquitin-protein transferase activity;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: ubiquitin ligase complex;plasma membrane;perinuclear region of cytoplasm
• Molecular function: molecular_function;protein binding;ubiquitin conjugating enzyme binding;ubiquitin-like protein binding;cullin family protein binding