DCUN1D1

defective in cullin neddylation 1 domain containing 1

Basic information

Region (hg38): 3:182938073-182985953

Links

ENSG00000043093 ∙ NCBI:54165 ∙ OMIM:605905 ∙ HGNC:18184 ∙ Uniprot:Q96GG9 ∙ 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 DCUN1D1 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCUN1D1 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			3			3
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	3	0	0

Variants in DCUN1D1

This is a list of pathogenic ClinVar variants found in the DCUN1D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-182961303-A-G		not specified	Uncertain significance (Jul 19, 2023)
3-182961345-A-G		not specified	Uncertain significance (Dec 14, 2021)
3-182963968-C-G		not specified	Uncertain significance (Dec 07, 2021)
3-182963984-C-T		not specified	Uncertain significance (Oct 27, 2022)
3-182965756-A-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCUN1D1	protein_coding	protein_coding	ENST00000292782	7	47880

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0147	123561	0	1	123562	0.00000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.98	67	131	0.512	0.00000638	1738
Missense in Polyphen		4	21.066	0.18988		321
Synonymous	0.0884	42	42.7	0.983	0.00000208	420
Loss of Function	3.62	1	17.2	0.0582	9.27e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000889	0.00000889
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of an E3 ubiquitin ligase complex for neddylation. Promotes neddylation of cullin components of E3 cullin-RING ubiquitin ligase complexes. Acts by binding to cullin-RBX1 complexes in the cytoplasm and promoting their nuclear translocation, enhancing recruitment of E2-NEDD8 (UBE2M-NEDD8) thioester to the complex, and optimizing the orientation of proteins in the complex to allow efficient transfer of NEDD8 from the E2 to the cullin substrates. Involved in the release of inhibitory effets of CAND1 on cullin-RING ligase E3 complex assembly and activity (PubMed:25349211, PubMed:28581483). Acts also as an oncogene facilitating malignant transformation and carcinogenic progression (By similarity). {ECO:0000250|UniProtKB:Q9QZ73, ECO:0000269|PubMed:25349211, ECO:0000269|PubMed:28581483}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.783
• ghis: 0.666

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcun1d1
• Phenotype: hematopoietic system phenotype; immune system phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: post-translational protein modification;protein neddylation;positive regulation of ubiquitin-protein transferase activity;positive regulation of protein neddylation
• Cellular component: ubiquitin ligase complex;nucleus;cytosol
• Molecular function: protein binding;ubiquitin conjugating enzyme binding;ubiquitin-like protein binding;cullin family protein binding