DCUN1D4

defective in cullin neddylation 1 domain containing 4

Basic information

Region (hg38): 4:51842999-51916837

Links

ENSG00000109184 ∙ NCBI:23142 ∙ OMIM:612977 ∙ HGNC:28998 ∙ Uniprot:Q92564 ∙ 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 DCUN1D4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCUN1D4 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in DCUN1D4

This is a list of pathogenic ClinVar variants found in the DCUN1D4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-51863444-G-C		not specified	Uncertain significance (Sep 29, 2022)
4-51863458-T-C		not specified	Uncertain significance (Sep 17, 2021)
4-51863502-A-G		not specified	Uncertain significance (Nov 08, 2022)
4-51863685-A-G		not specified	Likely benign (Jul 12, 2022)
4-51863689-G-T		not specified	Uncertain significance (Jan 04, 2024)
4-51863697-G-A		not specified	Uncertain significance (Dec 19, 2022)
4-51877852-C-G		not specified	Uncertain significance (Mar 11, 2022)
4-51886620-T-G		not specified	Uncertain significance (Jul 14, 2022)
4-51891784-A-C		not specified	Uncertain significance (Jun 11, 2021)
4-51891800-A-G		not specified	Uncertain significance (Sep 29, 2023)
4-51891817-C-G		not specified	Uncertain significance (Oct 22, 2021)
4-51899334-A-G		not specified	Uncertain significance (Jul 06, 2021)
4-51899342-T-A		not specified	Uncertain significance (Mar 23, 2023)
4-51913562-A-C		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCUN1D4	protein_coding	protein_coding	ENST00000334635	11	73838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0475	0.952	125726	0	11	125737	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.685	123	146	0.841	0.00000683	1941
Missense in Polyphen		31	52.005	0.5961		696
Synonymous	-0.191	52	50.3	1.03	0.00000253	474
Loss of Function	2.90	6	20.0	0.300	9.44e-7	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.000103	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Intolerance Scores

• loftool: 0.232
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.543
• ghis: 0.694

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00304

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcun1d4

Gene ontology

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