DCUN1D2

defective in cullin neddylation 1 domain containing 2

Basic information

Region (hg38): 13:113455819-113490951

Previous symbols: [ "C13orf17" ]

Links

ENSG00000150401 ∙ NCBI:55208 ∙ ∙ HGNC:20328 ∙ Uniprot:Q6PH85 ∙ 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 DCUN1D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCUN1D2 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in DCUN1D2

This is a list of pathogenic ClinVar variants found in the DCUN1D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-113458042-C-T		not specified	Uncertain significance (Oct 05, 2023)
13-113458097-C-T		not specified	Uncertain significance (Sep 26, 2024)
13-113459321-C-T		not specified	Uncertain significance (May 30, 2024)
13-113459332-A-G		not specified	Uncertain significance (Dec 07, 2023)
13-113459333-T-C		not specified	Uncertain significance (Mar 01, 2023)
13-113459347-A-G		not specified	Uncertain significance (Mar 28, 2023)
13-113459350-T-C		not specified	Uncertain significance (Jan 04, 2024)
13-113459375-A-G		not specified	Uncertain significance (Oct 08, 2024)
13-113459377-G-A		not specified	Uncertain significance (Jun 22, 2023)
13-113461074-G-C		not specified	Uncertain significance (Dec 08, 2021)
13-113474151-C-T		not specified	Uncertain significance (Oct 20, 2024)
13-113474157-T-C		not specified	Uncertain significance (May 03, 2023)
13-113474190-C-G		not specified	Uncertain significance (Jun 07, 2024)
13-113474205-C-T		not specified	Uncertain significance (Apr 12, 2023)
13-113480579-G-A		not specified	Uncertain significance (Mar 06, 2023)
13-113480665-A-G		not specified	Uncertain significance (Jul 17, 2023)
13-113480701-T-G		not specified	Uncertain significance (Dec 16, 2022)
13-113483872-T-C		not specified	Uncertain significance (Dec 02, 2024)
13-113483876-T-C		not specified	Uncertain significance (Feb 13, 2023)
13-113483914-T-A		not specified	Uncertain significance (Jan 08, 2024)
13-113483932-C-T		not specified	Likely benign (Dec 28, 2023)
13-113483951-G-T		not specified	Uncertain significance (Jan 30, 2024)
13-113483959-T-C		not specified	Uncertain significance (May 30, 2024)
13-113483965-T-G		not specified	Uncertain significance (Oct 12, 2021)
13-113483968-G-A		not specified	Uncertain significance (Mar 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCUN1D2	protein_coding	protein_coding	ENST00000478244	7	35134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.97e-8	0.175	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.118	142	146	0.973	0.00000826	1733
Missense in Polyphen		20	26.071	0.76714		349
Synonymous	0.779	51	58.6	0.870	0.00000402	452
Loss of Function	0.203	12	12.8	0.939	5.41e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potently stimulates the neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes from the NEDD8- conjugating E2 enzyme UBC12. Neddylation of cullins play an essential role in the regulation of SCF-type complexes activity. {ECO:0000269|PubMed:23201271}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.507
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.0826
• hipred: N
• hipred_score: 0.350
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.157

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcun1d2

Gene ontology

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