CUL9

cullin 9, the group of Armadillo like helical domain containing|RBR E3 ubiquitin ligases|Cullins

Basic information

Region (hg38): 6:43182184-43224587

Links

ENSG00000112659 ∙ NCBI:23113 ∙ OMIM:607489 ∙ HGNC:15982 ∙ Uniprot:Q8IWT3 ∙ 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 CUL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CUL9 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				4	2	6
missense			207	15		222
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				3		3
non coding						0
Total	0	0	207	20	2

Variants in CUL9

This is a list of pathogenic ClinVar variants found in the CUL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43184323-C-T		not specified	Uncertain significance (Nov 21, 2024)
6-43184337-C-A		not specified	Uncertain significance (May 05, 2023)
6-43184341-A-T		not specified	Conflicting classifications of pathogenicity (Jul 01, 2023)
6-43184377-G-C		not specified	Uncertain significance (Aug 28, 2024)
6-43184530-G-A		not specified	Uncertain significance (Nov 17, 2022)
6-43184546-T-C		not specified	Uncertain significance (Oct 08, 2024)
6-43184547-G-C		CUL9-related disorder	Likely benign (Apr 11, 2023)
6-43184585-A-C		not specified	Uncertain significance (Dec 22, 2023)
6-43184594-G-C		not specified	Uncertain significance (Mar 21, 2024)
6-43184606-G-A			Likely benign (Jul 01, 2023)
6-43184615-G-A		not specified	Uncertain significance (Nov 12, 2024)
6-43184616-A-G		CUL9-related disorder	Uncertain significance (Aug 15, 2024)
6-43184628-C-A		CUL9-related disorder	Benign (Dec 20, 2019)
6-43184635-G-A		not specified	Uncertain significance (Dec 06, 2021)
6-43184702-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-43184711-G-T		not specified	Uncertain significance (Mar 24, 2023)
6-43184766-C-T		CUL9-related disorder	Benign (Jan 02, 2020)
6-43184775-C-G		not specified	Uncertain significance (Dec 14, 2021)
6-43184776-G-C		CUL9-related disorder	Benign (Jun 12, 2019)
6-43184802-G-T		not specified	Uncertain significance (Jan 23, 2023)
6-43184818-C-T		CUL9-related disorder	Likely benign (Jul 29, 2019)
6-43184835-A-G		CUL9-related disorder	Benign (Oct 28, 2019)
6-43184840-A-G		not specified	Uncertain significance (Dec 15, 2022)
6-43184861-G-A		not specified	Uncertain significance (Aug 28, 2024)
6-43185493-A-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CUL9	protein_coding	protein_coding	ENST00000252050	40	42413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00809	124966	5	777	125748	0.00311

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.10	1154	1.49e+3	0.774	0.0000929	16322
Missense in Polyphen		421	635.21	0.66277		7260
Synonymous	0.423	589	602	0.978	0.0000366	5161
Loss of Function	8.27	25	125	0.201	0.00000679	1314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00169
Ashkenazi Jewish	0.00179	0.00179
East Asian	0.000163	0.000163
Finnish	0.00162	0.00162
European (Non-Finnish)	0.00431	0.00430
Middle Eastern	0.000163	0.000163
South Asian	0.00569	0.00560
Other	0.00343	0.00343

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Core component of a Cul9-RING ubiquitin-protein ligase complex, a complex that mediates ubiquitination and subsequent degradation of BIRC5 and is required to maintain microtubule dynamics and genome integrity. Acts downstream of the 3M complex, which inhibits CUL9 activity, leading to prevent ubiquitination of BIRC5 (PubMed:24793696). Cytoplasmic anchor protein in p53/TP53- associated protein complex. Regulates the subcellular localization of p53/TP53 and subsequent function (PubMed:12526791, PubMed:17332328). {ECO:0000269|PubMed:12526791, ECO:0000269|PubMed:17332328, ECO:0000269|PubMed:24793696}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.536
• rvis_EVS: -2.21
• rvis_percentile_EVS: 1.36

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.608
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cul9
• Phenotype: neoplasm; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: microtubule cytoskeleton organization;ubiquitin-dependent protein catabolic process;regulation of mitotic nuclear division;protein ubiquitination;post-translational protein modification
• Cellular component: cytosol;cullin-RING ubiquitin ligase complex
• Molecular function: protein binding;ATP binding;transferase activity;ubiquitin protein ligase binding;metal ion binding