CUL3
protein-codingcullin 3, the group of Cullins
Gene summary
This gene encodes a member of the cullin protein family. The encoded protein plays a critical role in the polyubiquitination and subsequent degradation of specific protein substrates as the core component and scaffold protein of an E3 ubiquitin ligase complex. Complexes including the encoded protein may also play a role in late endosome maturation. Mutations in this gene are a cause of type 2E pseudohypoaldosteronism. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Mar 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~115.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0030994
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0013782
Submitter: ClinGen
The *CUL3* gene is located on chromosome 2 at q36.2 and encodes cullin-3, a scaffolding component of the Cullin-RING ligase (CRL) complex that belongs to a class of E3 ubiquitin ligases that mediate polyubiquitination of specific target proteins destined for degradation. E3 ligases containing CUL3 interact with KLHL3 and are involved in controlling blood pressure in the body by regulating the amount of WNK1 and WNK4 available. *CUL3* mutation was first reported in relation to autosomal dominant Pseudohypoaldosteronism, type II (PHA2E) in 2012 (Boyden et al., PMID: 22266938). This disorder is also known as Gordon syndrome, and familial hyperkalemic hypertension. The preferred disease name suggested for this disorder is ‘Familial hypertension with hyperkalaemia - CUL3’. The disorder is characterized by hyperkalemia, hypertension, metabolic acidosis and suppressed plasma renin levels despite a normal glomerular filtration rate. *CUL3* mutation has also been associated with autosomal dominant Neurodevelopmental disorder with or without autism or seizures. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, although both conditions have an AD inheritance, there is a difference in molecular mechanism and in clinical phenotype. Therefore, the following disease entities have been split into two distinct disease entities: Pseudohypoaldosteronism, type IIE (OMIM:614496) and Neurodevelopmental disorder with or without autism or seizures (OMIM:619239). Autosomal dominant Neurodevelopmental disorder with or without autism or seizures has been curated separately by the ID/Austim GCEP on 1/16/2021. Nine variants (intronic, canonical splice, splice donor, splice acceptor, splice enhancer) that have been reported in 8 probands in 4 publications (PMIDs: 22266938, 24266877, 29511623, 34480842) are included in this curation. More evidence is available in the literature, but the maximum score for genetic evidence (12 points) has been reached. The mechanism of pathogenicity appears to be loss of function. This gene-disease association is also supported by expression studies, protein interaction studies, and mouse models. (PMIDs: 29869755, 26286618). In summary, *CUL3* is definitively associated with autosomal dominant familial hypertension with hyperkalaemia - CUL3. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time.
Inheritance Pattern: AD
Disease ID:MONDO:0030994
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0100038
Submitter: ClinGen
Variants in the CUL3 gene were first reported in individuals with complex neurodevelopmental disorder in 2012 (O'Roak et al., PMID 22495309; Kong et al., PMID 22914163). The gene-disease relationship was originally suggested by large cohort studies focusing on autism spectrum disorder, developmental delay, and intellectual disability (O'Roak et al., PMID 22495309; McRae et al., PMID 28135719; Stessman et al., PMID: 28191889). In addition to these features, other variable clinical features may include seizures, congenital heart defects, skeletal anomalies, and dysmorphic facial features (Thiffault et al., PMID 30311385; Nakashima et al., PMID 32341456). The phenotypic spectrum is still emerging as most reported patients were part of large cohort studies where only neurodevelopmental phenotypes were described. More than 30 truncating and missense variants in CUL3 have been documented in 15 publications, with the majority being de novo. Of note, we did not score any variants documented to be inherited from a parent, due to incomplete information about the affected status of the parents in large cohort studies. CUL3 is highly intolerant to loss of function variants (pLI=1) and highly constrained for missense variants (Z score=4.75) according to gnomAD v2.1.1. Evidence supporting this gene-disease relationship also includes experimental data. Three independent studies in heterozygous constitutive or conditional knockout mouse models showed behavioral abnormalities, including social and cognitive deficits, altered neuronal excitability, and defective cortical neuronal migration (Rapanelli et al., PMID 31455858; Dong et al., PMID 31780330; Morandell et al., doi: https://doi.org/10.1101/2020.01.10.902064). CUL3 encodes a E3 ubiquitin ligase and has been demonstrated to interact with RHOBTB2, KLHL15, and LZTR1 (Wilkins et al., PMID 15107402; Ferretti et al., PMID 27561354; Abe et al., PMID 31337872), which are implicated in neurodevelopmental disorders. Of note, variants in CUL3 leading to exon 9 skipping exert a dominant-negative effect and are associated with a different disorder, autosomal dominant pseudohypoaldosteronism type II, characterized by hypertension, hyperkalaemia, metabolic acidosis and normal renal function (OMIM #614496). In summary, CUL3 is definitively associated with complex neurodevelopmental disorder. This classification was approved by the ClinGen Intellectual Disability and Autism Gene Curation Expert Panel on 11/04/20 (SOP Version 8).
Inheritance Pattern: AD
Disease ID:MONDO:0013782
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0013782
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0013782
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Neurologic; Renal
Intervention: Renal
Rationale: Treatment (eg, correction of physiologic abnormalities by thiazide diuretics) can be effective
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CUL3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003590.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 9 | 73 | 4 | 89 |
| missense | 8 | 17 | 183 | 13 | 221 | |
| nonsense | 15 | 6 | 4 | 1 | 26 | |
| start loss | 1 | 1 | ||||
| frameshift | 30 | 31 | 8 | 69 | ||
| splice donor/acceptor (+/-2bp) | 8 | 9 | 11 | 28 | ||
| Total | 62 | 65 | 216 | 87 | 4 | 434 |
Highest pathogenic variant AF is 0.0000065717704
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003581.1 | 16 | MANE Select | |
| Ensembl | ENSP00000264414.4 | 16 | MANE Select | |
| RefSeq | NP_001244126.1 | 15 | Standard | |
| RefSeq | NP_001244127.1 | 16 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ubiquitin mediated proteolysis - Homo sapiens (human)
- Hedgehog signaling pathway - Homo sapiens (human)
- HH-Ncore
- Hereditary Leiomyomatosis and Renal Cell Carcinoma Pathway
- Hedgehog Signaling Pathway
Biological Process
- G1/S transition of mitotic cell cycle
- negative regulation of transcription by RNA polymerase II
- MAPK cascade
- protein polyubiquitination
- trophectodermal cellular morphogenesis
Molecular Function
- ubiquitin-protein transferase activity
- Notch binding
- protein binding
- cyclin binding
- POZ domain binding
Cellular Component
- Golgi membrane
- nucleoplasm
- cytoplasm
- polar microtubule
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264414
- Coding exons
- 16
- Length
- 115244
- Individuals with no LoFs
- 125719
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125727
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 4.75 | 145 | 419 | 0.346 | 0.0000222 | 5098 |
| Missense (PolyPhen) | 37 | 160.33 | 0.23077 | 2018 | ||
| Synonymous | -1.10 | 155 | 139 | 1.12 | 0.00000720 | 1382 |
| Loss of Function | 5.28 | 4 | 40.1 | 0.0997 | 0.00000218 | 504 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00021 | 0.00020 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Core component of multiple cullin-RING-based BCR (BTB- CUL3-RBX1) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. BCR complexes and ARIH1 collaborate in tandem to mediate ubiquitination of target proteins (PubMed:27565346). As a scaffold protein may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin- protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1. The functional specificity of the BCR complex depends on the BTB domain-containing protein as the substrate recognition component. BCR(KLHL42) is involved in ubiquitination of KATNA1. BCR(SPOP) is involved in ubiquitination of BMI1/PCGF4, BRMS1, H2AFY and DAXX, GLI2 and GLI3. Can also form a cullin-RING-based BCR (BTB-CUL3- RBX1) E3 ubiquitin-protein ligase complex containing homodimeric SPOPL or the heterodimer formed by SPOP and SPOPL; these complexes have lower ubiquitin ligase activity. BCR(KLHL9-KLHL13) controls the dynamic behavior of AURKB on mitotic chromosomes and thereby coordinates faithful mitotic progression and completion of cytokinesis. BCR(KLHL12) is involved in ER-Golgi transport by regulating the size of COPII coats, thereby playing a key role in collagen export, which is required for embryonic stem (ES) cells division: BCR(KLHL12) acts by mediating monoubiquitination of SEC31 (SEC31A or SEC31B) (PubMed:22358839, PubMed:27716508). BCR(KLHL3) acts as a regulator of ion transport in the distal nephron; by mediating ubiquitination of WNK4 (PubMed:23387299, PubMed:23453970, PubMed:23576762). The BCR(KLHL20) E3 ubiquitin ligase complex is involved in interferon response and anterograde Golgi to endosome transport: it mediates both ubiquitination leading to degradation and 'Lys-33'-linked ubiquitination (PubMed:20389280, PubMed:21840486, PubMed:21670212, PubMed:24768539). The BCR(KLHL21) E3 ubiquitin ligase complex regulates localization of the chromosomal passenger complex (CPC) from chromosomes to the spindle midzone in anaphase and mediates the ubiquitination of AURKB (PubMed:19995937). The BCR(KLHL22) ubiquitin ligase complex mediates monoubiquitination of PLK1, leading to PLK1 dissociation from phosphoreceptor proteins and subsequent removal from kinetochores, allowing silencing of the spindle assembly checkpoint (SAC) and chromosome segregation (PubMed:23455478). The BCR(KLHL22) ubiquitin ligase complex is also responsible for the amino acid-stimulated 'Lys-48' polyubiquitination and proteasomal degradation of DEPDC5. Through the degradation of DEPDC5, releases the GATOR1 complex-mediated inhibition of the TORC1 pathway (PubMed:29769719). The BCR(KLHL25) ubiquitin ligase complex is involved in translational homeostasis by mediating ubiquitination and subsequent degradation of hypophosphorylated EIF4EBP1 (4E-BP1) (PubMed:22578813). The BCR(KBTBD8) complex acts by mediating monoubiquitination of NOLC1 and TCOF1, leading to remodel the translational program of differentiating cells in favor of neural crest specification (PubMed:26399832). Involved in ubiquitination of cyclin E and of cyclin D1 (in vitro) thus involved in regulation of G1/S transition. Involved in the ubiquitination of KEAP1, ENC1 and KLHL41. In concert with ATF2 and RBX1, promotes degradation of KAT5 thereby attenuating its ability to acetylate and activate ATM. The BCR(KCTD17) E3 ubiquitin ligase complex mediates ubiquitination and degradation of TCHP, a down-regulator of cilium assembly, thereby inducing ciliogenesis (PubMed:25270598). The BCR(KLHL24) E3 ubiquitin ligase complex mediates ubiquitination of KRT14, controls KRT14 levels during keratinocytes differentiation, and is essential for skin integrity (PubMed:27798626). {ECO:0000269|PubMed:10500095, ECO:0000269|PubMed:11311237, ECO:0000269|PubMed:15897469, ECO:0000269|PubMed:15983046, ECO:0000269|PubMed:16524876, ECO:0000269|PubMed:17543862, ECO:0000269|PubMed:18397884, ECO:0000269|PubMed:19261606, ECO:0000269|PubMed:19995937, ECO:0000269|PubMed:20389280, ECO:0000269|PubMed:21670212, ECO:0000269|PubMed:21840486, ECO:0000269|PubMed:22085717, ECO:0000269|PubMed:22358839, ECO:0000269|PubMed:22578813, ECO:0000269|PubMed:22632832, ECO:0000269|PubMed:23387299, ECO:0000269|PubMed:23453970, ECO:0000269|PubMed:23455478, ECO:0000269|PubMed:23576762, ECO:0000269|PubMed:24768539, ECO:0000269|PubMed:25270598, ECO:0000269|PubMed:26399832, ECO:0000269|PubMed:27565346, ECO:0000269|PubMed:27716508, ECO:0000269|PubMed:27798626, ECO:0000269|PubMed:29769719}.;
- Disease
- DISEASE: Pseudohypoaldosteronism 2E (PHA2E) [MIM:614496]: An autosomal dominant disorder characterized by severe hypertension, hyperkalemia, hyperchloremia, hyperchloremic metabolic acidosis, and correction of physiologic abnormalities by thiazide diuretics. {ECO:0000269|PubMed:22266938}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- LoFtool
- 0.416
- RVIS EVS
- -0.14
- RVIS percentile EVS
- 43.29
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |