CUL3

protein-coding

cullin 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

NM_003590.5

Inheritance

AD

ClinVar variants

P:127U:216B:91

Top phenotype

Pseudohypoaldosteronism, type IIE

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr2:224,470,150-224,585,397

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~115.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorder with or without autism or seizuresDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0030994

Submitter: G2P

pseudohypoaldosteronism type 2EDEFINITIVE

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.

neurodevelopmental disorder with or without autism or seizuresSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030994

Submitter: Labcorp Genetics (formerly Invitae)

complex neurodevelopmental disorderDEFINITIVE

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).

pseudohypoaldosteronism type 2ESUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0013782

Submitter: Orphanet

pseudohypoaldosteronism type 2ESTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013782

Submitter: Labcorp Genetics (formerly Invitae)

pseudohypoaldosteronism type 2ESTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013782

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Pseudohypoaldosteronism, type IIEAD

Manifestation: Neurologic; Renal

Intervention: Renal

Rationale: Treatment (eg, correction of physiologic abnormalities by thiazide diuretics) can be effective

Refs: 22266938; 31696658; 31780330; 32341456; 33097317Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CUL3 variants in ClinVar

20 Conditions Cataloged
not providedTotal: 379
Neurodevelopmental disorder with or without autism or seizuresTotal: 105
Pseudohypoaldosteronism type 2ETotal: 78
Inborn genetic diseasesTotal: 48
CUL3-related disorderTotal: 20
not specifiedTotal: 14
Pseudohypoaldosteronism type 2ATotal: 14
Intellectual disabilityTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
9
clinvar
73
clinvar
4
clinvar
89
missense
8
clinvar
17
clinvar
183
clinvar
13
clinvar
221
nonsense
15
clinvar
6
clinvar
4
clinvar
1
clinvar
26
start loss
1
clinvar
1
frameshift
30
clinvar
31
clinvar
8
clinvar
69
splice donor/acceptor (+/-2bp)
8
clinvar
9
clinvar
11
clinvar
28
Total6265216874434

Highest pathogenic variant AF is 0.0000065717704

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003590.5RefSeqNP_003581.116MANE Select
ENST00000264414.9EnsemblENSP00000264414.416MANE Select
NM_001257197.2RefSeqNP_001244126.115Standard
NM_001257198.2RefSeqNP_001244127.116Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense4.751454190.3460.00002225098
Missense (PolyPhen)37160.330.230772018
Synonymous-1.101551391.120.000007201382
Loss of Function5.28440.10.09970.00000218504

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish0.000210.00020rare
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.0000180.000018rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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