RHOBTB2

protein-coding

Rho related BTB domain containing 2, the group of Rho family GTPases|BTB domain containing

Gene summary

The protein encoded by this gene is a small Rho GTPase and a candidate tumor suppressor. The encoded protein interacts with the cullin-3 protein, a ubiquitin E3 ligase necessary for mitotic cell division. This protein inhibits the growth and spread of some types of breast cancer. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

MANE transcript

NM_015178.3

Inheritance

AD, AR

ClinVar variants

P:20U:313B:445

Top phenotype

Developmental and epileptic encephalopathy 64

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr8:22,987,417-23,020,509

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~33.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

developmental and epileptic encephalopathy, 64STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0033373

Submitter: Labcorp Genetics (formerly Invitae)

complex neurodevelopmental disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: PanelApp Australia

developmental and epileptic encephalopathy, 64STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0033373

Submitter: PanelApp Australia

developmental and epileptic encephalopathy, 64STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0033373

Submitter: G2P

complex neurodevelopmental disorderDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: ClinGen

*RHOBTB2* was first reported in relation to autosomal recessive complex neurodevelopmental disorder in 2020 (Maddirevula et al., PMID: 33456446). Phenotypic features in individuals with biallelic *RHOBTB2* variants include intellectual disability, hypotonia and/or hypertonia, microcephaly, seizures, and movement disorders. Reported seizure types include absence, febrile, and generalized tonic clonic seizures with onset typically in neonatal period and infancy (PMID: 37165955). Of note, there have also been many reported cases of individuals with *de novo* heterozygous missense variants in *RHOBTB2* and complex neurodevelopmental disorder. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in inheritance pattern and molecular mechanism, with the autosomal recessive (AR) presentation being primarily loss of function variants and the autosomal dominant (AD) presentation being primarily missense variants. Therefore, the curations for AD and AR complex neurodevelopmental disorder have been split, and cases with AD *RHOBTB2* variants have been curated separately by the Epilepsy GCEP. Eight homozygous variants reported in eight probands from 2 publications are included in this curation (PMIDs: 33456446, 37165955). Additionally, one individual with compound heterozygous nonsense and canonical splice site variants has also been reported (PMID: 37165955). The mechanism of pathogenicity appears to be loss of function, as reported variants are nonsense, frameshift and splice site in probands with biallelic variants (PMID: 37165955). There was no experimental evidence utilized for this curation. In summary, there is definitive evidence supporting the relationship between *RHOBTB2* and AR complex neurodevelopmental disorder. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen Epilepsy GCEP on the meeting date January 16, 2024 (SOP Version 10).

developmental and epileptic encephalopathy, 64MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0033373

Submitter: Ambry Genetics

complex neurodevelopmental disorderDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: ClinGen

*RHOBTB2* was first reported in relation to autosomal dominant complex neurodevelopmental disorder in 2016 (Lopes et al., PMID 26740508). Phenotypic features in individuals with *de novo* missense *RHOBTB2* variants include intellectual disability, microcephaly, seizures, paroxysmal movement disorders, dystonia, chorea, dyskinesia, dysmorphic features and abnormal brain MRI findings. Reported seizure types include febrile, generalized tonic clonic, myoclonic, and focal seizures, with onset in neonatal period and infancy (Langhammer et al, PMID: 37165955). Of note, there have also been reported cases of individuals with biallelic loss of function variants in *RHOBTB2* and complex neurodevelopmental disorder. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in inheritance pattern and molecular mechanism, with the autosomal recessive (AR) presentation being primarily loss of function variants and the autosomal dominant (AD) presentation being primarily missense variants. Therefore, the curations for AD and AR complex neurodevelopmental disorder have been split, and cases with AR *RHOBTB2* variants have been curated separately by the Epilepsy GCEP. Fourteen missense variants reported in 24 individuals from five publications are included in this curation (PMIDs: 26740508, 29276004, 29768694, 33504645, 37165955). Of note, many of these variants are reported to be *de novo*. Genotype-phenotype correlation has been demonstrated; individuals with pathogenic variants in the two BTB domains generally have more severe to profound intellectual disability with epilepsy and movement disorder, while *de novo* pathogenic missense variants in the GTPase domain are associated with more variable neurodevelopmental presentations with or without epilepsy (PMID: 37165955). The mechanism of pathogenicity of the missense variants in *RHOBTB2* is not well understood, and there was no experimental evidence utilized for this curation. In summary, there is definitive evidence supporting the relationship between *RHOBTB2* and AD complex neurodevelopmental disorder. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen Epilepsy GCEP on the meeting date January 16, 2024 (SOP Version 10).

complex neurodevelopmental disorderDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: LiferaOmics

ClinGen RHOBTB2–related complex neurodevelopmental disorder (AR) – Definitive – Approval: 2024 ClinGen Evidence Breakdown Genetic Evidence = 12.0 points (max reached) Based on: • PMID: 33456446 • PMID: 37165955 Experimental Evidence = 0 points (no experimental evidence used in the ClinGen AR curation) ClinGen Total = 12.0 Genetic Evidence – Our Case Family 1 – one proband. Case-level (biallelic predicted null in AR model; homozygous frameshift; no consanguinity → no −0.5 applied) = 1.5; Segregation = 0; Case-control = 0 Family 1 total = 1.5 Our Case Total = 1.5 / 12 Updated Total Genetic Evidence (ClinGen + Our Case) ClinGen genetic evidence: 12.0 (cap reached) Our additional case: +1.5 Updated genetic total = 12.0 (cap maintained) Experimental Evidence (unchanged from ClinGen) ClinGen experimental evidence = 0 Updated Overall Score Genetic evidence = 12.0 Experimental evidence = 0 Updated total = 12.0 Brief curation summary (AR scope) ClinGen classifies RHOBTB2 as Definitive for autosomal recessive complex neurodevelopmental disorder, supported by multiple independent probands with biallelic loss-of-function variants (nonsense/frameshift/splice), reported across PMIDs 33456446 and 37165955, with replication over time and no contradictory evidence noted.

Clinical Genomic Database (CGD)

Developmental and epileptic encephalopathy 64AR

Manifestation: Craniofacial; Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 29276004Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RHOBTB2 variants in ClinVar

13 Conditions Cataloged
not providedTotal: 803
Inborn genetic diseasesTotal: 117
not specifiedTotal: 60
Developmental and epileptic encephalopathy, 64Total: 56
RHOBTB2-related disorderTotal: 41
SeizureTotal: 2
See casesTotal: 2
Dystonic disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015178.3. 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
2
clinvar
281
clinvar
6
clinvar
289
missense
3
clinvar
15
clinvar
273
clinvar
111
clinvar
35
clinvar
437
nonsense
1
clinvar
10
clinvar
5
clinvar
16
start loss
1
clinvar
1
frameshift
1
clinvar
17
clinvar
6
clinvar
24
splice donor/acceptor (+/-2bp)
10
clinvar
1
clinvar
11
Total41631340441778

Highest pathogenic variant AF is 0.0000013684178

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015178.3RefSeqNP_055993.29MANE Select
ENST00000251822.7EnsemblENSP00000251822.79MANE Select
NM_001160036.2RefSeqNP_001153508.110Standard
NM_001160037.2RefSeqNP_001153509.110Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ubiquitin mediated proteolysis - Homo sapiens (human)
  • Signal Transduction
  • Rho GTPase cycle
  • Signaling by Rho GTPases

Biological Process

  • cell morphogenesis
  • actin filament organization
  • Rho protein signal transduction
  • cell migration
  • actin cytoskeleton organization

Molecular Function

  • GTPase activity
  • protein binding
  • GTP binding
  • protein kinase binding

Cellular Component

  • cytoplasm
  • cytosol
  • cytoskeleton
  • plasma membrane
  • cell projection

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000519685
Coding exons
10
Length
32783
Individuals with no LoFs
125713
Homozygous LoFs
0
Heterozygous LoFs
35
Defined
125748
p
0.000139
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.663224870.6610.00003254910
Missense (PolyPhen)80191.110.41861982
Synonymous0.3791891960.9660.00001301516
Loss of Function3.831034.10.2930.00000216325

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000430.00043rare
Latino/Admixed American0.000200.00020rare
Ashkenazi Jewish0.000100.000099rare
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.000130.00013rare
South Asian0.0000650.000065rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec
0.150

Intolerance Scores

LoFtool
0.614
RVIS EVS
-0.97
RVIS percentile EVS
8.9

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.946

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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