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GeneBe

RORB

RAR related orphan receptor B, the group of RAR related orphan receptors

Basic information

Region (hg38): 9:74497334-74693177

Links

ENSG00000198963NCBI:6096OMIM:601972HGNC:10259Uniprot:Q92753AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • complex neurodevelopmental disorder (Moderate), mode of inheritance: AD
  • epilepsy (Moderate), mode of inheritance: AD
  • epilepsy, idiopathic generalized, susceptibility to, 15 (Strong), mode of inheritance: AD
  • epilepsy, idiopathic generalized, susceptibility to, 15 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Epilepsy, idiopathic generalized, susceptibilty to, 15ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic27352968

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RORB gene.

  • not provided (264 variants)
  • Epilepsy, idiopathic generalized, susceptibility to, 15 (17 variants)
  • Inborn genetic diseases (16 variants)
  • Seizure (3 variants)
  • RORB-related condition (2 variants)
  • Neurodevelopmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RORB 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
37
clinvar
11
clinvar
48
missense
1
clinvar
4
clinvar
126
clinvar
2
clinvar
133
nonsense
9
clinvar
3
clinvar
12
start loss
2
clinvar
2
frameshift
8
clinvar
1
clinvar
3
clinvar
12
inframe indel
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
7
clinvar
1
clinvar
8
splice region
?
0
non coding
?
1
clinvar
32
clinvar
8
clinvar
41
Total 18 16 134 71 19

Variants in RORB

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

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

Position Type Phenotype Significance ClinVar
9-74497978-T-C Uncertain significance (Jun 30, 2019)1306466
9-74497978-T-G Uncertain significance (Oct 22, 2023)2770599
9-74497981-G-C Uncertain significance (Aug 16, 2021)1483936
9-74497989-C-T Conflicting classifications of pathogenicity (Jun 01, 2022)1695250
9-74498003-C-A Benign (Nov 02, 2022)1528222
9-74498003-C-T Benign (Nov 03, 2022)1610805
9-74630275-C-T Likely benign (Apr 18, 2022)2127492
9-74630281-G-A Epilepsy, idiopathic generalized, susceptibility to, 15 Likely pathogenic (Dec 14, 2018)690378
9-74630294-T-G Uncertain significance (Jun 18, 2022)2008088
9-74630300-C-T Uncertain significance (Jul 15, 2022)1878889
9-74630301-A-C Likely benign (Mar 25, 2021)1544307
9-74630313-T-TG Pathogenic (May 06, 2022)2134793
9-74630316-C-T Likely benign (Jul 29, 2022)1947724
9-74630317-G-A Uncertain significance (Oct 22, 2022)1722048
9-74630329-G-A Uncertain significance (Jan 14, 2022)1519722
9-74630330-G-T Uncertain significance (Jun 24, 2022)2010063
9-74630333-TC-T Pathogenic (Apr 14, 2022)1678868
9-74630340-C-T Likely benign (Jul 19, 2022)1546650
9-74630341-G-A Uncertain significance (May 18, 2023)1410644
9-74630343-A-C Likely benign (Jun 15, 2022)2007340
9-74630349-C-T Benign (Nov 01, 2023)782753
9-74630351-CAT-C Pathogenic (Sep 09, 2021)1404805
9-74630355-T-C Likely benign (Nov 20, 2023)1620529
9-74630355-T-G Uncertain significance (Apr 17, 2023)2094337
9-74630370-A-T Uncertain significance (May 27, 2022)2193303

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RORBprotein_codingprotein_codingENST00000376896 10195813
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000085900000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.081162540.4560.00001353033
Missense in Polyphen886.3110.0926881042
Synonymous0.008801011010.9990.00000635827
Loss of Function4.78026.60.000.00000134304

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Nuclear receptor that binds DNA as a monomer to ROR response elements (RORE) containing a single core motif half-site 5'-AGGTCA-3' preceded by a short A-T-rich sequence. Considered to have intrinsic transcriptional activity, have some natural ligands such as all-trans retinoic acid (ATRA) and other retinoids which act as inverse agonists repressing the transcriptional activity. Required for normal postnatal development of rod and cone photoreceptor cells. Modulates rod photoreceptors differentiation at least by inducing the transcription factor NRL-mediated pathway. In cone photoreceptor cells, regulates transcription of OPN1SW. Involved in the regulation of the period length and stability of the circadian rhythm. May control cytoarchitectural patterning of neocortical neurons during development. May act in a dose-dependent manner to regulate barrel formation upon innervation of layer IV neurons by thalamocortical axons. May play a role in the suppression of osteoblastic differentiation through the inhibition of RUNX2 transcriptional activity (By similarity). {ECO:0000250}.;
Pathway
Circadian rhythm - Homo sapiens (human);NHR;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

pRec
0.178

Intolerance Scores

loftool
rvis_EVS
-0.41
rvis_percentile_EVS
26.23

Haploinsufficiency Scores

pHI
0.807
hipred
Y
hipred_score
0.817
ghis
0.594

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.922

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rorb
Phenotype
growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; reproductive system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process
regulation of transcription, DNA-templated;transcription initiation from RNA polymerase II promoter;G protein-coupled receptor signaling pathway;visual perception;intracellular receptor signaling pathway;amacrine cell differentiation;eye photoreceptor cell development;regulation of circadian rhythm;steroid hormone mediated signaling pathway;negative regulation of osteoblast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;retinal rod cell development;retinal cone cell development;rhythmic process;retina development in camera-type eye;cellular response to retinoic acid
Cellular component
nucleus;nucleoplasm
Molecular function
RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;steroid hormone receptor activity;nuclear receptor activity;protein binding;transcription factor binding;zinc ion binding;melatonin receptor activity