RHOBTB3

Rho related BTB domain containing 3, the group of BTB domain containing

Basic information

Region (hg38): 5:95713522-95824383

Links

ENSG00000164292 ∙ NCBI:22836 ∙ OMIM:607353 ∙ HGNC:18757 ∙ Uniprot:O94955 ∙ 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 RHOBTB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHOBTB3 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						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in RHOBTB3

This is a list of pathogenic ClinVar variants found in the RHOBTB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-95731968-G-A		not specified	Uncertain significance (Oct 06, 2021)
5-95736894-A-G		not specified	Uncertain significance (Mar 11, 2024)
5-95736935-G-A		not specified	Uncertain significance (Sep 20, 2023)
5-95737016-T-C		not specified	Uncertain significance (Mar 14, 2023)
5-95737024-G-A		not specified	Uncertain significance (Jun 16, 2024)
5-95748375-G-A		not specified	Uncertain significance (Dec 19, 2023)
5-95748377-A-C		not specified	Uncertain significance (Dec 19, 2023)
5-95752264-T-C		not specified	Uncertain significance (Jun 18, 2024)
5-95752300-A-G		not specified	Uncertain significance (Apr 19, 2024)
5-95755590-A-G		not specified	Uncertain significance (Sep 25, 2023)
5-95755592-T-G		not specified	Uncertain significance (Feb 23, 2023)
5-95755645-A-C		not specified	Uncertain significance (Jan 17, 2024)
5-95755740-A-C		not specified	Uncertain significance (Dec 19, 2023)
5-95763565-G-C		not specified	Uncertain significance (Jun 09, 2022)
5-95768101-A-G		not specified	Uncertain significance (May 07, 2024)
5-95768157-G-A		not specified	Uncertain significance (Nov 18, 2022)
5-95780375-A-G		not specified	Uncertain significance (Jan 23, 2024)
5-95780407-A-G		not specified	Uncertain significance (Mar 19, 2024)
5-95783805-T-C		not specified	Uncertain significance (Jan 17, 2024)
5-95783880-A-T		not specified	Uncertain significance (Jun 07, 2024)
5-95783941-T-C		not specified	Uncertain significance (Jan 23, 2024)
5-95793068-G-A		not specified	Uncertain significance (Nov 20, 2023)
5-95793098-C-T		not specified	Uncertain significance (Nov 17, 2023)
5-95793107-A-G		not specified	Uncertain significance (Dec 08, 2023)
5-95793148-C-T		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHOBTB3	protein_coding	protein_coding	ENST00000379982	12	110862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000424	0.998	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	250	338	0.740	0.0000168	4056
Missense in Polyphen		63	84.005	0.74995		1065
Synonymous	-0.319	135	130	1.04	0.00000714	1128
Loss of Function	2.73	14	30.2	0.463	0.00000153	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000384
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000178	0.000167
Middle Eastern	0.000327	0.000326
South Asian	0.000232	0.000229
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rab9-regulated ATPase required for endosome to Golgi transport. Involved in transport vesicle docking at the Golgi complex, possibly by participating in release M6PRBP1/TIP47 from vesicles to permit their efficient docking and fusion at the Golgi. Specifically binds Rab9, but not other Rab proteins. Has low intrinsic ATPase activity due to autoinhibition, which is relieved by Rab9. {ECO:0000269|PubMed:19490898}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Intolerance Scores

• loftool: 0.693
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.231
• hipred: Y
• hipred_score: 0.585
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.867

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rhobtb3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system 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); limbs/digits/tail phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: actin filament organization;establishment or maintenance of cell polarity;Rho protein signal transduction;regulation of cell shape;male gonad development;actin cytoskeleton organization;regulation of actin cytoskeleton organization;retrograde transport, endosome to Golgi
• Cellular component: cytoplasm;cytosol;plasma membrane;cell cortex;trans-Golgi network membrane;cell projection;extracellular exosome
• Molecular function: GTPase activity;protein binding;ATP binding;GTP binding;ATPase activity;Rab GTPase binding;protein kinase binding