RND3

Rho family GTPase 3, the group of Rho family GTPases

Basic information

Region (hg38): 2:150468195-150539011

Previous symbols: [ "ARHE" ]

Links

ENSG00000115963 ∙ NCBI:390 ∙ OMIM:602924 ∙ HGNC:671 ∙ Uniprot:P61587 ∙ 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 RND3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RND3 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					2	2
missense			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	3

Variants in RND3

This is a list of pathogenic ClinVar variants found in the RND3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-150470030-G-A		not specified	Benign (Dec 12, 2023)
2-150470081-G-C		not specified	Uncertain significance (Feb 17, 2022)
2-150470103-G-A		not specified	Uncertain significance (Jan 04, 2024)
2-150470118-T-G		not specified	Uncertain significance (Sep 11, 2024)
2-150470120-G-T		not specified	Uncertain significance (Jan 15, 2025)
2-150470148-C-T		not specified	Uncertain significance (Oct 25, 2022)
2-150470166-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-150470170-A-G			Benign (Mar 29, 2018)
2-150470226-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-150470228-A-G		not specified	Uncertain significance (Jan 06, 2023)
2-150471671-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-150471672-T-C			Likely benign (Jun 01, 2025)
2-150474883-G-A		not specified	Uncertain significance (Jan 20, 2025)
2-150487269-T-G		not specified	Uncertain significance (Sep 16, 2021)
2-150487354-C-T		not specified	Uncertain significance (Feb 05, 2024)
2-150487375-T-C		not specified	Uncertain significance (Jan 15, 2025)
2-150487403-T-C			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RND3	protein_coding	protein_coding	ENST00000375734	5	70817

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.967	0.0331	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	85	140	0.608	0.00000767	1606
Missense in Polyphen		27	60.635	0.44528		681
Synonymous	-0.694	62	55.4	1.12	0.00000334	451
Loss of Function	3.01	0	10.6	0.00	4.46e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds GTP but lacks intrinsic GTPase activity and is resistant to Rho-specific GTPase-activating proteins.

Recessive Scores

• pRec: 0.163

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.453
• hipred: Y
• hipred_score: 0.853
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.676

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnd3
• Phenotype: craniofacial phenotype; muscle phenotype; growth/size/body region phenotype; renal/urinary system phenotype; skeleton 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); hearing/vestibular/ear 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: actin filament organization;cell adhesion;Rho protein signal transduction;regulation of cell shape;actin cytoskeleton organization;regulation of cell migration;establishment or maintenance of actin cytoskeleton polarity;regulation of actin cytoskeleton organization;actin filament bundle assembly
• Cellular component: Golgi membrane;cytoplasm;plasma membrane;focal adhesion;cell cortex;cell division site;intracellular membrane-bounded organelle
• Molecular function: GTPase activity;protein binding;GTP binding;protein kinase binding