RHOT1

ras homolog family member T1, the group of EF-hand domain containing|Miro like atypical Rho GTPases

Basic information

Region (hg38): 17:32142453-32253374

Previous symbols: [ "ARHT1" ]

Links

ENSG00000126858 ∙ NCBI:55288 ∙ OMIM:613888 ∙ HGNC:21168 ∙ Uniprot:Q8IXI2 ∙ 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 RHOT1 gene.

• Inborn genetic diseases (13 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHOT1 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in RHOT1

This is a list of pathogenic ClinVar variants found in the RHOT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-32171097-A-G		not specified	Uncertain significance (Nov 22, 2023)
17-32176201-A-G		not specified	Uncertain significance (Aug 22, 2023)
17-32182840-A-G		not specified	Uncertain significance (Sep 25, 2023)
17-32192231-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-32193188-A-G		not specified	Uncertain significance (Jan 26, 2022)
17-32193225-C-A		not specified	Uncertain significance (Mar 29, 2022)
17-32199460-C-T		not specified	Uncertain significance (Jul 12, 2023)
17-32202818-A-G		not specified	Uncertain significance (Sep 20, 2023)
17-32202862-A-G		not specified	Uncertain significance (Sep 13, 2023)
17-32203944-T-C		not specified	Uncertain significance (Nov 05, 2021)
17-32208123-G-A		not specified	Uncertain significance (Aug 17, 2021)
17-32208162-T-G		not specified	Uncertain significance (Jan 24, 2024)
17-32208261-C-G		not specified	Uncertain significance (Apr 05, 2023)
17-32209372-C-T		not specified	Uncertain significance (May 04, 2022)
17-32209421-T-A		not specified	Uncertain significance (Aug 08, 2022)
17-32211124-G-A		not specified	Uncertain significance (Feb 17, 2024)
17-32211142-C-T		not specified	Uncertain significance (Apr 27, 2022)
17-32211172-A-G		not specified	Uncertain significance (Oct 06, 2023)
17-32211185-C-G		not specified	Uncertain significance (Jan 16, 2024)
17-32211267-G-A			not provided (-)
17-32224620-G-A		not specified	Uncertain significance (Feb 13, 2024)
17-32224729-G-A		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHOT1	protein_coding	protein_coding	ENST00000358365	21	110921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.799	0.201	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.47	230	362	0.635	0.0000179	4569
Missense in Polyphen		40	107.97	0.37049		1376
Synonymous	1.62	101	124	0.815	0.00000619	1243
Loss of Function	4.97	9	44.9	0.200	0.00000248	530

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000113	0.000109
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.000113	0.000109
South Asian	0.0000993	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial GTPase involved in mitochondrial trafficking. Probably involved in control of anterograde transport of mitochondria and their subcellular distribution. {ECO:0000269|PubMed:12482879, ECO:0000269|PubMed:16630562}.
• Pathway: Mitophagy - animal - Homo sapiens (human);Signal Transduction;Post-translational protein modification;Metabolism of proteins;Rho GTPase cycle;Signaling by Rho GTPases;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.709
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.204
• hipred: Y
• hipred_score: 0.639
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.419

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rhot1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory 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); normal 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); cellular phenotype; skeleton phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: rhot1b
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: mitochondrion organization;Rho protein signal transduction;regulation of mitochondrion organization;protein deubiquitination;cellular homeostasis;establishment of mitochondrion localization by microtubule attachment;regulation of neurotransmitter secretion;mitochondrion transport along microtubule;regulation of small GTPase mediated signal transduction;mitochondrial outer membrane permeabilization;regulation of organelle transport along microtubule
• Cellular component: mitochondrion;mitochondrial outer membrane;cytosol;plasma membrane;membrane;integral component of mitochondrial outer membrane
• Molecular function: molecular_function;GTPase activity;calcium ion binding;protein binding;GTP binding