RHOT2

ras homolog family member T2, the group of Miro like atypical Rho GTPases|EF-hand domain containing

Basic information

Region (hg38): 16:668100-674174

Previous symbols: [ "C16orf39", "ARHT2" ]

Links

ENSG00000140983 ∙ NCBI:89941 ∙ OMIM:613889 ∙ HGNC:21169 ∙ Uniprot:Q8IXI1 ∙ 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 RHOT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHOT2 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				1	5	6
missense			47	9	1	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	47	10	6

Variants in RHOT2

This is a list of pathogenic ClinVar variants found in the RHOT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-668359-T-G		not specified	Uncertain significance (Dec 18, 2023)
16-668389-T-G		not specified	Uncertain significance (Apr 18, 2023)
16-668400-T-C		not specified	Uncertain significance (Dec 10, 2024)
16-668509-A-T		not specified	Uncertain significance (Mar 07, 2024)
16-668521-G-A		not specified	Uncertain significance (Jun 18, 2024)
16-668533-C-A		not specified	Uncertain significance (May 01, 2024)
16-668542-G-A		not specified	Uncertain significance (May 02, 2023)
16-668545-C-T		not specified	Uncertain significance (May 10, 2024)
16-668683-G-A		not specified	Likely benign (May 25, 2022)
16-668688-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-668690-G-C		not specified	Uncertain significance (Oct 01, 2024)
16-669553-G-A		not specified	Uncertain significance (Apr 09, 2024)
16-669569-T-C		not specified	Uncertain significance (Nov 29, 2023)
16-669593-C-T		not specified	Uncertain significance (Oct 16, 2024)
16-669612-C-T			Likely benign (Jul 21, 2018)
16-670126-C-G		not specified	Uncertain significance (May 27, 2022)
16-670129-A-G		not specified	Uncertain significance (Mar 27, 2023)
16-670165-C-G		not specified	Uncertain significance (Jan 24, 2024)
16-670253-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-670259-A-C		not specified	Uncertain significance (May 23, 2023)
16-670293-G-A		not specified	Uncertain significance (Dec 14, 2021)
16-670341-T-C		not specified	Uncertain significance (Oct 30, 2023)
16-670350-G-A		not specified	Uncertain significance (Sep 14, 2022)
16-670460-C-T		not specified	Uncertain significance (Jun 17, 2024)
16-670480-A-G		not specified	Uncertain significance (Jun 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHOT2	protein_coding	protein_coding	ENST00000315082	19	6089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.90e-27	0.0000582	125363	0	131	125494	0.000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.40	479	400	1.20	0.0000273	3940
Missense in Polyphen		126	109.63	1.1493		1147
Synonymous	-4.66	267	186	1.43	0.0000143	1272
Loss of Function	-0.503	38	34.8	1.09	0.00000175	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000792	0.000780
Ashkenazi Jewish	0.000307	0.000298
East Asian	0.000555	0.000544
Finnish	0.000290	0.000277
European (Non-Finnish)	0.000663	0.000644
Middle Eastern	0.000555	0.000544
South Asian	0.000717	0.000654
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 (By similarity). {ECO:0000250, ECO:0000269|PubMed:16630562}.
• Pathway: Mitophagy - animal - Homo sapiens (human);Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.803
• rvis_EVS: -1.12
• rvis_percentile_EVS: 6.61

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.170
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rhot2
• Phenotype: skeleton phenotype; normal phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

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