RHOT2
protein-codingras homolog family member T2, the group of Miro like atypical Rho GTPases|EF-hand domain containing
Gene summary
This gene encodes a member of the Rho family of GTPases. The encoded protein is localized to the outer mitochondrial membrane and plays a role in mitochondrial trafficking and fusion-fission dynamics. [provided by RefSeq, Nov 2011]
- C16orf39
- ARHT2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RHOT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138769.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 5 | 8 | ||
| missense | 136 | 18 | 1 | 155 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 146 | 19 | 6 | 171 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_620124.1 | 19 | MANE Select | |
| Ensembl | ENSP00000321971.4 | 19 | MANE Select | |
| RefSeq | NP_001339204.1 | 19 | Standard | |
| RefSeq | NP_001339205.1 | 18 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mitophagy - animal - Homo sapiens (human)
- Signal Transduction
- Rho GTPase cycle
- Signaling by Rho GTPases
Biological Process
- mitochondrion organization
- Rho protein signal transduction
- regulation of mitochondrion organization
- cellular homeostasis
- mitochondrion transport along microtubule
Molecular Function
- GTPase activity
- calcium ion binding
- protein binding
- GTP binding
Cellular Component
- mitochondrion
- cytosol
- plasma membrane
- membrane
- integral component of mitochondrial outer membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000315082
- Coding exons
- 19
- Length
- 6089
- Individuals with no LoFs
- 125363
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 131
- Defined
- 125494
- p
- 0.000522
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.40 | 479 | 400 | 1.20 | 0.0000273 | 3940 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00044 | 0.00043 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.00031 | 0.00030 | rare |
| East Asian | 0.00056 | 0.00054 | rare |
| Finnish | 0.00029 | 0.00028 | rare |
| European (Non-Finnish) | 0.00066 | 0.00064 | rare |
| South Asian | 0.00072 | 0.00065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- LoFtool
- 0.803
- RVIS EVS
- -1.12
- RVIS percentile EVS
- 6.61
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.943
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |