TMEM230
Basic information
Region (hg38): 20:5068232-5113087
Previous symbols: [ "C20orf30" ]
Links
Phenotypes
GenCC
Source:
- Parkinson disease (Moderate), mode of inheritance: Semidominant
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM230 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 | 12 | |||||
| missense | 18 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 3 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 3 | 3 | ||||
| non coding | 14 | |||||
| Total | 1 | 0 | 23 | 16 | 14 |
Highest pathogenic variant AF is 0.0000131
Variants in TMEM230
This is a list of pathogenic ClinVar variants found in the TMEM230 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMEM230 | protein_coding | protein_coding | ENST00000342308 | 5 | 13264 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000181 | 0.480 | 125727 | 0 | 20 | 125747 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.360 | 84 | 93.8 | 0.895 | 0.00000490 | 1139 |
| Missense in Polyphen | 10 | 21.532 | 0.46442 | 278 | ||
| Synonymous | 0.444 | 35 | 38.5 | 0.909 | 0.00000204 | 390 |
| Loss of Function | 0.325 | 6 | 6.92 | 0.867 | 2.97e-7 | 98 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000618 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000272 | 0.000272 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000441 | 0.0000439 |
| Middle Eastern | 0.000272 | 0.000272 |
| South Asian | 0.000261 | 0.000261 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in trafficking and recycling of synaptic vesicles. {ECO:0000269|PubMed:27270108}.;
- Disease
- DISEASE: Parkinson disease (PARK) [MIM:168600]: A complex neurodegenerative disorder characterized by bradykinesia, resting tremor, muscular rigidity and postural instability. Additional features are characteristic postural abnormalities, dysautonomia, dystonic cramps, and dementia. The pathology of Parkinson disease involves the loss of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies (intraneuronal accumulations of aggregated proteins), in surviving neurons in various areas of the brain. The disease is progressive and usually manifests after the age of 50 years, although early-onset cases (before 50 years) are known. The majority of the cases are sporadic suggesting a multifactorial etiology based on environmental and genetic factors. However, some patients present with a positive family history for the disease. Familial forms of the disease usually begin at earlier ages and are associated with atypical clinical features. {ECO:0000269|PubMed:27270108}. Note=The gene represented in this entry may be involved in disease pathogenesis. Genetic variants in TMEM230 and DNAJC13 have been found in the same large multigenerational family with adult-onset Parkinson disease. The pathological role of each gene and therefore the exact molecular basis of the disease is unclear. {ECO:0000305|PubMed:27270108}.;
Recessive Scores
- pRec
- 0.0918
Haploinsufficiency Scores
- pHI
- 0.158
- hipred
- N
- hipred_score
- 0.306
- ghis
- 0.613
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmem230
- Phenotype
Gene ontology
- Biological process
- synaptic vesicle transport
- Cellular component
- early endosome;late endosome;autophagosome;endoplasmic reticulum;trans-Golgi network;synaptic vesicle;integral component of membrane;cell junction;recycling endosome
- Molecular function