TOP1MT
Basic information
Region (hg38): 8:143304384-143359979
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (188 variants)
- not_specified (101 variants)
- Premature_ovarian_insufficiency (1 variants)
- Sensorineural_hearing_loss_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOP1MT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000052963.3. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 41 | 52 | ||||
missense | 142 | 14 | 164 | |||
nonsense | 5 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
Total | 0 | 0 | 159 | 55 | 14 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TOP1MT | protein_coding | protein_coding | ENST00000329245 | 14 | 55596 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.44e-34 | 2.00e-7 | 125367 | 0 | 381 | 125748 | 0.00152 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.109 | 393 | 387 | 1.02 | 0.0000255 | 3914 |
Missense in Polyphen | 146 | 135.24 | 1.0796 | 1548 | ||
Synonymous | 0.134 | 163 | 165 | 0.987 | 0.0000120 | 1143 |
Loss of Function | -1.70 | 45 | 34.3 | 1.31 | 0.00000197 | 368 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00400 | 0.00393 |
Ashkenazi Jewish | 0.00212 | 0.00209 |
East Asian | 0.00191 | 0.00190 |
Finnish | 0.000791 | 0.000786 |
European (Non-Finnish) | 0.00137 | 0.00135 |
Middle Eastern | 0.00191 | 0.00190 |
South Asian | 0.00162 | 0.00160 |
Other | 0.00149 | 0.00147 |
dbNSFP
Source:
- Function
- FUNCTION: Releases the supercoiling and torsional tension of DNA introduced during duplication of mitochondrial DNA by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then rotates around the intact phosphodiester bond on the opposing strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). {ECO:0000250, ECO:0000269|PubMed:11526219}.;
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.985
- rvis_EVS
- -0.44
- rvis_percentile_EVS
- 24.71
Haploinsufficiency Scores
- pHI
- 0.185
- hipred
- N
- hipred_score
- 0.219
- ghis
- 0.491
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.190
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Top1mt
- Phenotype
- liver/biliary system phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- DNA replication;DNA topological change
- Cellular component
- nucleus;chromosome;mitochondrion;mitochondrial nucleoid
- Molecular function
- DNA binding;DNA topoisomerase type I activity