TOMM7
Basic information
Region (hg38): 7:22812628-22822849
Links
Phenotypes
GenCC
Source:
- Garg-Mishra progeroid syndrome (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Garg-Mishra progeroid syndrome | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic | 36282599; 36299998 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM7 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in TOMM7
This is a list of pathogenic ClinVar variants found in the TOMM7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-22813187-T-C | TOMM7-related early onset Leigh disease | Uncertain significance (-) | ||
| 7-22818025-C-T | not specified | Uncertain significance (Apr 08, 2022) | ||
| 7-22818033-G-C | not specified | Uncertain significance (Oct 14, 2023) | ||
| 7-22822694-G-A | Garg-Mishra progeroid syndrome | Pathogenic (Nov 13, 2023) | ||
| 7-22822707-A-G | See cases • Garg-Mishra progeroid syndrome | Pathogenic/Likely pathogenic (Nov 13, 2023) | ||
| 7-22822754-T-C | not specified | Uncertain significance (Mar 07, 2023) | ||
| 7-22822757-G-T | not specified | Uncertain significance (Nov 30, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TOMM7 | protein_coding | protein_coding | ENST00000358435 | 3 | 10220 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00977 | 0.616 | 125743 | 0 | 4 | 125747 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.153 | 31 | 28.7 | 1.08 | 0.00000130 | 353 |
| Missense in Polyphen | 5 | 5.2373 | 0.95469 | 68 | ||
| Synonymous | -1.96 | 18 | 10.1 | 1.79 | 5.16e-7 | 102 |
| Loss of Function | 0.336 | 3 | 3.70 | 0.811 | 1.57e-7 | 40 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for assembly and stability of the TOM complex. Positive regulator of PRKN translocation to damaged mitochondria. Acts probably by stabilizing PINK1 on the outer membrane of depolarized mitochondria. {ECO:0000269|PubMed:18331822, ECO:0000269|PubMed:24270810}.;
- Pathway
- Mitophagy - animal - Homo sapiens (human);Metabolism of proteins;Pink/Parkin Mediated Mitophagy;Mitophagy;Mitochondrial protein import
(Consensus)
Intolerance Scores
- loftool
- 0.474
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.0902
- hipred
- N
- hipred_score
- 0.435
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0314
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tomm7
- Phenotype
Gene ontology
- Biological process
- protein targeting to mitochondrion;protein import into mitochondrial matrix;regulation of protein stability;positive regulation of mitophagy in response to mitochondrial depolarization;positive regulation of protein targeting to mitochondrion
- Cellular component
- mitochondrion;mitochondrial outer membrane;mitochondrial outer membrane translocase complex;integral component of membrane
- Molecular function
- protein binding;protein transmembrane transporter activity