TMOD4
Basic information
Region (hg38): 1:151169986-151176284
Links
Phenotypes
GenCC
Source:
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 TMOD4 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 | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 0 |
Variants in TMOD4
This is a list of pathogenic ClinVar variants found in the TMOD4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-151170526-A-C | not specified | Uncertain significance (Apr 15, 2024) | ||
| 1-151170533-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
| 1-151170615-C-G | not specified | Uncertain significance (Jun 02, 2023) | ||
| 1-151170933-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
| 1-151171464-A-G | not specified | Uncertain significance (May 28, 2024) | ||
| 1-151171488-G-A | not specified | Uncertain significance (Apr 24, 2023) | ||
| 1-151171697-T-A | not specified | Uncertain significance (Jan 18, 2023) | ||
| 1-151171722-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
| 1-151171761-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
| 1-151172270-C-T | not specified | Uncertain significance (Oct 12, 2022) | ||
| 1-151172307-G-A | not specified | Uncertain significance (Feb 14, 2023) | ||
| 1-151172325-T-C | not specified | Uncertain significance (Mar 06, 2023) | ||
| 1-151173557-C-A | not specified | Uncertain significance (Mar 02, 2023) | ||
| 1-151173615-C-G | not specified | Uncertain significance (Jan 06, 2023) | ||
| 1-151174477-C-T | not specified | Uncertain significance (Nov 19, 2022) | ||
| 1-151174517-G-A | not specified | Uncertain significance (May 13, 2022) | ||
| 1-151174825-A-T | not specified | Uncertain significance (Aug 12, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMOD4 | protein_coding | protein_coding | ENST00000295314 | 9 | 6299 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.83e-8 | 0.657 | 125602 | 1 | 144 | 125747 | 0.000577 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.715 | 177 | 206 | 0.860 | 0.0000115 | 2284 |
| Missense in Polyphen | 63 | 71.729 | 0.87831 | 834 | ||
| Synonymous | 1.05 | 61 | 72.4 | 0.842 | 0.00000378 | 642 |
| Loss of Function | 1.25 | 15 | 21.2 | 0.708 | 0.00000127 | 218 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00188 | 0.00188 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000490 | 0.000489 |
| Finnish | 0.00333 | 0.00329 |
| European (Non-Finnish) | 0.000158 | 0.000158 |
| Middle Eastern | 0.000490 | 0.000489 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.000653 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Blocks the elongation and depolymerization of the actin filaments at the pointed end. The Tmod/TM complex contributes to the formation of the short actin protofilament, which in turn defines the geometry of the membrane skeleton.;
- Pathway
- Striated Muscle Contraction;Muscle contraction
(Consensus)
Recessive Scores
- pRec
- 0.129
Intolerance Scores
- loftool
- 0.458
- rvis_EVS
- 0.33
- rvis_percentile_EVS
- 73.41
Haploinsufficiency Scores
- pHI
- 0.281
- hipred
- N
- hipred_score
- 0.350
- ghis
- 0.498
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmod4
- Phenotype
Zebrafish Information Network
- Gene name
- tmod4
- Affected structure
- fast muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased width
Gene ontology
- Biological process
- muscle contraction;myofibril assembly;pointed-end actin filament capping
- Cellular component
- striated muscle thin filament;myofibril
- Molecular function
- tropomyosin binding;actin filament binding