MYO1D
Basic information
Region (hg38): 17:32492522-32877177
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 MYO1D 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 | 5 | |||||
| missense | 49 | 53 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 3 | 3 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 49 | 4 | 6 |
Variants in MYO1D
This is a list of pathogenic ClinVar variants found in the MYO1D 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 |
|---|---|---|---|---|---|
| MYO1D | protein_coding | protein_coding | ENST00000318217 | 22 | 384656 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.28e-12 | 1.00 | 125655 | 0 | 93 | 125748 | 0.000370 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.36 | 487 | 579 | 0.841 | 0.0000344 | 6652 |
| Missense in Polyphen | 159 | 216.13 | 0.73567 | 2502 | ||
| Synonymous | 0.109 | 207 | 209 | 0.990 | 0.0000123 | 1870 |
| Loss of Function | 3.36 | 29 | 56.2 | 0.516 | 0.00000329 | 638 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000867 | 0.000867 |
| Ashkenazi Jewish | 0.000398 | 0.000397 |
| East Asian | 0.000383 | 0.000381 |
| Finnish | 0.000417 | 0.000416 |
| European (Non-Finnish) | 0.000354 | 0.000343 |
| Middle Eastern | 0.000383 | 0.000381 |
| South Asian | 0.000301 | 0.000294 |
| Other | 0.000498 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements. Their highly divergent tails are presumed to bind to membranous compartments, which would be moved relative to actin filaments (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.154
Intolerance Scores
- loftool
- rvis_EVS
- -0.64
- rvis_percentile_EVS
- 16.71
Haploinsufficiency Scores
- pHI
- 0.888
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.553
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.922
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Myo1d
- Phenotype
Gene ontology
- Biological process
- negative regulation of phosphatase activity;forebrain development;cellular localization;early endosome to recycling endosome transport
- Cellular component
- endosome;smooth endoplasmic reticulum;cytosol;brush border;basolateral plasma membrane;myosin complex;axon;axolemma;cytoplasmic vesicle;neuron projection;neuronal cell body;myelin sheath;plasma membrane raft;extracellular exosome;apical dendrite
- Molecular function
- microfilament motor activity;calmodulin binding;ATP binding;protein domain specific binding;actin-dependent ATPase activity;calcium-dependent protein binding;actin filament binding