MYL9
Basic information
Region (hg38): 20:36541497-36551447
Links
Phenotypes
GenCC
Source:
- megacystis-microcolon-intestinal hypoperistalsis syndrome 4 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Megacystis-microcolon-intestinal hypoperistalsis syndrome 4 | AR | Gastrointestinal; Renal | Individuals have been described as benefiting from surgical interventions, including related to renal anomalies and nephrolithiasis; Multivisceral transplantation has been described | Gastrointestinal; Genitourinary; Musculoskeletal; Ophthalmologic; Renal | 27481187; 29453416; 33031641 |
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 MYL9 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in MYL9
This is a list of pathogenic ClinVar variants found in the MYL9 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 |
|---|---|---|---|---|---|
| MYL9 | protein_coding | protein_coding | ENST00000279022 | 3 | 8342 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0198 | 0.757 | 125728 | 0 | 18 | 125746 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.17 | 83 | 119 | 0.698 | 0.00000773 | 1176 |
| Missense in Polyphen | 17 | 30.866 | 0.55077 | 364 | ||
| Synonymous | 0.375 | 43 | 46.2 | 0.930 | 0.00000332 | 301 |
| Loss of Function | 0.841 | 3 | 5.04 | 0.596 | 2.13e-7 | 63 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000146 | 0.000146 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000277 | 0.000272 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000711 | 0.0000703 |
| Middle Eastern | 0.000277 | 0.000272 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Myosin regulatory subunit that plays an important role in regulation of both smooth muscle and nonmuscle cell contractile activity via its phosphorylation. Implicated in cytokinesis, receptor capping, and cell locomotion. {ECO:0000269|PubMed:11942626, ECO:0000269|PubMed:2526655}.;
- Pathway
- Focal adhesion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Tight junction - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Focal Adhesion;Striated Muscle Contraction;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Developmental Biology;Smooth Muscle Contraction;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;EPH-Ephrin signaling;EPHA-mediated growth cone collapse;RHO GTPases Activate ROCKs;RHO GTPases activate PAKs;RHO GTPases activate PKNs;RHO GTPases activate CIT;Muscle contraction;RHO GTPase Effectors;Signaling by Rho GTPases;Sema4D induced cell migration and growth-cone collapse;Sema4D in semaphorin signaling;Semaphorin interactions;Axon guidance;Integrin-linked kinase signaling;Transcriptional regulation by RUNX1
(Consensus)
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- loftool
- 0.626
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.284
- hipred
- N
- hipred_score
- 0.455
- ghis
- 0.646
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.982
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Myl9
- Phenotype
Gene ontology
- Biological process
- muscle contraction;regulation of muscle contraction;regulation of megakaryocyte differentiation;platelet aggregation
- Cellular component
- stress fiber;cytosol;muscle myosin complex;Z disc
- Molecular function
- calcium ion binding;structural constituent of muscle;myosin heavy chain binding