GeneBe

MYO9A

myosin IXA, the group of Myosin heavy chains, class IX

Basic information

Region (hg38): 15:71822291-72118577

Links

ENSG00000066933 ∙ NCBI:4649 ∙ OMIM:604875 ∙ HGNC:7608 ∙ Uniprot:B2RTY4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • myasthenic syndrome, congenital, 24, presynaptic (Strong), mode of inheritance: AR
  • myasthenic syndrome, congenital, 24, presynaptic (Strong), mode of inheritance: AR
  • myasthenic syndrome, congenital, 24, presynaptic (Limited), mode of inheritance: AR
  • presynaptic congenital myasthenic syndrome (Supportive), mode of inheritance: AD
  • myasthenic syndrome, congenital, 24, presynaptic (Limited), mode of inheritance: Unknown
  • arthrogryposis syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Myasthenic syndrome, congenital, 24, presynapticARMusculoskeletal; NeurologicIndividuals have been described as benefiting from medical management (with pyridostigmine and 3,4-DAP)Musculoskeletal; Neurologic26752647; 27259756

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYO9A gene.

  • Inborn_genetic_diseases (304 variants)
  • not_provided (99 variants)
  • Myasthenic_syndrome,_congenital,_24,_presynaptic (27 variants)
  • MYO9A-related_disorder (27 variants)
  • Focal_segmental_glomerulosclerosis (4 variants)
  • not_specified (2 variants)
  • Bronchiectasis (2 variants)
  • Flexion_contracture (2 variants)
  • See_cases (2 variants)
  • Presynaptic_congenital_myasthenic_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYO9A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006901.4. 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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
35
clinvar
8
clinvar
 47
missense
1
clinvar
317
clinvar
29
clinvar
9
clinvar
 356
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
 2
Total 0 2 321 65 17

Highest pathogenic variant AF is 0.00000136885

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MYO9Aprotein_codingprotein_codingENST00000356056 41296287
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.4890.51112556911781257480.000712
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.7411561.33e+30.8660.000070916794
Missense in Polyphen278414.050.671415226
Synonymous-0.2304664601.010.00002214745
Loss of Function8.31301340.2240.000008111606

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001020.00102
Ashkenazi Jewish0.000.00
East Asian0.005300.00523
Finnish0.0001860.000185
European (Non-Finnish)0.0002300.000229
Middle Eastern0.005300.00523
South Asian0.0007570.000719
Other0.001150.00114

dbNSFP

Source: dbNSFP

Function
FUNCTION: Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements. Regulates Rho by stimulating it's GTPase activity in neurons, has a role in the regulation of neuronal morphology and function. {ECO:0000250|UniProtKB:Q9Z1N3}.;
Pathway
Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

pRec
0.113

Intolerance Scores

loftool
0.0452
rvis_EVS
-0.7
rvis_percentile_EVS
14.79

Haploinsufficiency Scores

pHI
0.766
hipred
Y
hipred_score
0.652
ghis
0.568

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.831

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Myo9a
Phenotype
cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
visual perception;bioluminescence;cell junction assembly;intracellular signal transduction;positive regulation of GTPase activity;establishment of epithelial cell apical/basal polarity;regulation of small GTPase mediated signal transduction
Cellular component
cytosol;integral component of membrane;unconventional myosin complex
Molecular function
motor activity;actin binding;GTPase activator activity;protein binding;ATP binding;metal ion binding