MYO9A

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

Basic information

Region (hg38): 15:71822290-72118577

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myasthenic syndrome, congenital, 24, presynaptic	AR	Musculoskeletal; Neurologic	Individuals have been described as benefiting from medical management (with pyridostigmine and 3,4-DAP)	Musculoskeletal; Neurologic	26752647; 27259756

ClinVar

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

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.

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			4	31	10	45
missense			154	17	14	185
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1		1		2
splice region			1	3	2	6
non coding			1	3	50	54
Total	0	1	159	52	74

Variants in MYO9A

This is a list of pathogenic ClinVar variants found in the MYO9A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-71826436-G-C			Benign (May 13, 2021)
15-71826584-A-T		Inborn genetic diseases	Uncertain significance (Jul 19, 2022)
15-71826657-G-A		Inborn genetic diseases	Uncertain significance (May 20, 2024)
15-71826660-C-A		Inborn genetic diseases	Uncertain significance (Mar 12, 2024)
15-71826665-A-C		Inborn genetic diseases	Uncertain significance (Apr 05, 2023)
15-71826680-G-A		Inborn genetic diseases	Uncertain significance (Aug 04, 2021)
15-71826697-C-G		MYO9A-related disorder	Uncertain significance (Sep 05, 2023)
15-71826716-T-G			Benign (May 04, 2021)
15-71826742-C-T			Likely benign (Jan 08, 2018)
15-71826744-G-T		Inborn genetic diseases	Uncertain significance (May 29, 2024)
15-71826765-T-C		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
15-71826774-G-A		Inborn genetic diseases	Uncertain significance (Feb 13, 2024)
15-71826777-T-C		Inborn genetic diseases	Uncertain significance (Oct 21, 2021)
15-71826845-C-T		Inborn genetic diseases	Uncertain significance (Apr 05, 2023)
15-71826905-G-A		Inborn genetic diseases	Uncertain significance (Dec 16, 2022)
15-71826950-A-G		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
15-71826953-G-A		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
15-71826982-C-A		Inborn genetic diseases	Uncertain significance (Oct 06, 2021)
15-71827003-C-G		Myasthenic syndrome, congenital, 24, presynaptic	Uncertain significance (-)
15-71827011-C-G		Myasthenic syndrome, congenital, 24, presynaptic	Uncertain significance (Nov 18, 2022)
15-71827050-C-CA		MYO9A-related disorder	Likely benign (Jun 11, 2019)
15-71827082-C-T			Benign (May 24, 2021)
15-71827228-C-T			Benign (May 14, 2021)
15-71827899-T-C		MYO9A-related disorder	Benign (May 05, 2021)
15-71827917-T-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYO9A	protein_coding	protein_coding	ENST00000356056	41	296287

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.489	0.511	125569	1	178	125748	0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	1156	1.33e+3	0.866	0.0000709	16794
Missense in Polyphen		278	414.05	0.67141		5226
Synonymous	-0.230	466	460	1.01	0.0000221	4745
Loss of Function	8.31	30	134	0.224	0.00000811	1606

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.00	0.00
East Asian	0.00530	0.00523
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.00530	0.00523
South Asian	0.000757	0.000719
Other	0.00115	0.00114

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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