MYO1A

myosin IA, the group of Myosin heavy chains, class I

Basic information

Region (hg38): 12:57028516-57051198

Previous symbols: [ "MYHL", "DFNA48", "BBMI" ]

Links

ENSG00000166866 ∙ NCBI:4640 ∙ OMIM:601478 ∙ HGNC:7595 ∙ Uniprot:Q9UBC5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nonsyndromic genetic hearing loss (Refuted Evidence), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal dominant 48	AD	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	12596055; 12736868
The condition has variable age of onset and severity

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYO1A gene.

• not provided (70 variants)
• not specified (56 variants)
• Inborn genetic diseases (37 variants)
• Autosomal dominant nonsyndromic hearing loss 48 (5 variants)
• Nonsyndromic Hearing Loss, Dominant (4 variants)
• MYO1A-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYO1A 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				10	3	13
missense			51	20	6	77
nonsense					1	1
start loss						0
frameshift						0
inframe indel			2		1	3
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1	14	17	32
Total	0	0	54	44	28

Variants in MYO1A

This is a list of pathogenic ClinVar variants found in the MYO1A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57028736-T-C			Likely benign (Jul 20, 2018)
12-57028759-T-C		not specified	Conflicting classifications of pathogenicity (Jul 25, 2017)
12-57028777-C-G		not specified	Uncertain significance (Aug 16, 2022)
12-57028792-T-G			Likely benign (Mar 19, 2018)
12-57028796-T-C		not specified	Uncertain significance (Jan 13, 2014)
12-57028802-G-A		not specified	Uncertain significance (Dec 20, 2023)
12-57028811-T-C		not specified	Likely benign (Jun 11, 2021)
12-57028815-G-T		not specified	Uncertain significance (May 06, 2022)
12-57028857-G-C		not specified	Uncertain significance (Nov 17, 2022)
12-57028861-T-G		not specified	Benign (Dec 31, 2019)
12-57028944-A-T			Benign (Jul 05, 2018)
12-57029038-G-A			Likely benign (Jul 04, 2018)
12-57029142-C-T		not specified	Uncertain significance (Jul 16, 2021)
12-57029150-G-A		not specified	Benign (May 09, 2017)
12-57029152-A-G			Likely benign (Apr 27, 2018)
12-57029165-G-A		not specified	Uncertain significance (Sep 14, 2021)
12-57029183-C-T		MYO1A-related disorder	Likely benign (Mar 21, 2019)
12-57029217-C-T		not specified	Conflicting classifications of pathogenicity (Sep 09, 2018)
12-57029218-G-A		not specified	Benign (Dec 31, 2019)
12-57029219-C-T		not specified	Uncertain significance (Jun 13, 2022)
12-57029250-C-T		Malignant tumor of prostate	Uncertain significance (-)
12-57029304-C-T			Likely benign (May 26, 2021)
12-57029413-T-C			Benign (Jun 21, 2018)
12-57029440-T-C		not specified • MYO1A-related disorder	Conflicting classifications of pathogenicity (Mar 28, 2019)
12-57029472-C-A		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYO1A	protein_coding	protein_coding	ENST00000442789	27	22682

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.90e-46	3.48e-8	124283	7	1458	125748	0.00584

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.495	588	555	1.06	0.0000340	6804
Missense in Polyphen		236	210.32	1.1221		2618
Synonymous	0.333	216	222	0.972	0.0000130	2029
Loss of Function	-0.578	66	61.1	1.08	0.00000375	710

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0100	0.0100
Ashkenazi Jewish	0.00636	0.00637
East Asian	0.00517	0.00518
Finnish	0.00342	0.00342
European (Non-Finnish)	0.00621	0.00604
Middle Eastern	0.00517	0.00518
South Asian	0.00686	0.00682
Other	0.00719	0.00703

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in directing the movement of organelles along actin filaments. {ECO:0000305}.

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• loftool: 0.187
• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.31

Haploinsufficiency Scores

• pHI: 0.0697
• hipred: N
• hipred_score: 0.200

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.899

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myo1a
• Phenotype: digestive/alimentary phenotype

Gene ontology

• Biological process: sensory perception of sound;microvillus assembly;vesicle localization
• Cellular component: cytoplasm;microvillus;brush border;basal plasma membrane;basolateral plasma membrane;apical plasma membrane;lateral plasma membrane;myosin complex;cortical actin cytoskeleton;filamentous actin;plasma membrane raft
• Molecular function: motor activity;calmodulin binding;ATP binding;actin filament binding