MYO16

myosin XVI, the group of Myosin heavy chains, class XVI|Protein phosphatase 1 regulatory subunits|Ankyrin repeat domain containing

Basic information

Region (hg38): 13:108596151-109208005

Links

ENSG00000041515 ∙ NCBI:23026 ∙ OMIM:615479 ∙ HGNC:29822 ∙ Uniprot:Q9Y6X6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYO16 gene.

• Inborn genetic diseases (86 variants)
• not provided (53 variants)
• MYO16-associated developmental delay (1 variants)
• MYO16-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYO16 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				16	14	30
missense		1	81	14	5	101
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					4	4
non coding				2	2	4
Total	0	1	81	32	21

Variants in MYO16

This is a list of pathogenic ClinVar variants found in the MYO16 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-108665911-T-C		MYO16-related disorder	Benign (Dec 31, 2019)
13-108665916-C-A		not specified	Uncertain significance (Jan 09, 2024)
13-108665917-C-G			Likely benign (Sep 21, 2018)
13-108665952-C-T		not specified	Uncertain significance (Nov 17, 2023)
13-108665961-T-C		not specified	Uncertain significance (Feb 16, 2023)
13-108665968-A-G		MYO16-related disorder	Benign (Apr 05, 2019)
13-108666022-G-A		MYO16-related disorder	Benign/Likely benign (Dec 31, 2019)
13-108666025-C-T			Benign (Dec 31, 2019)
13-108666084-C-T		not specified	Uncertain significance (Oct 25, 2023)
13-108666104-A-G		not specified	Likely benign (Feb 03, 2022)
13-108712653-G-T		MYO16-related disorder	Likely benign (Oct 28, 2019)
13-108712701-C-T			Likely benign (Dec 13, 2018)
13-108712702-G-A		not specified	Uncertain significance (Nov 30, 2022)
13-108727441-G-T		not specified	Uncertain significance (Feb 23, 2023)
13-108727458-G-T		not specified	Uncertain significance (Apr 11, 2023)
13-108727495-A-G		not specified	Uncertain significance (Dec 13, 2023)
13-108727509-G-A		not specified	Uncertain significance (Mar 08, 2024)
13-108785665-A-G		not specified	Uncertain significance (Jan 25, 2024)
13-108785736-T-A		MYO16-related disorder	Benign (Oct 18, 2019)
13-108793536-C-T		not specified	Uncertain significance (Feb 23, 2023)
13-108793537-G-T		not specified	Uncertain significance (Jan 23, 2023)
13-108793560-A-G		not specified	Uncertain significance (Mar 01, 2023)
13-108793562-G-A		not specified	Uncertain significance (Nov 10, 2021)
13-108793621-A-G		not specified	Uncertain significance (Nov 03, 2022)
13-108793628-A-C		not specified	Likely benign (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYO16	protein_coding	protein_coding	ENST00000356711	34	611856

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00149	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	917	1.01e+3	0.909	0.0000576	12060
Missense in Polyphen		267	377.53	0.70723		4647
Synonymous	-0.143	429	425	1.01	0.0000279	3597
Loss of Function	7.20	16	89.5	0.179	0.00000485	1061

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000241
Ashkenazi Jewish	0.00	0.00
East Asian	0.000376	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.000376	0.000326
South Asian	0.0000654	0.0000653
Other	0.000531	0.000489

dbNSFP

Source: dbNSFP

• 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. May be involved in targeting of the catalytic subunit of protein phosphatase 1 during brain development. Activates PI3K and concomitantly recruits the WAVE1 complex to the close vicinity of PI3K and regulates neuronal morphogenesis (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0927

Intolerance Scores

• loftool: 0.234
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.365
• hipred: Y
• hipred_score: 0.639
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Myo16
• 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)

Gene ontology

• Biological process: negative regulation of cell population proliferation;cerebellum development;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleoplasm;cytoplasm;plasma membrane;myosin complex;perinuclear region of cytoplasm
• Molecular function: motor activity;protein binding;ATP binding;actin filament binding