MYO16

protein-coding

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

Gene summary

This gene encodes an unconventional myosin protein. The encoded protein has been proposed to act as a serine/threonine phosphatase-1 targeting or regulatory subunit. Studies in a rat cell line suggest that this protein may regulate cell cycle progression. A variant within this gene may be associated with susceptibility to schizophrenia and elevated expression of this gene has been observed in the frontal cortex of human schizophrenia patients. [provided by RefSeq, Mar 2017]

MANE transcript

NM_001198950.3

Inheritance

—

ClinVar variants

P:1U:307B:77

Top phenotype

MYO16-related disorder

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr13:108,596,152-109,208,005

External References & Databases

Ensembl (ENSG00000041515)

Transcript & Mutation Effects

hg38 • Region Span ~611.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MYO16 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 316

not providedTotal: 56

MYO16-related disorderTotal: 45

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Prostate cancerTotal: 1

MYO16-associated developmental delayTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001198950.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	24 clinvar	18 clinvar	47
missense		1 clinvar	297 clinvar	27 clinvar	8 clinvar	333
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	1	307	51	26	385

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001198950.3	RefSeq	NP_001185879.1	35	MANE Select
ENST00000457511.7	Ensembl	ENSP00000401633.3	35	MANE Select
NM_015011.3	RefSeq	NP_055826.1	34	Standard
ENST00000251041.10	Ensembl	ENSP00000251041.5	24	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of cell population proliferation
cerebellum development
negative regulation of G1/S transition of mitotic cell cycle

Molecular Function

motor activity
protein binding
ATP binding
actin filament binding

Cellular Component

nucleoplasm
cytoplasm
plasma membrane
myosin complex
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356711
Coding exons: 34
Length: 611856
Individuals with no LoFs: 125710
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 125748
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.03	917	1.01e+3	0.909	0.0000576	12060
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00033	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.000065	0.000065	rare
Other	0.00053	0.00049	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.186

Gene Damage Prediction

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