MYO1C

myosin IC, the group of Myosin heavy chains, class I|B-WICH chromatin-remodelling complex subunits

Basic information

Region (hg38): 17:1464185-1492686

Links

ENSG00000197879 ∙ NCBI:4641 ∙ OMIM:606538 ∙ HGNC:7597 ∙ Uniprot:O00159 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant nonsyndromic hearing loss (Supportive), mode of inheritance: AD
• autosomal dominant nonsyndromic hearing loss (Disputed Evidence), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYO1C gene.

• not provided (140 variants)
• Inborn genetic diseases (63 variants)
• not specified (23 variants)
• Anophthalmia-microphthalmia syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYO1C 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				22	10	32
missense			62	10	8	80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	4	7
non coding				28	73	101
Total	0	0	62	60	91

Variants in MYO1C

This is a list of pathogenic ClinVar variants found in the MYO1C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-1465529-G-A			Benign (May 14, 2021)
17-1465617-C-T			Benign (Jul 17, 2018)
17-1465784-G-A			Benign (Aug 06, 2018)
17-1465796-C-T			Benign (Jul 05, 2018)
17-1465839-T-C			Benign (Jun 16, 2018)
17-1466044-T-C			Benign (Jun 20, 2021)
17-1466072-G-A			Benign (Nov 12, 2018)
17-1466961-T-C			Benign (Nov 12, 2018)
17-1467165-T-C			Benign (Jun 22, 2018)
17-1467248-C-A		not specified	Benign (May 09, 2017)
17-1467257-G-A			Likely benign (May 21, 2018)
17-1467285-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-1467335-C-T			Likely benign (Mar 01, 2022)
17-1467426-C-T			Benign (Jun 22, 2018)
17-1467432-GCC-G			Likely benign (Aug 06, 2018)
17-1467445-C-T			Benign (Jun 16, 2018)
17-1467449-G-A			Likely benign (Jul 05, 2018)
17-1467459-C-T			Benign (Jun 13, 2018)
17-1467485-C-G		not specified	Uncertain significance (Sep 26, 2023)
17-1467508-C-T		not specified	Uncertain significance (Jan 06, 2023)
17-1467551-G-A		MYO1C-related disorder	Likely benign (Oct 04, 2019)
17-1467579-T-TG			Benign (Dec 26, 2018)
17-1467629-C-A			Benign (Jul 01, 2018)
17-1467794-T-C			Benign (Aug 23, 2019)
17-1467804-A-G			Benign (May 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYO1C	protein_coding	protein_coding	ENST00000359786	32	28715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.64e-14	1.00	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.637	703	657	1.07	0.0000483	6858
Missense in Polyphen		276	259.2	1.0648		2704
Synonymous	-3.63	352	275	1.28	0.0000203	2087
Loss of Function	3.70	34	66.6	0.511	0.00000387	702

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000823	0.000815
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000274	0.000272
Finnish	0.000157	0.000139
European (Non-Finnish)	0.000286	0.000281
Middle Eastern	0.000274	0.000272
South Asian	0.000366	0.000327
Other	0.000490	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. Involved in glucose transporter recycling in response to insulin by regulating movement of intracellular GLUT4-containing vesicles to the plasma membrane. Component of the hair cell's (the sensory cells of the inner ear) adaptation-motor complex. Acts as a mediator of adaptation of mechanoelectrical transduction in stereocilia of vestibular hair cells. Binds phosphoinositides and links the actin cytoskeleton to cellular membranes. {ECO:0000269|PubMed:24636949}.
• Pathway: Insulin Signaling;B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);Vesicle-mediated transport;Membrane Trafficking;Translocation of GLUT4 to the plasma membrane (Consensus)

Recessive Scores

• pRec: 0.212

Intolerance Scores

• loftool: 0.0331
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.63

Haploinsufficiency Scores

• pHI: 0.248
• hipred: Y
• hipred_score: 0.637
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.724

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myo1c
• Phenotype: skeleton phenotype; hearing/vestibular/ear 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: myo1cb
• Affected structure: pronephric glomerular basement membrane
• Phenotype tag: abnormal
• Phenotype quality: increased thickness

Gene ontology

• Biological process: protein targeting;protein targeting to membrane;vesicle transport along actin filament;positive regulation of cell migration;positive regulation of actin filament polymerization;positive regulation of cell migration by vascular endothelial growth factor signaling pathway;Fc-gamma receptor signaling pathway involved in phagocytosis;positive regulation of gene expression, epigenetic;mRNA transport;cellular response to interferon-gamma;positive regulation of protein targeting to membrane;positive regulation of cellular response to insulin stimulus;positive regulation of vascular endothelial growth factor signaling pathway;regulation of bicellular tight junction assembly
• Cellular component: stress fiber;nuclear pore;nucleoplasm;nucleolus;cytoplasm;cytosol;plasma membrane;microvillus;brush border;basal plasma membrane;membrane;lateral plasma membrane;unconventional myosin complex;nuclear body;cytoplasmic vesicle membrane;filamentous actin;ruffle membrane;membrane raft;phagocytic vesicle;stereocilium membrane;extracellular exosome
• Molecular function: microfilament motor activity;signaling receptor binding;protein binding;calmodulin binding;ATP binding;protein C-terminus binding;Ral GTPase binding;actin-dependent ATPase activity;actin filament binding