MYOM3

myomesin 3, the group of I-set domain containing|Myosin binding proteins

Basic information

Region (hg38): 1:24056035-24112135

Links

ENSG00000142661 ∙ NCBI:127294 ∙ OMIM:616832 ∙ HGNC:26679 ∙ Uniprot:Q5VTT5 ∙ 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 MYOM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYOM3 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		4
missense			114	5		119
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding						0
Total	0	0	115	9	0

Variants in MYOM3

This is a list of pathogenic ClinVar variants found in the MYOM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-24057371-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-24057428-G-A		not specified	Uncertain significance (Jan 06, 2023)
1-24057468-G-A		not specified	Uncertain significance (Apr 10, 2023)
1-24057534-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-24057544-A-G			Likely benign (Oct 01, 2022)
1-24057555-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-24057606-C-T		not specified	Likely benign (Oct 05, 2023)
1-24057624-G-T		not specified	Uncertain significance (May 30, 2023)
1-24058943-G-C		not specified	Uncertain significance (Jun 29, 2023)
1-24058952-G-A		not specified	Uncertain significance (Feb 12, 2024)
1-24061960-T-G		not specified	Uncertain significance (Jan 09, 2024)
1-24062034-G-T		not specified	Uncertain significance (Jan 31, 2024)
1-24062077-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-24062083-C-T		not specified	Uncertain significance (Oct 16, 2023)
1-24063151-A-G		not specified	Uncertain significance (Sep 26, 2023)
1-24063200-G-A			Likely benign (Jan 01, 2023)
1-24063216-A-G		not specified	Uncertain significance (Nov 13, 2023)
1-24064087-C-A		not specified	Uncertain significance (May 11, 2022)
1-24064114-C-A		not specified	Uncertain significance (Dec 13, 2022)
1-24064148-C-A		not specified	Uncertain significance (Nov 17, 2022)
1-24064156-A-G		not specified	Uncertain significance (Apr 23, 2024)
1-24065835-C-T		Flexion contracture	Benign (-)
1-24065902-A-C		not specified	Uncertain significance (Jun 11, 2021)
1-24065912-C-T			Likely benign (Mar 01, 2023)
1-24065923-C-T		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYOM3	protein_coding	protein_coding	ENST00000374434	36	56141

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.43e-47	0.00000215	122862	26	1920	124808	0.00783

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.654	908	854	1.06	0.0000537	9228
Missense in Polyphen		280	263.66	1.062		2939
Synonymous	-0.654	378	362	1.04	0.0000250	2831
Loss of Function	0.726	76	83.1	0.914	0.00000430	937

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00540	0.00539
Ashkenazi Jewish	0.00238	0.00239
East Asian	0.0270	0.0268
Finnish	0.000466	0.000464
European (Non-Finnish)	0.00301	0.00297
Middle Eastern	0.0270	0.0268
South Asian	0.0309	0.0305
Other	0.00432	0.00430

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May link the intermediate filament cytoskeleton to the M-disk of the myofibrils in striated muscle. {ECO:0000250}.

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.963
• rvis_EVS: 1.16
• rvis_percentile_EVS: 92.65

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.219
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.117

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myom3

Gene ontology

• Biological process: muscle contraction;skeletal muscle thin filament assembly;skeletal muscle myosin thick filament assembly;sarcomere organization;cardiac muscle fiber development;cardiac myofibril assembly;cardiac muscle tissue morphogenesis;striated muscle myosin thick filament assembly
• Cellular component: striated muscle thin filament;sarcomere;Z disc;M band
• Molecular function: structural constituent of muscle;protein homodimerization activity;actin filament binding;muscle alpha-actinin binding